Latest improvements for CLC Genomics Server

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CLC Genomics Server 7.5.4

Release date: 2017-03-22

All changes in this release have also been fixed on the CLC Genomics Server 9.x and 8.5.x lines at time of writing.

Improvements

  • All NCBI server communication is now encrypted (uses HTTPS).
  • Updated BLAST executables to be compatible with macOS Sierra. This change only affects Mac users.

Bug fixes

  • For the Basic Variant DetectionLow Frequency Variant Detection and Fixed Ploidy Variant Detection tools:
     
    • Fixed an issue where the count and read count could be reported as marginally higher than they actually were in a small minority of cases. For the affected variants, this could then also result in variant frequencies being reported that were slightly higher than they should have been, in some cases above 100%. Variants affected by this issue are a small subset of variants where the variant affected overlapped another potential variant and where only the affected variant was then reported. This change could lead to a small decrease in the number variants reported compared to earlier versions of the CLC software, due to a variant no longer passing the count or read count filtering constraints. The impact of this change is expected to be low. For example, in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after this fix was implemented.
    • Fixed an issue where the coverage of a longer variant that contained another variant was reported for both the longer variant and the contained variant. The coverage for the contained variant is now reported correctly.
    • Fixed a bug where count, read count, and forward- and reverse read count could be incorrect for variants found in overlapping regions of a pair of reads and where the variant was originally identified as being adjacent to one or more other variants.
    • Fixed an issue affecting coverage calculation for SNVs without immediately adjacent variants when using paired read data: if the second read of a pair containing the variant did not meet the requirements of the quality filter, neither the first nor second read of that pair contributed to the coverage calculated for the variant.
    • Fixed an issue where for a SNV without immediate neighboring variants, overlapping reads of a pair that had conflicting base calls for that variant position contributed to the values calculated for coverage, read coverage, and read count of that variant.
    • Fixed an issue where the forward and/or reverse count for a longer variant, supported by paired reads with both children having the same direction, could be too low. The forward count and reverse count is now reported correctly.
  • Fixed an issue with the InDels and Structural Variants tool where an incorrect insertion could be called when the optimal alignment of a read's unaligned end around the breakpoint included a gap in the insertion sequence.
  • For the Identify Known Mutations from Sample Mappings tool:
    • Fixed an issue where reads in a sample mapping were not identified as supporting the presence of a known variant in cases where the first position of the variant region in the mapped read contained a gap.
    • Fixed an issue where a read containing a variant longer than a known variant being tested for was counted as supporting the known variant in cases where the first part of the read’s variant sequence is identical to that of the known variant.
    • Fixed an issue where overlapping reads of a pair having conflicting base calls for a variant position could contribute to the coverage calculated for that variant.

Compatibility

We recommend running the corresponding versions of clients for CLC Genomics Server. The following are the corresponding client software for the CLC Genomics Server 7.5.4:

  • CLC Genomics Workbench 8.5.4
  • Biomedical Genomics Workbench 2.5.4
  • CLC Command Line Tools 2.5.4

The following client software and versions are compatible with the CLC Genomics Server 7.5.4: 

  • CLC Genomics Workbench 8.5.3, 8.5.2, 8.5.1, 8.5, 8.0.3, 8.0.2, 8.0.1 and 8.0
  • Biomedical Genomics Workbench 2.5.3, 2.5.2, 2.5.1, 2.5, 2.1.2, 2.1.1 and 2.1
  • CLC Command Line Tools 2.5.3, 2.5.2, 2.5.1, 2.5, 2.0.3, 2.0.2, 2.0.1 and 2.0

Compatible client versions that are not the corresponding version can connect to CLC Genomics Server 7.5.4. Jobs can be launched on the server from such client software with the exception of jobs where the tool being run has changed between between the client software version and the server software version.

CLC Server Command Line Tools

Changes

  • Fixed an issue so that the download_pfam_database can now be run using the CLC Command Line Tools. This issue was also fixed in the CLC Server Command Line Tools 3.x line and above.


CLC Genomics Server 7.5.3

Release date: 2016-06-16

Improvements

  • When running a workflow on a CLC Genomics Server with grid nodes and using the classic job queuing option, the name of individual subjobs contains the name of the workflow element being run. Previously,  "Grid Executer" was the name reported for each subjob.

Bug fixes

  • Fixed an issue with the RNA-Seq Analysis tool that could arise when the "Genomes annotated with genes and transcripts" option was chosen: If two or more genes had the same name, and a transcript could be assigned to each from the mRNA track, then the value in the "Transcripts annotated" column in the GE track and in the TE track was 0. Furthermore, all counts for such genes were reported as zero, even when there were reads mapping to them.
  • Fixed an issue where the Motif Search tool incorrectly reported all match accuracies as either 0% or 100%.
  • Fixed an issue that prevented workflows containing an input modifying element but no outgoing connection from being run on the Server.

Compatibility

  • It is possible to use the CLC Genomics Workbench 8.5.3, 8.5.2, 8.5.1, 8.5, 8.0.3, 8.0.2, 8.0.1 and 8.0 to connect to the CLC Genomics Server 7.5.3. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, that would be a CLC Genomics Workbench 8.5.3 connecting to the CLC Genomics Server 7.5.3.
  • It is possible to use the Biomedical Genomics Workbench 2.5.3, 2.5.2, 2.5.1, 2.5, 2.1.2, 2.1.1 and 2.1 to connect to the CLC Genomics Server 7.5.3. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, that would be a Biomedical Genomics Workbench 2.5.3 connecting to CLC Genomics Server 7.5.3.

Advanced notice

  • From the autumn 2016 release, only 64 bit versions of the CLC Genomics Server, CLC Genomics Workbench, Biomedical Genomics Workbench, CLC Bioinformatics Database and CLC Assembly Cell will be made available. 32 bit versions of these will be discontinued from that time.
  • The Probabilistic Variant Detection (legacy) and Quality-based Variant Detection (legacy) tools will be removed from the Server and Workbenches in early 2017.

CLC Server Command Line Tools 2.5.3

This version of the CLC Server Command Line Tools is the corresponding client version for the CLC Genomics Server 7.5.3. This version of the CLC Server Command Line Tools can be used to connect to the CLC Genomics Server 7.5.3, 7.5.2, 7.5.1, 7.5, 7.0.3, 7.0.2, 7.0.1 and 7.0. However, we generally recommend running the corresponding client for the server version.


CLC Genomics Server 7.5.2

Release date: 2016-04-07

Retirements

  • The Biobase Genome Trax Download Server Extension has been retired because it is dependent on the Biobase GenomeTrax product, which will stop operating in 2016.

Bug fixes

  • The  Download Pfam Database tool has been updated to download version 29.
  • Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
  • When the InDels and Structural Variants tool is added to the workflow the "P-value Threshold" parameter did not show up in the Select settings wizard step under "Significance of unaligned ends breakpoints". This has been fixed.
  • BED Export: when exporting block list entries (such as connected exons from mRNA tracks), positions were absolute. This has been fixed: positions are now relative to the 'chromStart' position.
  • Fixed an issue where Map Reads to Reference would under rarely occurring circumstances report a persistence error.

Compatibility

  • It is possible to use the CLC Genomics Workbench 8.5.2, 8.5.1, 8.5, 8.0.3, 8.0.2, 8.0.1 and 8.0 to connect to the CLC Genomics Server 7.5.2. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, that would be a CLC Genomics Workbench 8.5.2 with the CLC Genomics Server 7.5.2.
  • It is possible to use the Biomedical Genomics Workbench 2.5.2, 2.5.1, 2.5, 2.1.2, 2.1.1 and 2.1 to connect to the CLC Genomics Server 7.5.2. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, that would be a Biomedical Genomics Workbench 2.5.2 with the CLC Genomics Server 7.5.2.

CLC Server Command Line Tools 2.5.2

Improvements

On Windows some temporary files named MIMEXXX.tmpwas not removed on exit

Compatibility

This version of the CLC Server Command Line Tools is the corresponding client version for the CLC Genomics Server 7.5.2. This version of the CLC Server Command Line Tools can be used to connect to the CLC Genomics Server 7.5.2, 7.5.1, 7.5, 7.0.3, 7.0.2, 7.0.1 and 7.0. However, we generally recommend running the corresponding client for the version of the CLC Genomics Server being connected to.


CLC Genomics Server 7.5.1

Release date: 2015-10-15

Bug fixes

  • Fixed an issue leading to an error during VCF export where the data involved had originally been imported from VCF files and the values in the QUAL field were integers.
  • Export of floating-point (decimal) numbers to VCF format were previously dependent on the specified locale. This has been fixed so that the decimal separator now always is a point.
  • Improved user feedback when configuring LDAP/AD configuration.
  • Fixed a problem where after import of a large volume of data, using the "Show results" option in the process tab resulted in an error.

Compatibility

  • It is possible to use the CLC Genomics Workbench 8.5.1, 8.5, 8.0.3, 8.0.2, 8.0.1 and 8.0 to connect to the CLC Genomics Server 7.5.1. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, that would be a CLC Genomics Workbench 8.5.1 with the CLC Genomics Server 7.5.1.
  • It is possible to use the Biomedical Genomics Workbench 2.5.1, 2.5, 2.1.2, 2.1.1 and 2.1 to connect to the CLC Genomics Server 7.5.1. We generally recommend running the corresponding version of the Workbench for the CLC Server. Here, that would be a Biomedical Genomics Workbench 2.5.1 with the CLC Genomics Server 7.5.1.


CLC Genomics Server 7.5

Release date: 2015-09-08

New server-specific features and improvements

  • Tools configured for use via the External Applications functionality can now be included within Workflows.
  • Metadata functionality has been added, allowing users to create tables of metadata, import metadata, and associate data elements with particular metadata.
  • LDAP and Active Directory authentication now supports LDAP over SSL (ldaps://) and Start TLS for encrypting LDAP communication.
  • The performance of the "Link Variants to 3D Structure" tool has been significantly improved when running on a grid or on a remote server.

Improvements shared with CLC Genomics Workbench

  • Improved use of multiple cores when running the Create Detailed Mapping Report.
  • Some applications require VCF formatted variant data to contain quality score values. We now calculate QUAL and annotate variants with the resulting value.
  • Improved memory management when handling large report elements. Batching on selected elements is now possible: it used to be restricted to selected folders.
  • One can now select "EST" as database when using the Search for Sequences at NCBI tool.
  • The output of the Reverse Complement Sequence now gets the suffix -RC attached to the name of the input instead of -1 before.
  • The Hierarchical Clustering of Samples tool can now be executed as part of workflows and on the server.

Bug fixes

  • Fixed an issue where if a job node addition failed, that same job node could not be added within the same Server session.
  • The "Save in separate folders" option is now available for tools being configured to run via the Server.
  • Fixed an issue with the Map Reads to Contigs tool that could be extremely slow when included in workflows with multiple inputs.
  • Fixed an issue to the Basic Variant DetectionFixed Ploidy Variant Detection and Low Frequency Variant Detection tools that happened for certain genomes when using masking tracks.
  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  • Improved memory management when handling large report elements.
  • Fixed a rare error in the Create Statistics for Target Regions tool. The error resulted in a failure when a target region only included the very last nucleotide of a chromosome.
  • Fixed an issue whereby Create Box Plot and Principal Component Analysis could sometimes be run with illegal arguments, leading to an error message.
  • Fixed a bug in the Predict Secondary Structure tool when the option to calculate the partition function was selected  for long molecules (>1000 nucleotides).
  • Fixed an issue where some filtering operations, such as "doesn't contain" did not act correctly when filtering table cells that contained multiple pieces of information.
  •  Fixed an issue where the count of objects in the recycle bin of an SQL data area could be inaccurate if some of the items were not found. (Only relevant for Servers with a Bioinformatics Database.)
  • Fixed an issue that required the installation of both mySQL and Oracle JDBC drivers, even if only one of these drivers is needed. (Only relevant for Servers with a Bioinformatics Database.)

Compatibility

  • CLC Genomics Workbench 8.5. It is possible to use the CLC Genomics Workbench 8.0.3, 8.0.2, 8.0.1 and 8.0 to connect, but we recommend upgrading the Workbench to use the corresponding version for the Server.
  • Biomedical Genomics Workbench 2.5.  It is possible to use the Biomedical Genomics Workbench 2.1.2, 2.1.1 and 2.1 and the CLC Cancer Research Workbench 2.0,  but we recommend upgrading the Workbench to use the corresponding version for the Server.


CLC Genomics Server 7.0.3

Release date: 2015-08-13

Bug fixes -  CLC Genomics Server specific

  • Resolved an issue with the grid integration where certain workflows run with a big number of inputs would result in the grid worker giving up waiting for input data
  • The analysis/workflow execution system now handles search algorithms specially so that search results are not modified. This eliminates a host of concurrency issues.
  • Fixed an issue associated with submitting CLC Server jobs as the root user when using AD/LDAP authentication that could resulting in a job node stalling if the AD/LDAP server was down.
  • For Servers that include a CLC Bioinformatics Database only: Postgresql and H2 database locations can now be configured without the need to install the MySQL and Oracle database connector.

Bug fixes shared with CLC Genomics Workbench and Biomedical Genomics Workbench

  • Fixed a read mapper bug that caused some reads to be incorrectly reported as unmapped when global alignment was selected.
  • Fixed a SOLiD NGS importer bug where import of very low quality, colorspace encoded paired-end sequence reads in fastq format could lead to paired sequence lists where the wrong reads area marked as pairs.
  • Fixed an issue with the sort order for paired reads in SAM/BAM exports in high coverage regions.
  • Fixed an issue where the Local Realignment tool when run with RNA-seq mapping could occasionally report a match that did not meet internal requirements as a valid match. This had a downstream effect when variant calling tools were run, and then failed upon encountering such a position. This issue has also been addressed in this release.
  • Fixed an issue where the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools would stop with an error when encountering a place in a read mapping containing a match that did not meet internal requirements of a valid match.
  • Fixed a bug that caused the mapper to enter an infinite loop if a reference of length 0 was used.
  • Fixed a rare bug that sometimes made the read mapper halt prematurely when several seeds were identified at the same reference position.
  • For Biomedical enabled CLC Genomics Servers only: In case of very low sample coverage, the Copy Number Variant Detection algorithm will now terminate the analysis early and an explanation is given in the reports.

Corresponding client software

  • CLC Genomics Workbench 8.0.3, 8.0.2, 8.0.1 and 8.0
  • Biomedical Genomics Workbench 2.1.2, 2.1.1 and 2.1
  • CLC Cancer Research Workbench 2.0.


CLC Genomics Server 7.0.2

Release date: 2015-06-15

Bug fixes specific to Genomics Server

  • Improved memory management for long-running server instances.
  • Fixed a rare error in the Create Statistics for Target Regions tool. The error resulted in a failure when a target region only included the very last nucleotide of a chromosome.
  • Decreased intensity of data integrity check to improve speed when adding new data areas or generating server setup reports.
  • Fixed an issue when copying data between areas on a Server where the data was generated by a Workbench plugin and the Server did not have that plugin installed.

Bug fixes shared with CLC Genomics Workbench

    • Fixed an issue with running BLAST at NCBI tool where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
    • Fixed an issue with master server - job node communication that has been observed sporadically on systems with large numbers of job nodes (>20).
    • Fixed bug in which Local Realignment could produce an illegal read mapping. This only happened for RNA-data.
    • The variant caller will now fail if it encounters an illegal RNA read mapping. If the variant caller fails with such a message, and if it was run on locally realigned data, then we suggest to re-run the local realignment to avoid the error.
    • BED importer truncates the names to 80 chars now.

Corresponding client software

  • CLC Genomics Workbench 8.0.2, 8.0.1 and 8.0
  • Biomedical Genomics Workbench 2.1.1 and 2.1
  • CLC Cancer Research Workbench 2.0.


CLC Genomics Server 7.0.1

Release date: 2015-04-16

New server-specific features and improvements

  • Former plugin "Duplicate Mapped Reads Removal" is now integrated under the name "Remove Duplicate Mapped Reads" and can be found in the NGS Core toolbox. Please uninstall this plugin as part of your Server upgrade process.

Improvements shared with CLC Genomics Workbench

  • BLAST has been upgraded to BLAST+ 2.2.30 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.2.30 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777
  • Particular annotation types (columns) can now be specified for export in Excel, HTML and tab delimited formats.
  • Added column to output of "Annotate and Merge Counts" indicating 3' or 5' direction when using "grouping on mature" parameter.
  • Increased the performance for gzip export.

Biomedical-enabled Genomics Servers only

  • For users holding a Biomedical Genomics Server Solution (previously called Cancer Research Server Solution), the Copy Number Variant (CNV) Detection plugin has been integrated and can be found in the 'Resequencing' toolbox. Please uninstall this plugin as part of your Server upgrade process.

Bug fixes

  • Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
  • Fixed an error with the administrative interface that did not reload the webpage after restarting the Server.
  • Fixed the SOLiD NGS importer to correctly import basespace encoded sequences in fastq files. It is still assumed that sequences originate from colorspace.
  • Fixed an error that occurred when running the Create Sequencing QC Report tool and requesting quality analysis reporting.
  • Fixed a rare error that caused the Amino Acid Change tool to crash if a CDS feature was less than 3 bases long.
  • Fixes and updates for automated genome downloads (Zea mays, C. elegans).
  • Fixed a bug in the probabilistic variant caller that caused it to fail for certain input.

Corresponding client software

  • CLC Genomics Workbench 8.0.1
  • Biomedical Genomics Workbench 2.1 (Servers with Biomedical extension)
  • CLC Server Command Line Tools 2.4.1.


CLC Genomics Server 7.0

Release date: 2015-02-24

New server-specific features and improvements

  • The layout of the process queue for jobs submitted to the server has been improved.
  • Genomics Server now supports IPv6.
  • It is now possible to set an upper limit to the number of jobs that can run concurrently on a given job node or a single server.
  • Access to grid presets on grid node setups can be restricted to particular groups of users.
  • The job node list in the server configuration interface now sorts job nodes by name and host name rather than the order they were added.
  • Adding database location can now be done with custom connection string.

Improvements shared with CLC Genomics Workbench

  • New tools:
    • Create Track from Experiment. This tool makes it possible to convert Experiments to Tracks. In the Experiment, the results of the statistical analysis are annotated on the experiment as additional columns. It can be advantageous to visualize the results of the statistical analysis as tracks.
    • Link Variants to 3D Protein Structure makes it possible to visualize amino acid changes on 3D protein structures. After running the tool on a variant table, variants can be visualized on 3D structures.
  • The Map Reads to Reference tool now supports both linear gap cost parameters and affine gap cost parameters. The addition of affine gap cost support allows you to get more accurate results for reads with stretches of insertions or deletions.
  • The read mapper used in the RNA-Seq Analysis tool has been upgraded to use the new read mapper described above. This upgrade enables you to run RNA-seq Analysis with as little as 6 GB RAM and at the same time improves your end results. However, you cannot yet use affine gap cost parameters in your RNA-Seq analysis.
  • MA plots, scatter plots and histograms can now accept expression tracks as input.
  • Performance of the Merge Read Mappings tool has been improved, especially in situations where the number of reference sequences is very large, such as when merging reads mapped against de novo assembly results.
  • The tool Amino Acid Changes has been expanded with an extra output that makes it possible to visualize amino acid changes in track format.
  • Improved PDB import of water molecules, DNA/RNA, and saccharides.
  • When importing PDB files, the resulting Molecule Project now contains citation information(PDB ID and primary reference), which can be found in the 'Show History' view.
  • Batching: Processes tab and analysis execution logs now display batch names in addition to analysis names for enhanced clarity.

Bug fixes

  • Fixed an error resulting in billions of reads being silently dropped when producing large read mappings against large counts of reference sequences. The error involves a read count overflow and the dropping of at least 2 billion reads per failure instance.
  • The tool Identify Graph Threshold Areas can now use negative values to define its threshold.
  • Fixed problem with import of BED files using external applications.
  • SAM/BAM import will no longer fail for alignments with POS = 0, but instead import them as though they were unmapped.
  • Fixed an issue that previously blocked the ability to run certain non-exclusive jobs on a single server or job node.

Changes

  • We now recommend restart of the server after installation of a server plugin. This can be done via the server administrator interface. A restart will cause any running or scheduled jobs to fail. To avoid disruptions during plugin installation, we have added a maintenance mode. Entering maintenance mode allows such jobs to run and complete, while restricting submission of new jobs.

Compatibility

  • This release can be used with CLC Server Command Line Tools 2.4.

Cancer-enabled Genomics Servers only

  • Plugins
    • New: Copy Number Variant Detection Plugin (beta)

CLC Server Command Line Tools

New Tools

    • link_to_structure
    • download_sequence_to_structure_db
    • extract_diff_exp_genes

Tools that have changed parameters

All Genomics Servers

    •  add_amino_acid_info Added option:
      • --filter-empty-cds
    • amino_acid_changes Added option:
      • --filter-empty-cds
    • contig_read_mapping Added options:
      • --deletion-extend-cost
      • --deletion-open-cost
      • --indel-mode
      • --insertion-extend-cost
      • --insertion-open-cost
    • download_genome Added option:
      • --download-chromosome-band
    • duplicate_mapped_reads_removal Added option:
      • --create-report
    • qc_target_sequencing Added option:
      • --create-coverage-graph
    • read_mapping Added options:
      • --deletion-extend-cost
      • --deletion-open-cost
      • --indel-mode
      • --insertion-extend-cost
      • --insertion-open-cost
    • statistics_target_regions Added option:
      • --create-coverage-graph
    • structural_variant_detection Added option:
      • --masking-track

Cancer-enabled Genomics Servers only

    • add_link_to_structure
    • download_3d_structure_information_db
    • mutation_tester_tool Added options:
      • --ignore-broken-pairs
      • --ignore-nonspecific-matches


CLC Genomics Server 6.5.6

Release date: 2015-08-18

Bug fixes shared with CLC Genomics Workbench

  • Fixed a bug that caused the mapper to enter an infinite loop if a reference of length 0 was used.
  • Fixed a rare bug that sometimes made the read mapper halt prematurely when several seeds were identified at the same reference position.
  • Fixed sort order for paired reads in SAM/BAM exports in high coverage regions.
  • The analysis/workflow execution system now handles search algorithms specially so that search results are not modified. This eliminates a host of concurrency issues.
  • Minor improvements in persistence.

Corresponding Client Software

  • CLC Genomics Workbench 7.5.X
  • Cancer Research Workbench 1.5.X (Servers with Cancer extension)
  • CLC Server Command Line Tools 2.4.X.


CLC Genomics Server 6.5.5

Release date: 2015-06-18

Bug fixes server-specific

    • Integrity checks on Server data areas have been made more conservative than previously, yielding substantial speed benefits when starting up or reconfiguring Servers with very large amounts of data.
    • Fixed issue with copying data held in a Server location where the data type is specific to a tool in a Workbench plugin that is not installed on the Server.
    • Fixed an issue where certain temporary files were written directly into the system temporary area rather than into the CLCTmp directory.

Bug fixes shared with CLC Genomics Workbench

  • Read-only folders are no longer offered as potential locations to save data bundled with a Workflow.
  • Fixed bug in which Local Realignment could produce an illegal read mapping. This only happened for RNA-data.
  • The variant caller will now fail if it encounters an illegal RNA read mapping. If the variant caller fails with such a message, and if it was run on locally realigned data, then we suggest to re-run the local realignment to avoid the error.

Corresponding client software

  • CLC Genomics Workbench 7.5.4
  • CLC Cancer Research Workbench 1.5.5 (Servers with Cancer extension)
  • CLC Server Command Line Tools 2.2.2.


CLC Genomics Server 6.5.4

Release date: 2015-04-23

Bug fixes server-specific

  • Fixed an issue with master server - job node communication that has been observed sporadically on systems with large numbers of job nodes (>20).
  • Improved memory management for long-running server instances.

Bug fixes shared with CLC Genomics Workbench

  • The filtering option in the Create Track from Experiment tool only considered the predicted fold-changes in the positive direction, so features that were reduced in expression were filtered out. This has now been fixed.
  • Fixed an issue with running blast searches at the NCBI where an NCBI-generated error about their CPU usage limit being exceeded was not being reported transparently and a result of "no hits" was being reported instead.
  • Fixed an issue with mapping of paired-end reads, where these were erroneously reported as broken pairs when the fragment size derived from the alignments of the two ends of the pair was longer than reference sequence
  • Improved memory management for long-running server instances
  • Fixed a bug in the probabilistic variant caller that caused it to fail for certain input.
  • When using the RNA-Seq Analysis tool with the "One reference sequence per transcript" option, the "Maximum number of hits for a read" option was sometimes not taken into account for multi-hit reads. This has been fixed.

Cancer Research-enabled Genomics Servers only

  • The filtering option in the Extract Differentially Expressed Genes tool only considered the predicted fold-changes in the positive direction, so features that were reduced in expression were filtered out. This has now been fixed. The change also affects the workflow: "Identify and Annotate Differentially Expressed Genes and Pathways", as the tool is also included in this workflow.
  • Fixed issue where when the options  "Keep only selected annotations" in the "Remove information from variants" tool was selected, the Coverage, Count and Frequency columns did not appear in the output.

Corresponding client software

  • CLC Genomics Workbench 7.5.3
  • Cancer Research Workbench 1.5.4 (Servers with Cancer extension)
  • CLC Server Command Line Tools 2.4.1.


CLC Genomics Server 6.5.3

Release date: 2015-02-17

Bug fixes shared with CLC Genomics Workbench

  • Fixed an error resulting in billions of reads being silently dropped when producing large read mappings against large counts of reference sequences. The error involves a read count overflow and the dropping of at least 2 billion reads per failure instance.   
  • Amino Acid Change tool: In cases where an mRNA track does not overlap all annotations in the CDS track, "Coding Region Changes" were not added to variants that overlap a CDS but not an mRNA annotation. This has been fixed.
  • Small RNA Analysis -> Annotate and Merge Counts: When you choose to create a “grouped on mature” output, the small RNAs are grouped by both the 5’ and the 3’ mature sequences separately in the “grouped on mature” output. The column heading has therefore been changed to show "Mature" instead of "Mature 5'".  
  • The Low Frequency Variant caller could end up in an infinite loop in certain corner cases. This is now fixed. 
  • Fixed problem with import of BED files using external applications. 
  • Fixed a bug in the QC report creation step of the ChIP-seq analysis. 
  • Fixed a bug for color space reads in RNA-Seq Analysis that caused all exon-exon matches to be filtered away. 
  • Fixed a bug that in some cases caused an error when annotating read sequence lists with the GFF/GTF/GVF annotation tool.

Compatibility

  • This release can be used with CLC Server Command Line Tools 2.2.2

CLC Server Command Line Tools - Bug fixes

  • Fixed problem running Workflows using the Command Line Tools, where unusual characters, such as quotes, were included in unlocked parameters.


CLC Genomics Server 6.5.2

Release date: 2014-12-03

This release contains fixes to issues seen sporadically on CLC Servers with job nodes, where the main symptom is the occasional occurrence of irreproducible errors related to locating data when you run a job. If you are running a single server, or a master server with grid nodes, or if your job node setup is running without problems, then you do not need to upgrade to this version.

Bug fixes

  • Fixed an issue seen sporadically on CLC Servers with job node setups where jobs failed due to problems locating results files even when those files were in place and intact.
  • Fixed a problem that arose when validating parameters in Workflows on the Server where more than one Workflow being validated referred to the same underlying data.
  • Fixed an issue related to the licensing of job nodes.
  • License conditions on job nodes changed to better support multi-job processing.

Compatibility

The CLC Genomics Server 6.5.2 is compatible with the CLC Genomics Workbench 6.5.1 and the CLC Command Line Tools 2.2.1. The CLC Genomics Server 6.5.2 with Cancer Research Add-on is compatible with the CLC Cancer Research Workbench 1.5.2 and the CLC Command Line Tools 2.2.1.


CLC Genomics Server 6.5.1

Release date: 2014-10-28

New features and improvements

  • "Filter Annotations on Name" can now insert names to filter on from significantly bigger files. Previously the limit for the file size was 10KB, this has now been increased to 20MB.
  • RNA-Seq Analysis: The ENSEMBL gene id of each gene, where available, has been added as an additional column to the gene expression track output.
  • Improved performances of the ChIP-seq Analysis tool for genomes with a large number of chromosomes.
  • It is now possible to run a workflow without an optional input.

Bug fixes

  • Fixed a problem that prevented BLAST operations when choosing to run these on the CLC Server.
  • The AAC tool did not annotate variants in 3' UTR with their DNA-level change using the HGVS c.xxx format. This affects any analysis done with Gx 7.5 or earlier based on ENSEMBL CDS tracks from older versons. The AAC analysis should be redone using Gx 7.5.1 for correct annotation. Important: Please also check the description in the MWB 7.5 release notes of a bug fix in the translation of CDS annotations to protein sequences that was wrong in cases where the reading frame was not +1 or -1 in CDS annotations imported from ENSEMBL.
  • A bug has been fixed in the Set Up Experiment tool. Exon-related expression values can now only be selected when present in the individual samples.
  • When creating a subset of a paired experiment, the sub-experiment no longer appeared as being paired. This bug has been fixed and sub-experiments created in previous versions should recover the pairing information when accessed with this version of the workbench.
  • Pfam filtering bug fixed. Previously, Pfam only reported the first domain of each type in a query and as a consequence many domains were missed. We recommend that users whose research depends on Pfam annotations re-run the tool on their data. Fixed problem importing VCF files using the AO and RO genotype field.
  • Fixed problem importing certain VCF files.
  • Fixed a bug in the 'Maximum Likelihood Phylogeny' tool that failed when generating bootstrap values for certain input alignments.
  • The Blast text results have been improved so they show the correct query and subject positions regardless of strand.
  • Fixed problem with import of read mappings with supplementary alignments. When importing read mappings with supplementary alignments, supplementary alignments are not imported. Previously import of such read mappings caused import errors.
  • Fixed a bug in the Annotate and Merge Counts tool that in rare cases resulted in incorrect sorting and crash.

CLC Server Command Line Tools - Changes

  • The Command Line Tool will no longer wait for child processes of the processes it starts, to complete. This is a technical change that does not affect the performance.


CLC Genomics Server 6.0.5

Release date: 2014-05-28

Changes

An option to change the way workflows are submitted to the grid has been introduced. The behaviour of the previous version (and if the property is unset or set to false) is to submit each individual job in the workflow when its dependencies have been executed. The consequence of this is that jobs from different workflows are interleaved in execution. If many workflows are executed at the same time, this means that total run time of a workflow becomes very unpredictable. By creating a properties file in the server installation directory: /settings/grid.propertiescontaining one line: "com.clcbio.server.configuration.grid.lsfPreserveWorkflowOrder = true, and restarting the server, a new behavior can be switched on. With this new behavior all jobs of the workflow are submitted at once, supplying the grid with the dependency information. The consequence of this is that all jobs belonging to one workflow are placed next to each other in the execution queue on the grid. The general execution order of the jobs is therefore, that the workflow submitted first will be completed before jobs from the next workflow is run. It should be noted that if the grid has sufficient resources and all elements of the first workflow are waiting for the execution of an element, elements from the next workflow will be executed. For this release, this behavior is only supported for LSF grids. One drawback of submitting the entire workflow at once is that a large number of grid jobs are created (#elements-per-workflow x #workflows). The server creates a new thread for each job on the grid, which it uses to poll for status with 5 second intervals. This does not work very well if there are many grid jobs. By adding a line: com.clcbio.server.configuration.grid.groupedPolling = true in the /settings/grid.properties file and restarting the server, this is changed such that a single thread is used to poll the status of all grid jobs. This reduces both the number of threads used but also allows for more efficient polling techniques against the DRMAA library. The behavior described above is expected to be the default behavior with next major release of the CLC Genomics Server (check latest improvements notes for confirmation).


CLC Genomics Server 6.0.4

Release date: 2014-05-14

Bug fixes

  • Fixed a bug in RNA-Seq Analysis regarding the calculation of RPKM. This error was introduced with the new RNA-Seq tool in CLC Genomics Server 6.0. When calculating RPKM, the total number of gene reads was used instead of total exon reads. This will only have a significant impact in case there are many intron reads mapped to this gene. With this release we have fixed the bug, and we recommend all users that base their analysis of RPKM values to re-run all RNA-Seq analyses conducted with CLC Genomics Server 6.0 - 6.0.3. Please note that the legacy RNA-Seq plugin is not affected by this bug.
  • Fixed a bug in the Filter against Control Reads tool which meant that variants that are of type "Replacement" and which also introduce an insertion were not properly removed by the filter, even if there were reads supporting them. We recommend all customers that have relied on this tool for processing data with this tool in CLC Genomics Server 6.0.X to run the tool again in the 6.0.4 version.
  • Fixed bug that sometimes caused the workbench to crash when running "Local Realignment" on mappings generated with other mappers and imported as BAM files.
  • Fixed problem with some parts of workflow not being executed if there was multiple branches in workflow.

Changes

  • Users running RNA-seq analyses with only gene annotations can now choose whether to calculate  the RPKM for these genes (i.e. genes without transcripts) or not.


CLC Genomics Server 6.0.3

Release date: 2014-04-07

Changes

Adding support for CLC Cancer Research Workbench: If you have purchased a CLC Genomics Server with added support for Cancer Research, you will receive an additional license that will allow Cancer Research-specific tools to be executed on the CLC Genomics Server.


CLC Genomics Server 6.0.2

Release date: 2014-03-20

Bug fixes

  • Fixed problem with the amino acid changes tool that reported all variants within coding regions as non-synonymous. This error was introduced with Genomics Workbench 7.0.2


CLC Genomics Server 6.0.1

Release date: 2014-03-14

New features and improvements

  • Improved parameter specification for RNA-seq Analysis
  • It is now possible to perform both batched and non-batched import of VCF files without genotype information
  • Statistical Analysis: Improved reporting of invalid input to the tools "On Gaussian Data" and "On Proportions"
  • Fasta export:
    • Fasta export with trimming is now much faster and consumes less memory
    • Fasta export now reports progress while executing
    • When the "Remove trimmed regions" option is set, the Fasta export will ignore sequences in which all nucleotides are covered by a Trim annotation
  • Translate to Protein (Batch Process):
    • There are now options for specifying whether to translate the coding regions or extract translations from the annotations
    • The log has been made more detailed and informative
    • If the result is just a single protein sequence, the output will be just that, otherwise all sequences are output as a list
    • If the tool estimates that the number of protein sequences to be produced is greater than 1.000.000, it will create protein sequences without history, and it will not copy the common name, latin name, and taxonomy fields

Changes

  • When importing a VCF file. If multiple count tags are present in a VCF file, the VCF tags are prioritized in the following order: 1) CLCAD2, 2) AD, 3) AO
  • In the "Amino Acid Changes" tool, the description of coding region changes at the DNA level now complies with HGVS recommended nomenclature with regard to variants in untranslated regions. Examples: "c.-4A>C" describes a SNV four bases upstream of the start codon, while "c.*4A>C" describes a SNV four bases downstream of the stop codon

Bug fixes

  • After annotating variants with the tool "Annotate from Known Variants" a small fraction of the MNVs disappeared. This has now been fixed
  • Fixed problem where "InDels and Structural Variation" crashed for certain data
  • Fixed "Filter Based on Overlap" accepting expression tracks as inputs but not knowing how to handle them
  • Fixed error in mapping long reads as part of de-novo assembly, Read Mapping Legacy plugin, RNA-Seq Legacy plugin, and Transcript Discovery plugin
  • A rare error has been fixed in the Secondary Peak Calling tool
  • Fixed a bug that in certain cases made the De Novo Assembly fail
  • Fixed a bug that in certain cases made the RNA-Seq Analysis fail
  • Fixed a bug that made access to data impossible because of a failed rename operation
  • A problem importing Ensembl version 75 files has been addressed. If you have previously imported Ensembl version 75 files, please see the FAQ entry for full details of what to do


CLC Genomics Server 6.0

Release date: 2014-02-11

New server-specific features and improvements

  • New recycle bin concept with individual recycle bins and automatic clean-up.
    • Each user has an individual recycle bin to avoid problems when deleting data where permissions are applied
    • No other users have access to the recycle bin (except server administrators)
    • The server administrator can access and empty all recycle bins
    • All recycle bins on the server can be configured to be automatically emptied when the data is older than 100 days. This can be set in the server administration user interface
    • Special note for customers with database locations: when starting the new server version, the user connecting to the database must have permissions to create tables and indexes in the database in order to perform an automatic upgrade of the data location to the new recycle bin concept. This permission is only needed the first time the server starts up. If it is not desirable to grant these permissions to this user, it is possible to upgrade the database using the CLC Bioinformatics Database Tool.
  • Gateway cloning tools now available on the server
  • Statistical analysis tools now available on the server
  • Create track list now available on the server
  • Motif search now available on the server
  • Signal Peptide prediction is now available on the server
  • Node setup
    • It's easier to populate the fields in the job distributions part of the administration interface.
    • The display name of the server is shown in the top graphics of the administration interface
    • An option to Resync Job Nodes has been added to help in cases where job nodes get out of sync with the master node
  • Queue management with job nodes has been simplified and better tailored to executing workflows
    • Workflow jobs are handled in a special way on servers using job nodes. Once a workflow has started (after having made it to the top of the queue), the sub-processes that are part of the workflow are automatically placed at the top of the queue. This will ensure that the workflow is not punished for being split into several parts. Previously, work flows could end up being effectively blocked in the queue because the sub-processes would always start from the bottom of the queue.
    • The buttons to move jobs up and down in the queue have been removed since this would conflict with the way workflow jobs are handled
  • Improved performance when setting permissions on folders, especially important on systems linked to directories with large amounts of users.
  • Zip export is now available on all server products

Improvements shared with CLC Genomics Workbench

  • Copying data in the Navigation Area runs much faster and uses less memory than before. This is a great improvement which also kicks in when moving data between a CLC Genomics Server and a Workbench.
  • RNA-Seq on tracks: A substantial update of the popular RNA-Seq Analysis tool together with new statistical tools for analysis of differential expression form a great improvement for all users working with RNA-Seq.
    • The output of the RNA-Seq Analysis is based on tracks and includes tracks with the read mapping, expression values and fusion genes.
    • The gene-level and transcript-level expression results are now output as two different tracks. Downstream analysis can be performed on either.
    • A new column "Relative RPKM" on the transcript-level expression track can be used to see the relative expression of alternative transcripts for a gene.
    • Experiments based on the new expression tracks can be used for browsing the track list with read mappings and annotations.
    • It is now possible to map the reads against the full genome as well as gene regions.
    • The new read mapping algorithm introduced with CLC Genomics Server 5.5 is now also used for RNA-Seq. This means that mapping is faster but for some data sets it will also require more memory. For a human data set using the latest annotation sets (obtained through the Download Reference Genome Data), there is a minimum requirement at 16GB of RAM and we recommended 24 GB of RAM. If this causes problems, it is still possible to make use of the old RNA-Seq Analysis tool which is available as a plugin.
    • The parameters have been changed and updated to make use of tracks and includes a more explicit way of controlling what reference annotations should be used (if any).
    • The fusion genes table has been changed into an annotation track.
    • Variant tracks can be annotated with expression values from expression tracks.
  • New statistical testbased on EdgeR:
    • The tools available for statistical analysis of differential expression have been extended to also include the 'Exact Test' (developed by Robins and Smyth and implemented in the EdgeR Bioconductor package). The test is applicable to comparisons of pairs of groups and implicitly performs TMM normalization.
  • New functionality for phylogenetic trees (was previously part of a beta plugin)
    • Tool to reconstruct phylogenetic trees based on k-mers. This approach avoids the computationally intensive step of constructing a multiple alignment of the input sequences. The k-mer based reconstruction tool is especially useful for whole genome phylogenetic reconstruction where the genomes are closely related.
    • Tool performing a statistic evaluation of different substitution models to be used with maximum likelihood tree construction. The output of this tool is a report that lists the recommended settings to be used when constructing phylogenetic trees based on maximum likelihood.
    • Added an option for using the Kimura 80 substitution model when creating trees with distance based methods.
    • Distance-based tree reconstruction methods can now reconstruct trees from protein alignments using the Jukes-Cantor substitution model or the Kimura protein ML distance estimate.
    • A user defined start tree can now be supplied to the ML inference tool.
  • Tracks:
    • The speed of the Annotate with known variants and Filter against Known Variants tools have been greatly improved when using a large reference database like dbSNP.
    • Table filtering of tracks: it is not possible to use "overlaps" and "doesn't overlap" when filtering on the region column. This allows for quicker inspection if any of the variants or annotations overlap a particular position.
    • Tooltips on variant tracks in track lists now include the number of variants in the track.
    • The Identify Graph Threshold Areas tool is now capable of identifying intervals with higher-than-average reads. This is obtained by setting a “window-size” parameter in the "Identify Graph Threshold Areas" wizard that specifies the width of the window around every position that is used to calculate an average value for that position.
    • Previously, when importing variants from VCF files and from UCSC, a small number of variants were ignored because they were not proper replacements or MNVs because they contained reference bases at the ends. These variants are now trimmed and properly imported. This also affects the Download Reference Genome Data tool.
  • Workflows:
    • Possibility to have bulk configuration of elements. This enables to set the same reference data for multiple elements at once.
    • Workflows can be added inside a workflow. The inner workflow is "unfolded" into the single elements.
    • Parameters can now be renamed in the editor by the creator during configuration of the elements.
    • Workflows with invalid/unknown elements are laid out nicer and more consistent.
    • The sidepanel has now an option to display rulers in the editor to indicate better the size of a workflow (particularly when exporting)
    • Fit Width now fits the entire workflow in the editor by zooming out.
    • The sidepanel has a new section "Minimap" which shows an outline of the whole workflow. It allows to navigate the workflow in the view and also supports zooming
    • One can change the design of the workflow editor via the sidepanel (removed the old designs in the preferences)
    • Better validation when configuring parameters in workflows
    • If a tool receives inputs from at least two tools, the inputs can now be ordered via the context menu on the connections or the input part of the target element.
    • The name of an output in the workflow can be set by configuring the output element
    • Parameters of a workflow run can now be exported to various formats via the wizard
    • It is now possible to reset a reference parameter. Before it was only possible by removing the whole element and add it again.
    • In the workbench the installed workflows are now sorted alphabetically.
    • The graphics export of a workflow now knows about the scale and one can now export the whole workflow or only the current view.
    • A cpw file can now be dragged into the workflow manager and will be installed.
    • Further speed improvements on working with larger workflows in the editor
    • New tools that are now workflow-enabled:
  • Amino acid changes:
    • There are two new columns reporting amino acid changes for the longest transcript. Previously, amino acid changes would be reported for all transcripts, and this information is still available, but many users prefer just to use the longest transcript, and this information is now available in two new columns: one for the change on the protein level, and one for the change on the coding DNA level.
    • Variants up- and downstream of the coding regions are now annotated with a coding DNA position as long as they are inside the transcript. In order for this to be reported, the amino acid changes tool has to be supplied with an mRNA track which will be used to determine whether the variant included in the transcript.
  • Extract consensus sequence is now able to copy annotations from both existing consensus sequence and the reference sequence.
  • When extracting consensus sequence from a mapping, conflict and low coverage annotations now include the position on the reference.
  • Read mappings can now be exported to a tabular file including detailed per-base information on coverage and nucleotide composition including insertions and deletions.
  • Trim annotations can be used to trim off sequences when exporting to fasta.
  • Secondary peak calling has been improved: it now only detects peaks that have a distinct peak shape, only peaks that fall within the same interval as the top peak are called. In addition, trim annotations are taken into account so that no peaks are called within trimmed regions. This greatly reduced false positive calls. Finally, the annotations now include information about the secondary peak's fraction of the maximum peak height.
  • Limitations on export of Excel 2010 files (xlsx) are removed:
    • Multiple tables can be exported to one xlsx file
    • Reports can be exported to xlsx
    • Hyperlinks are preserved in xlsx files
  • SignalP prediction has been updated to be server-, batch- and workflow enabled.
  • Assemble Sequences tools now accept sequence lists as input.
  • REBASE restriction enzyme list updated to version 310.

Bug fixes

  • The log of a server executed workflow now states when the workflow has been cancelled.
    • A workflow with elements which provide additional inputs could not be batched.
  • Various bugs in the extract consensus sequence tool have been fixed.
  • Tracks with many "chromosomes" took up extra disk space. These are now more compressed.
  • Fixed crash when creating a detailed mapping report.
  • When translating to protein, ambiguous nucleotides potentially resulting in stop codons were not translated properly, and only the codons resulting in an amino acid were represented in the protein. Now the stop codons are also represented by an X in the protein sequence.
  • Prevented multiple error dialogs from being shown on top of each other.

Changes

  • The De novo assembly legacy plugin has been discontinued and is no longer available for this release.

Compatibility

  • This release can be used with CLC Server Command Line Tools 2.1
  • This release is using the read mapping and de novo assembler that corresponds to CLC Assembly Cell 4.2.1

CLC Server Command Line Tools

New tools

  • add_att_b_sites
  • bp_reaction
  • create_track_list
  • empirical_analysis_dge
  • gaussian_statistical_analysis
  • kmer_tree_construction
  • lr_reaction
  • model_testing
  • motif_search
  • proportion_based_statistical_analysis

Tools that have added parameters

  • amino_acid_changes
    • --mrna-track
  • consensus_sequence_extraction
    • --keep-consensus-annotations
    • --transfer-reference-annotations
  • graph_threshold
    • --window-size

Tools that have changed parameters

  • import: some importers have new names to comply with conventions
    • com.clcbio.baseimplementation.importplugins.TrimLinkerLibraryImportPlugin is now trim_adapter_list
    • com.clcbio.genomics.base.algo.rnaseq.smallrna.MirBaseImporter is now mir_base
  • rna_seq: parameters removed
    • --colorspace
    • --downstream
    • --exon-discovery
    • --exon-discovery-min-coverage
    • --exon-discovery-min-length
    • --exon-discovery-min-reads
    • --expression-level
    • --len-fraction
    • --max-distance
    • --min-distance
    • --min-similarity
    • --mismatch
    • --organism
    • --strand-specific
    • --upstream
    • --use-annotations
  • rna_seq: parameters added
    • --auto-detect-paired-distances
    • --color-error-cost
    • --color-space
    • --deletion-cost
    • --genes
    • --global-alignment
    • --insertion-cost
    • --length-fraction
    • --mapping-type
    • --mismatch-cost
    • --mrna
    • --reference-type
    • --similarity-fraction


CLC Genomics Server 5.5.2

Release date: 2013-10-30

Bug fixes

  • Fixed: The automatic Grid Worker deployment during start up of the server deleted license.properties and vmoptions files.


CLC Genomics Server 5.5.1

Release date: 2013-10-21

New features

  • VCF export allows you to enforce diploid reporting of the variants. This will enable the VCF files to be parsed with other software relying on each line to report two alleles. As part of this, the CLCAD field is replaced with CLCAD2 (read more in the user manual).

Changes

  • Variant comparison tools are workflow-enabled
  • When importing Genbank nucleotide sequences, the Server will determine whether it is DNA or RNA based on the sequence rather than the description in the file.

Bug fixes

  • Fixed: An important issue with the interpretation of ensembl-style gtf files when using the Download Genomes functionality or the Import Tracks functionality. This issue only affects version 5.5 of the Genomics Server. If you have downloaded gene annotations using Download Genomes or have chosen to import ensembl-style gtf annotation files using the tool Import | Tracks using version 5.5 of the Genomics Server, then we highly recommend that you delete the annotation tracks you have generated, and perform the download or import again.  Annotations from earlier versions of the Server are not affected by this issue.
  • Fixed inconsistencies when importing variant files from UCSC, affecting variants on the negative strand where the allele sequence is longer than one base. This affects dbSNP tracks downloaded using the Download Genome tool, and we highly recommend that you delete any variant tracks imported or downloaded from UCSC, and perform the import or download again.
  • Fixed: Filter Against Control Reads was using only the first control reads track, if multiple ones were selected. The issue affected both 5.0 and 5.5 versions. If you used multiple control read tracks simultaneously to filter variants, we strongly recommend that you redo the analysis.
  • Fixed: Unresponsive administration interface when connected to Active Directory systems with many users
  • From CLC Server Command Line Tools It is now possible to export to a local folder.
  • Export is now possible on Grid systems.
  • SAM/BAM import: reads mapped to reference sequences that were not provided during import is no longer included in the list of unmapped reads. They are not imported at all, and a note in the history of the imported data records how many reads were ignored.
  • Improvements and fixes to the Indel and Structural Variation tool:
    • Improved the detection of insertions and deletions from self-mapping evidence particularly relevant for amplicon data
    • Fixed: a bug which caused some variants to be called as 'replacements' that should be called as 'insertions' or deletions
    • Fixed: a bug which caused the structural variantions to go undetected for long unaligned ends
  • Fixed: in Trio Analysis, homozygous variants on chr Y and MT and male X were wrongly marked as de novo mutations when not found in the father. The parameters for Trio Analysis have been changed as part of this.
  • Fixed: SAM and BAM export now supports direct gzip and zip compression of the files.
  • Fixed: Local Realignment fails on certain data sets
  • Fixed: out of memory error when performing bootstrapping with ML tree construction methods.


CLC Genomics Server 5.0.6

Release date: 2013-07-19

Bug fixes

  • Fixed problem listing user groups from Active Directory


CLC Genomics Server 5.0.5

Release date: 2013-07-09

Bug fixes

  • Fixed problems downloading and importing COSMIC variation data introduced in CLC Genomics Server 5.0.4: Sex chromosomes and mitochondrial genome were not annotated. We recommend everybody having downloaded or imported COSMIC variations with CLC Genomics Server 5.0.4 to re-do the download or import and re-run all analysis where this COSMIC variant track has been used.
  • Various minor bug fixes.


CLC Genomics Server 5.0.4

Release date: 2013-05-15

Bug fixes

  • Fixed problem in workflows introduced in CLC Genomics Server 5.0.3: only part of the workflow was executed in workflows that branch right after the input element.
  • Fixed issue with automated association of chromosome names during import of track data for some non-human organisms.


CLC Genomics Server 5.0.3

Release date: 2013-05-08

Bug fixes

  • The Create Statistics for Target Regions tool begins counting the reference positions at 0 rather than at 1. This causes a discrepancy with the reference position reported in other tools.
  • Fixed errors of line breaks in annotation notes
  • ChIP-Seq annotations were not added when running ChIP-Seq on the Genomics Server. The fix means that workflows using ChIP-Seq will be broken and needs to be re-configured by deleting the ChIP-Seq element and adding it again.
  • Create mapping graph tracks caused problems when part of workflows


CLC Genomics Server 5.0.2

Release date: 2013-03-19

Improvements

  • An update to the de novo assembly algorithm means that it will only include Ns in the contigs when doing scaffolding, or if the reads themselves contain Ns. Previously, ambiguities in the graph behind the assembly resulted in regions of Ns, but these have turned out to be problematic for customers submitting their results to NCBI, so the algorithm is now taking extra care to avoid this.
  • VCF export: headers mentioning the name and version producing the VCF file, and the identifier of the origin variant track is also encoded as a CLC URL in the header. The installer of the Workbench will per default associate the CLC URL with the Workbench, so that it can directly open the file. Alternatively, the id can be pasted into the search field in the Workbench to retrieve it.
  • GVF can now be exported on the server.
  • Adapter trim list can now be imported on the server.

Bug fixes

  • If the local hostname of the server computer did not resolve to an IP-address, it was not possible to connect to the Server from a Workbench. This has now been fixed.
  • Import or download of UCSC variant tracks was only done partially with no warning to the user. Only variants on chr1 were annotated. This has now been fixed, but we strongly recommend all users downloading or importing variant data from UCSC using Genomics Workbench 6.0 to re-run the import/download using the new version.
  • Trio analysis tool did not report a reference allele as a de novo mutation, even if both mother and father only had variant alleles at this position. This has now been fixed so that reference alleles are not considered special when analyzing the inheritance.
  • The RNA-Seq Analysis produced only single reads in the unmapped reads list. This has now been fixed, and we encourage customers using paired reads as input and performing downstream analysis of the unmapped reads to rerun the RNA-Seq Analysis.
  • In the GO Enrichment Analysis tool for variant data, some columns were missing. This has now been fixed.
  • When trimming paired data, section 4 in the report did not show the right number of reads used as input.
  • Several errors related to workflow configuration and execution have been fixed.
  • An error occurring when using variant tracks from old versions in the Compare Variants tool has been fixed.
  • Annotations were added by the Find Open Reading Frames tool, even though the option to add annotations was not selected. This is now fixed.
  • Fixed an out-of-memory problem in the Create Alignment tool.
  • The result of the Target Regions Statistics tool is now named after the input file.
  • Various bug-fixes


CLC Genomics Server 5.0.1

Release date: 2013-01-23

Improvements

  • The RNA-Seq tool supports strand-specific mapping of paired reads.

Bug fixes

  • Workflows including variant detection need to be upgraded. The variant detection elements need to be re-created and connected.
  • New versions of the Chrome browser caused web interface to flicker
  • Fixed error in probabilistic variant detection that caused it to crash.
  • Fixed an error in the trim report: When several trim methods were chosen, the numbers did not accurately reflect the number of sequences trimmed in each step.
  • Fixed an error in the figure showing the paired distance in the RNA-Seq results report
  • Fixed an error when translating DNA to protein. When more than 10 sequences were produced, the resulting protein sequence included X instead of * as stop symbol. We advice customers to re-run any analyses with the translation tool when using more than 10 sequences as input.
  • Fixed error in target region statistics when some regions were 0 bases long.
  • Link to reference sequence were missing from the history of mapping results, this is now fixed.
  • Unmapped reads from de novo assemblies were not passed on to the next element in a workflow, this is now fixed.
  • Various minor bug-fixes


CLC Genomics Server 5.0

Release date: 2013-01-08

New server-specific features

New features shared with CLC Genomics Workbench

  • Workflow: there are several important new features for workflows
    • It is possible to control which parameters should be locked or unlocked. This means that the creator of the workflow can decide which parameters should be left open for adjustment when the workflow is executed.
    • Several tools are now workflow-enabled:
    • Workflow compatibility: with this release, all of the tools in the Resequencing folder and the Trim tool have changed. This is mainly due to the change in the variant format (explained below). Workflows using these tools need to be updated by deleting the tool, adding it again and restoring the connections and parameters that have been modified. When you open the workflow editor, the workflow elements that need to be updated are high-lighted in red. For installed workflows, this needs to be done in the original workflow design, and the installer needs to be re-built and installed again. We are sorry for the inconvenience caused by this, and we are working on a solution to make the upgrade mechanisms for the next release much more smooth.
  • Variant detection and resequencing
    • New variant data format. We recommend all users of the variant detection tools to read the change notesin the manual for this release. The main features are:
      • Variants are reported with one entry per allele. This means that heterozygous variants are represented as two lines, including one line for the reference allele.
      • Variants were previously joined to form MNVs. The MNV concept has been replaced by linkage groups that mark that two variants have been observed together and assures that tools like Amino Acid Changes will produce correct results.
      • As a consequence, the variant types have been updated.
    • As a consequence of the new data format, the Filter against Variant Databasetool has been updated:
      • The auto-link feature is now obsolete
      • There are now three modes of filtering (learn more here). The filter for exact matches replaces the Haplotype Comparison tool which has been removed from this release
    • New tool for annotating variants with flanking sequence from the reference
    • New tool for removing reference allele variants
  • De novo assembly
    • Automatic paired distance estimation is now part of the de novo assembly
    • Guidance only option is now able to use single reads as well as paired reads
    • The number of Ns deriving from ambiguities in the graph data structure built by the assembler is reduced. Note that this does not refer to Ns inserted as part of scaffolding.
    • Fixed problem causing scaffold annotations to be removed when updating contig sequences based on mapping
    • Improved the scaffolding accuracy for overlapping contigs.
  • Mapping reads to circular chromosomes is now fully supported
    • All algorithms and exporters support circular mappings
    • When downloading genomes using the Download Genome tool, circular chromosomes are marked as circular. If this information is important for the further analysis, please download or import a new copy of the reference genome, since this information is not part of existing tracks. Circular and linear versions of the same chromosome can
  • New tool for extracting consensus sequence from a read mapping or BLAST result:
    • A number of options for handling low-coverage regions, including putting in Ns or splitting the consensus sequence
    • Ability to decide for ambiguity or voting scheme taking quality scores into account when dealing with conflicts. A noise threshold can be added for the ambiguity option.
    • Consensus sequence are annotated with important events (low-coverage regions and conflicts).
    • Ability to run in batch and be part of workflows
  • New tool for merging overlapping pairs
  • Tracks
    • VCF export of variant tracks: Please note that you have to input both the variant track and the reference genome sequence track for Export.
  • Trim:
    • Runs on multiple cores. This will greatly speed up trim on computers with multiple cores.
    • The definition of adapters for adapter trim has changed from the preferences to its own filein the Navigation Area. This makes it easier to manage large sets of adapters, it solves some usability problems related to the old dialog, and it makes it possible to work with adapter trim from the CLC Genomics Server Command Line Tools. Adapters can be imported directly using the standard import framework, or they can be created from scratch by manually adding in the adapter list editor.
  • Target region statistics:
    • The minimum coverage value is use throughout the coverage report and tracks for defining low coverage thresholds
    • Additional table and plot in the report showing how many target regions have a certain percentage of the region above the low coverage threshold.
    • Additional information in the track: median coverage and fraction of fragment covered by the minimum coverage
    • New output type: per-base coverage table can now be created
  • Detailed mapping reportincludes more information:
    • The tables for non-specific and non-perfect matches display the fraction of all mapped reads in addition to the number of reads
    • Overview plot of lengths of insertions and deletions in the read alignments
    • Tables and plots showing differences between reads and reference for each base.
    • Information about quality score distribution for matches and mismatches
    • Distribution of mismatches on read position
    • Information about number of reads with unaligned ends and distribution of lengths of the unaligned ends
  • RNA-Seq: fusion gene table has been changed to list broken pairs rather than gene combinations. The pairs can be extracted to a sequence list for further investigation.
  • Import of tabular mapping files is no longer supported. This format was produced by the early Illumina pipelines (with Eland) and this is no longer relevant. The SAM format has taken the place as the de facto standard for mapping data.
  • Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
  • Find Open Reading Frames can be run in batch and workflows
  • Translate to protein can be run in batch and workflows
  • Restriction map: Excel export now creates a sheet for both the cut sites table and the restriction map.
  • Alignments can be used as input for finding primer binding sites.
  • BLAST results and 3D structures can be exported as text.
  • Export to fastq now supports sequences up to 32k in length
  • Naming of output from de novo assembly and read mapping made consistent

Bug fixes

  • Fixed a number of mapper errors causing the mapper to crash.
  • Fixed a problem in the read mapper when estimating paired distances. This lead to very few reads mapping as pairs.
  • Fixed problem of not correctly formatting qualifiers in EMBL export.
  • Test on proportions: Fixed an error caused by the wrong group being used as reference, which means that the positive values should have been negative and vice versa.
  • Various bug fixes.

CLC Server Command Line Tools

This release of the CLC Genomics Server 5.0 is compatible with CLC Server Command Line Tools 1.7

New tools

  • alignment
  • annotate_variant_flank
  • consensus_sequence_extraction
  • convert_to_dna
  • convert_to_rna
  • filter_reference_variants
  • find_open_reading_frames
  • merge_overlapping_pairs
  • trio_analysis

Tools that have changed names

  • annotate_against_database_track has been renamed to annotate_from_known_variants
  • filter_against_variant_database has been renamed to filter_against_known_variants
  • merge_tracks has been renamed to merge_annotation_tracks

Tools that have been removed

  • ngs_import_tabular is no longer relevant because it was directed at the very first Illumina pipelines
  • filter_haplotype_comparison has been replaced by filter_against_known_variants

Tools that have changed parameters

  • amino_acid_changes
    • --CDSTrack changed into --cds-track for consistency reasons
  • compare_variants_within_group
    • --reference removed (no longer needed)
  • fisher_exact_test
    • --reference removed (no longer needed)
  • statistics_target_regions
    • --create-coverage-table (new output option)
  • filter_marginal_variants
    • --track removed (no longer needed)
  • trim
    • --adapters and min-count replaced by --trim-adapter-list
  • small_rna_sampling
    • --adapters and min-count replaced by --trim-adapter-list


CLC Genomics Server 4.5.2

Release date: 2012-12-07

Bug fixes

  • Fixed a number of mapper errors causing the mapper to crash.
  • Fixed a problem in the read mapper when estimating paired distances. This lead to very few reads mapping as pairs.
  • Fixed problem of not correctly formatting qualifiers in EMBL export.
  • Various bug fixes.


CLC Genomics Server 4.5.1

Release date: 2012-09-05

New features

Important: In Genomics Workbench 5.5, the Process Tagged Sequences tool would sometimes switch the sample names of the results. We strongly recommend everybody to update to the new version, and re-run all analyses made with this tool in Genomics Workbench 5.5.


CLC Genomics Server 4.5

Release date: 2012-08-09

New features

  • Re-sequencing tools
    • New variant caller: Probabilistic variant detection .
      • This is based on a probabilistic model in contrast to the quality-based variant caller that is based on quality analysis and cut-offs.
      • Supports genomes with a ploidy of 1, 2, 3 or 4.
      • Pre-filtering for non-specific matches and intact pairs
      • Post-filtering of homopolymer regions and forward/reverse reads balance
    • The old SNP and DIP detection tools are merged into one: Quality-based Variant Detection .
      • Pre-filtering for non-specific matches and intact pairs
      • Post-filtering of homopolymer regions and forward/reverse reads balance
    • Target regions statistics (previously a plug-in) is now integrated into the Workbench
      • A new parameter: Minimum coverage that will report the fraction of each region that is covered by at least this number of reads
      • Works on tracks: the regions of interest are defined in a track and the resulting per-region table is reported as a track
    • Annotation and filtering tools for variants
      • Annotate and filter against database variants (dbSNP, 1000 genomes or other databases that can be downloaded or imported)
      • Filtering of marginal variant calls based on average base quality, forward/reverse reads balance and frequency
      • Annotating variants with exon numbers
    • Variant comparison
      • Compare variants within group : Find variants that are shared between a number of samples
      • Fisher exact test : Compare variants between case and control groups to find variants that are more common in the case than in the control
      • Trio analysis : Compare child-father-mother variants to enable studies of inherited and de novo mutations
      • Filter against control reads : Compare a variant track against a control sample to remove variants that are also present in the control
      • Filter on haplotype comparison : Identifies variants that have the same haplotype in two samples.
    • Functional consequences of variants
      • GO enrichment analysis .This tool can be used to investigate the effect of candidate variants by analyzing the affected genes for a common functional role.
      • Amino acid changes : Classify synonymous and non-synonymous variants and see the effect on the protein.
      • Annotate with conservation scores : Annotate a variant with a score from conservation tracks that can be imported into the Workbench.
      • Predict splice site effect : A simple investigation to see if the variant is within two bases of an intron-exon boundary
  • Download of reference genome and annotations
    • Integrated download of reference genome sequences and annotations for selected organisms
    • Example : for human hg19, you can directly download sequences, genes and transcripts, variants from 1000 genomes, Hapmap, COSMIC, and dbSNP (incl. common SNPs).
  • Tracks
    • Genomic information for re-sequencing analysis can now be stored as tracks.
    • Great power for comparison and visualization because different kinds of data (reads, variants, genes etc) are not bundled into one static file but are separated into one file per data type. This means that different data sources can be compared and visualized in a flexible way.
    • All tools for re-sequencing has options to create and use tracks (e.g. read mapping, variant detection etc). More tools will be re-designed to work with tracks later.
    • Tools for converting between standard sequences and mappings and tracks:
      • Convert tracks to sequences, mappings etc
      • Convert sequences, mappings and annotations to tracks
    • Tools for filtering, annotating and merging tracks
    • Support for importing files as tracks from a number of new formats:
      • Fasta
      • VCF
      • BED
      • Wiggle
      • UCSC table format
      • GFF / GTF and GVF
      • Complete genomics master var files
  • Workflow
    • Workflows can be built in the Workbench to combine various tools from the Toolbox into one analysis, connecting the output from one tool to the input from another
    • Workflows can be distributed and installed either in the Workbench or in the CLC Genomics Server
    • The creator of the workflow can configure parameters for the workflow and these will be fixed when the workflow is distributed and installed
    • The creator of the workflow decides which of the output from the tools that should be saved and which should be discarded
    • Workflows can be run in batch , making it a powerful tool for crunching high numbers of samples through the same pipeline.
  • New read mapper
    • Great improvement of speed for mapping (white paper to be released soon)
    • Support for complex genomes with many repeats
    • Re-design of wizard for read mapping to make it simpler and easier to use. Options to control consensus sequence building and annotating with conflict annotations have been removed, since they have very little relevance for the amounts of data created by NGS platforms today
    • Color space mapping is still performed with the old mapper
    • Automatic calculation of paired distance (only for base space data)
    • Report includes percentage of reads instead of only counts
    • Changed strategy for placement of gaps: previous versions tried to cluster gaps into as few units as possible. This would sometimes cause problems for variant calling because this would in some situations place the gaps differently from read to read.
    • Please note that the memory requirements are different than for the old mapper. The memory requirements depend largely on the size of the reference genome. We will soon update our system requirements page to reflect this.
  • Sequencing QC report : Create summary statistics for sequencing data in various ways:
    • General statistics on read length etc
    • Quality statistics on quality scores
    • Over-representation analysis of subsequences
    • Analysis of duplicated reads

Special notes for customers already using the Genomics Gateway plug-in

  • Download tool for downloading genomic data replaces Ensembl download tool
  • Unlimited number of chromosomes in tracks
  • More streamlined conversion tools:
    • Convert tracks to sequences, mappings etc
    • Convert sequences, mappings and annotations to tracks
  • Export tracks to gff, vcf, sam
  • New tool for filtering marginal variant calls
  • New tool for annotating against database variants

CLC Server Command Line Tools

This release of the CLC Genomics Server 4.5 is compatible with CLC Server Command Line Tools 1.6

New tools

  • amino_acid_changes
  • annotate_against_database_track
  • annotate_conservation_score
  • annotate_exon_numbers
  • annotate_overlapping
  • blast_delete_index
  • blast_list_index_files
  • blast_ncbi
  • blast_set_db_locations
  • compare_variants_within_group
  • convert_from_tracks
  • convert_to_tracks
  • download_genome
  • extract_sequences
  • filter_against_control_reads
  • filter_against_variant_database
  • filter_annotation_names
  • filter_haplotype_comparison
  • filter_marginal_variants
  • filter_overlapping
  • fisher_exact_test
  • gc_contents_graph_track
  • go_enrichment_variants
  • import_tracks
  • mapping_graph_tracks
  • merge_tracks
  • predict_splice_site
  • probabilistic_variant_detection
  • sequencing_qc_report
  • statistics_target_regions

Tools that have changed names

  • dip_detection and snp_detection have been merged into quality-based_variant_detection
  • epcr has changed name to find_primer_binding_sites in order to reflect the name used elsewhere for this tool
  • merge_clusters has been renamed to merge_mappings to reflect the terminology used elsewhere

Tools that have changed parameters

  • chip_seq
    • –window-size changed into –window-shifted
  • detailed_mapping_report
    • –reference-or-contig-count removed
    • –separate-mapping-statistics removed
    • –create-table added
  • ngs_import_roche454
    • –flx-or-titanium-linker changed into –linker-sequence
  • read_mapping
    • options removed
      • –annotate-conflicts
      • –conflict-resolution-mode
      • –create-sequence-list
      • –do-split
      • –long-reads-alignment-mode
      • –long-reads-color-error-cost
      • –long-reads-color-space
      • –long-reads-deletion-cost
      • –long-reads-insertion-cost
      • –long-reads-length-fraction
      • –long-reads-match-cost
      • –long-reads-similarity-fraction
      • –map-as-long-reads
      • –map-as-single-reads
      • –mask-reference
      • –mask-reference-type
      • –match-mode
      • –maximum-alignment-count
      • –maximum-distance
      • –minimum-distance
      • –override-distance
      • –read-settings
      • –score-limit
      • –score-limit-offset
      • –short-reads-alignment-mode
      • –short-reads-color-error-cost
      • –short-reads-color-space
      • –short-reads-deletion-cost
      • –short-reads-insertion-cost
      • –short-reads-mismatch-cost
      • –short-reads-ungapped
      • –split-count
      • –split-index
      • –strand-specific
    • options added
      • –auto-detect-paired-distances
      • –collect-unmapped
      • –color-error-cost
      • –color-space
      • –deletion-cost
      • –global-alignment
      • –insertion-cost
      • –length-fraction
      • –masking-mode
      • –masking-track
      • –mismatch-cost
      • –non-specific-match-handling
      • –output-mode
      • –similarity-fraction


CLC Genomics Server 4.1

Release date: 2012-04-11

New features

Ion Torrent paired protocols are now supported for both fastq and sff files.


CLC Genomics Server 4.0.1

Release date: 2012-02-23

Bug fixes

  • Fixed: For grid set-ups: certain setups with OGE would run on a maximum of one core. (Refer to Genomics Server documentation for updated configuration information).
  • Fixed: Calculation of cDNA-level changes in variant detection failed in some situations.
  • Updated: Small RNA tools: the annotation tools now support recent changes to miRBase where mature and mature* nomenclature has been replaced with 3′ and 5′ mature regions.


CLC Genomics Server 4.0

Release date: 2012-02-13

New plug-ins and plug-in updates

  • Genomics Gateway plug-in updated
    • New tools for analyzing variants in groups of samples, enabling systematic analysis of genetic variants for whole genome, exome or targeted approaches.
      • Find Common Variations in Group. This can be used to find common variants in a group of variant tracks.
      • Fisher Exact Test. Comparing two groups of variant tracks (e.g. can be used for case-control studies). You can see which variants are found more common in the case compared to the control group using the Fisher Exact test.
      • Filter against Control Reads. This can be used to compare a single case variant track against a negative control from the same sample. It will check whether a certain number of the reads in the control sample have the same allele present as in the case variant.
    • New tools for functional annotation of variants
      • Go Enrichment Analysis for identifying significant gene ontology terms, which are annotated to genes having at least one variation.
      • Annotation with Conservation Scores. By importing a conservation score track (e.g. PhyloP Scores), variants can be annotated with a conservation score. Variants with a high score are assumed to alter functionally important regions.
    • New data structure.
      • All tracks are now saved as single files, and you can create a Track List to visualize them together.
      • A tool is available for data conversion from track sets to single tracks
    • New organization of the “Tool box” to provide a better overview
    • Support for batching and running tools on a Genomics Server
    • The Track List view supports drag and drop for adding and re-arranging tracks
    • Several Graph tracks can be created and displayed
    • Read the updated manual here.
  • Probabilistic Variant Detection Plug-in updated
    • The probability used as threshold for the algorithm is now reported in the output
    • Variants reported cDNA-level numbering and variant information compatible with www.hgvs.org/

Core server features and improvements

  • Possibility to import data from the Workbench on the Server. This was previously only possible with NGS data import.
  • BLAST database management: It is now possible to delete BLAST databases in the Web interface.
  • The blue dot indicating that a tool could be run on the server has been removed in order to provide a simpler user interface for new users.
  • External Applications: parameters for maximum number of cores and the name of the user logged in can be automatically provided by the server when the algorithm is executed.
  • Support for redirecting non-SSL port to SSL port when accessing the server’s web interface.
  • Command Line Tools: it is allowed to provide CLC urls with full path including the .clc file extension.

Algorithm features and improvements

  • New de novo assembler.
    • Scaffolding is integrated into the assembly. This means better resolution of contigs and insertion of Ns when two contigs cannot be joined in sequence but there is pair information that connects them.
    • New extended report for the assembly with information about nucleotide distribution, contig lengths measurements and scaffolding regions.
    • New parameter for specifying the maximum bubble size. There is a default value which is automatically calculated based on the input data.
    • New white paper with benchmarks and results from quality control.
    • The old de novo assembler is available as a plug-in. At the end of 2012, the plug-in will be discontinued, so it should only be used for backwards compatibility with results from older runs or if the new assembler fails.
  • SNP and DIP detection results include cDNA-level numbering and variant information compatible with www.hgvs.org/
  • SAM files exported from the Server now include basic information about read groups. Furthermore, read orientation for paired reads is now preserved when exporting to SAM and BAM files.
  • Improved exploitation of multi-core machines in read-mapping, RNA-Seq, and de-novo assembly.
  • Improved performance and memory management for high-throughput analyses in general.

Bug fixes

  • Export of BLAST results was not possible on the server.


CLC Genomics Server 3.6

Release date: 2011-11-29

New plug-ins and plug-in updates

  • New plug-in released: Ab Initio Transcript Discovery
    • Large gap mapper plug-in is renamed and now includes a tool for transcript discovery. Based on gapped alignments of RNA-Seq data, the plug-in identifies new transcripts and creates or extends annotations on the reference sequence that can be used for measuring gene expression using the RNA-Seq Analysis tool of the Genomics Workbench. The plug-in provides functionality a la Cufflinks/TopHat.
  • Genomics Gateway plug-in updated
    • New refiner: variant frequency. This allows you to filter a variation track, so that only the variants that have a frequency above a user-defined threshold remain. Note that the filter only applies to the frequency of non-reference alleles.
    • Performance improvements when visualizing read tracks
    • Fixed: CDS annotations from Ensembl did not include start codons
    • Fixed: Some variation tracks were not always recognized as variations. This means that the variation-specific refiners could not be used.
    • Fixed: Table view of annotation tracks could have a very large number of columns that are now combined into one column.
    • Fixed: There was an error when closing a view without saving changes. This could lead to subsequent errors when trying to rename tracks.
  • Structural variation plug-in updated
    • Only detection of insertions, deletions and interchromosomal variations are now supported.
    • The plug-in has a problem with repeats. The best way to work around this is to ignore non-specific matches when doing the mapping, to run the structural variant detection with a very stringent p-value cutoff and filter repeats out afterwards if possible (this could be by refinement with the microsatallite track from Biobase or another repeat track using the Genomics Gateway).
    • Integration of exporter to export results in circos format.
See a list of all plug-ins here. The pdf documentation of all plug-ins has been updated as well.

Core server features and improvements

  • The grid integration is now released out of beta
    • Core management: you can restrict the maximum number of cores that the Grid Worker is allowed to use. This is useful the execution node is shared with other jobs and the CLC Grid Worker needs to respect an assignment of the number of cores to use. This is mainly an issue for the De novo assembly and Read Mapping algorithms but the restriction applies to all algorithms that use several cores.
  • For Oracle databases: There are now two ways of connecting to an Oracle database. One is the traditional using SID style and the other is using thin-style service name. Existing installations do not need to be changed.

Algorithm features and improvements

  • BLAST is now available on the server
    • Creation of BLAST databases
    • Running BLAST jobs on the server against either databases on the server file system or temporary “on-the-fly” databases.
  • Process tagged sequences
    • A summary report is now available with an overview of the number of reads per bar code.
    • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol.
  • Find Binding Sites and Create Fragments improved:
    • Can now be run on the server
    • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G).
    • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table).
  • Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.
  • Enhancing the nomenclature of reporting amino acid changes in variant detection:
    • p. prefix included
    •  ? used for unknown (rather than non-standard “Unknown”)
    • = used to denote an allele which agrees with the reference sequence (rather than missing entries or entries like Ala45Ala)
    • [...] used around ,-separated lists of changes, each change coming from a different CDS annotation
    • [...];[...] scheme used to separate multiple alleles at same site

Bug fixes

  • Fixed: Import of SOLiD data failed when multiple sets of paired data was selected.
  • Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis.


CLC Genomics Server 3.5

Release date: 2011-10-12

New plug-ins and plug-in updates

Core server features and improvements

  • Permission control on file system. Previously, this feature was only available for customers with a Bioinformatics Database but now all server customers will be able to specify which users should have access to data on the server. This is done by logging in as admin through the Workbench and setting read and write permissions on folders.
  • SSL. The Server now supports secure connections from clients (either Workbench, Command Line Tools or the web interface)
  • Status icon in Workbench is now showing info on current server connection. Clicking the icon when not logged in will display the log-in dialog.
  • Permissions on server commands: server administrators can decide if certain groups should not be allowed to run certain analyses. This can be controlled also for each external application configuration.
  • Permissions on import/export directories: server administrators can decide if certain groups should not be allowed to access import/export directories
  • Web interface import and export from Import/Export directories on server file system
  • Support for attachments on Grid jobs. This means that you can run Next-Generation Sequencing data imports with data from the client file system when running on a grid. Previously you could only import data from the import/export directories.
  • Command Line Tools include a tool for setting permissions on folders on the server.

Algorithm features and improvements

  • De novo assembly improvements:
    • Word size can now be manually adjusted
    • When update contigs is not selected, the resulting mapping table will also include contigs where no reads map back. This means that the number of rows in the table will be identical to the number of “Simple contigs” produced by the de novo assembler. Previously contigs with less than two reads mapped back would be omitted from the table.
  • Merge Mapping Results will produce a mapping table when mapping tables are provided as input
  • Mapping tables now include a row for reference sequences where no reads map. This is done to provide consistency of results. Opening such an entry in the table will just open the reference sequence in the table.
  • SNP detection no longer ignores ambiguity bases in the reads. Each ambiguity code is treated as a separate variant; no merging of the possible variants covered by each ambiguity code is attempted (this typically only has an effect when using Sanger sequencing data since standard NGS platforms do not use ambiguity base calls).
  • SAM import and export format is now described in detail in the user manual.

Bug fixes

  • Fixed: Orientation of SOLiD mate-pair data was not set correctly on import. This meant that the reads were marked as broken pairs after mapping. We strongly recommend all users to re-run the import if using SOLiD mate pair data.
  • Fixed: Experiments tables can now be exported in Excel and csv formats
  • Fixed: If a combination of trim options is used, like quality trim or length trim in addition to adapter trimming on both strands, the reads could end up reverse complemented.
  • Fixed: Import of paired data generated by Illumina Casava 1.8 did not match the pairs correctly. Users are advised to re-import and re-analyze all data imported from Casava 1.8.
  • Fixed: De novo assembly sometimes failed on Mac OS 10.7 Lion.
  • Fixed: Errors for read mappings with the text “premature end of .cas file” have now been fixed. This has only been a problem on Windows.


CLC Genomics Server 3.2.2

Release date: 2011-07-14

Bug fixes

  • Fixed: A cache-related bug which would sometimes result in errors when running large jobs.
  • Fixed: A problem with interpretation of broken pairs on re-import from SAM format files.
  • Added missing Java VM-options to the CLC Grid Worker


CLC Genomics Server 3.2.1

Release date: 2011-06-27

Bug fixes

  • De novo assembly produced empty results
  • Paired distances for read mapping were not recorded correctly in history
  • Adapter trim with Command Line Tools: if multiple adapters were provided, only the first was used
  • Various minor bug-fixes


CLC Genomics Server 3.2

Release date: 2011-06-21

New and improved features

  • External applications is now running on grids
  • Secondary peak calling functionality is now available on the server
  • Import of GFF files is now available on the server
  • The High-throughput Sequencing Data Import Location has been redefined as a more general Import/Export location
  • CLC Server Command Line Tools is now released in a final version
  • Mapping
    • New mapping data format supports multiple alignments and allows for import and full visualization of Complete Genomics evidence files in SAM format
    • New plug-in for gapped read mapping of e.g. cDNA to genomes
  • New plugin to detect Structural variation
    • Action to detect structural genomic variation from paired read information
    • Action to detect copy-number variation (CNV) from coverage information
  • New and more flexible data structures to store information about paired data
  • All history entries will from now on include the version number of the software
  • Previous limit at 2 billion for the maximum number of reads in one analysis has been removed.
  • Reporting of amino acid changes in SNP and DIP detection now follows recommended nomenclature more closely w.r.t. changes that affect start codons and changes that cause indels at the amino acid level.
  • Performance of Excel 2010 exporter improved in terms of speed and memory requirements
  • Export of trace data in scf format.


CLC Genomics Server 3.1.1

Release date: 2011-04-06

RNA-Seq would crash when selecting prokaryote as organism type


CLC Genomics Server 3.1

Release date: 2011-04-05

New and improved features

  • Support for PBS Pro in addition to Oracle Grid Engine. Read more.
  • Import of Ion Torrent data. A special importer has been made for Ion Torrent data in fastq or sff format. Read more.
  • Grid integration redesigned to be more stable and easier to deploy. Existing users of the grid integration please contact [email protected] for upgrade instructions.
  • Import through Command Line Tools now works on grid set-ups. Read more.
  • Reporting merged SNPs is now optional. Read more.
  • SNP detection: When minimum paired coverage is set, reads from broken pairs will be completely ignored. Read more.
  • RNA-Seq: the transcript-level sample includes a column for the ratio of unique to total transcript reads. Note that this means that results generated with this version cannot be used in older versions. Read more.
  • Better support for color space SAM/BAM files.
  • Export in color space fastq format. When data is marked as color space, exporting in fastq format will produce a file with color encoding rather than bases.
  • Error reports from grid workers now include log files
  • Audit log files are archived to files every three months
  • Faster submission of bug report archives
  • List of grid presets in the Workbench dialog is now sorted, and the last selection of preset is preserved so that the first step can be skipped

Bug fixes

  • Fixed: The Gridworker would run out of memory on computers with large amounts of memory
  • Fixed: Import of csfasta paired data crashed when one read had a dot in the beginning of the sequence.
  • Import of paired qseq files: the read pairs are now joined correctly when importing paired qseq files
  • Fixed: Import of GO annotation files did not work
  • When processing tagged paired data sets, the status of the resulting files were not marked as paired. This means that subsequent analyses did not make use of the paired information.
  • Various minor bug fixes
Please note that you need to upgrade the Workbench plug-in in order to connect to the new server and you will also need to update the Command Line Tools client


CLC Genomics Server 3.0.1

Release date: 2011-02-18

Bug fixes

  • CHiP-seq analysis adjusted for the use of gapped aligner – CHiP-seq analysis with previous version should be redone
  • Improved support for Mac OS X systems with japanese language


CLC Genomics Server 3.0

Release date: 2011-01-26

New features

  • New way of running analyses on the server. Previously each analysis tool was duplicated in the Toolbox, but now the first step in the analysis wizard is about where the analysis should run.
  • Command Line Tools (will be available for beta test at selected customers medio January 2011)
    • A command line-based alternative to the Workbench as client
    • Enables using the server tools in a scripting environment
    • Note that this is not a stand-alone command line program – it is a client to the server
  • Oracle Grid Engine support (will be available for beta test at selected customers medio January 2011)
    • Jobs can be run on Oracle Grid Engine (formerly known as Sun Grid Engine)
    • Job status can be monitored from the Workbench
    • Seamless integration in the Workbench clients
  • External Applications re-design Read more
    • Sample scripts and configurations for Bowtie and Velvet integration available for download
    • New option to export and import external application configuration settings
    • New options for post-processing of analysis results see an example
    • New overview of parameter flows Read more
  • Check set-up tool for diagnostics of server setup Read more
  • Batching functionality of all high-throughput sequencing tools. It is now possible to start batch runs, e.g. running 12 samples through RNA-Seq Analysis in one go. Read more.
  • RNA-seq: transcript-level expression values and support for paired data
    • Included option to use paired information in RNA-seq. Read more.
    • Expression values can now be stratified into transcript level expression values, both for single and paired reads. Read more.
    • SOLiD data: new algorithm for mapping reads allows much higher fraction of reads to be mapped. Rather than a score limit, you now specify the stringency of the mapping using length and similarity fractions. Read more.
    • Similarity fraction for mapping of long reads is now available as a user-specified option (this was previously automatically set). Read more.
    • Simple reporting of putative gene fusions when using paired data. Read more.
    • Note about compatibility: Results from earlier versions should not be compared with results from this version.
  • SOLiD data: new algorithm for mapping reads allows much higher fraction of the reads to be mapped.
    • Rather than a score limit, you now specify the stringency of the mapping using length and similarity fractions. Read more..
    • Note about compatibility: Results from earlier versions should not be compared with results from this version.
  • Multiplexing: Process tagged sequencing data
    • De-multiplexing tool is now running on the server Read more
    • It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples. Read more.
    • You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses.
  • High-throughput Sequencing Import includes an option to place data into sub-folders (useful for batching subsequent analyses)
  • SNP detection reports adjacent SNPs within the same codon as one SNP. Read more.
  • De novo assembly: post-processing options when mapping reads back to contig sequences have been expanded. It is now possible to preserve the original contig sequences from the assembler (they used to be replaced by the consensus sequence from the mapping). Read more.
  • Support for exporting tables as tab-delimited files.
  • Memory allocation: the default memory allocation for the Server changes from 75% to 50% of available physical memory with a maximum at 50 GB.
  • New way of getting a license based on Order ID and automatic download of a license file. This makes it much easier to set up the server.
  • New licensing model replacing the Small, Medium and Large business editions.

Bug fixes

  • SNP detection bug with corrupt complementary CDS annotations.
  • SNP detection: color correction errors now count when filtering SNPs (this has become important with the new mapping algorithm for SOLiD data).
  • Time out in the communication between Workbench and Server is now recovered in most situations.
  • Various bug-fixes


CLC Genomics Server 2.6

Release date: 2010-10-28

Improvements

  • Create detailed mapping report now available on server

Bug fixes

  • SNP and DIP detection previously ignored overlapping pairs. Now they count (as one read) if the fulfill the quality criteria (SNP detection). In cases where the two parts of the pair disagree, the pair does not count. We recommend running all SNP and DIP detections based on overlapping pairs data sets again (this would be the case if the minimum distance when mapping the reads is lower than two times the read length). There is no need to re-run mappings – just the SNP/DIP detection.
  • ChIP-Seq: “nearest gene” reported not always right. This was the case for the last peak on each chromosome and also in cases where the order of the gene annotations in the reference file did not correspond to the order of the annotations on the actual sequence. We recommend running all ChIP-Seq Analyses again to get the correct reporting of nearest genes. There is no need to re-run the mappings.
  • Color space check box not checked per default when running color space data. We recommend checking the history of mappings based on color space data. If the history shows “Color space alignment = No”, you should re-run the mapping and consequent analyses.
  • Improved import of SAM/BAM files:
    • Better support for files from SOLiD Bioscope
    • Preliminary support for Complete Genomics files (The actual alignment is not represented completely – insertions that relates to a consensus sequence will be represented as unaligned ends in the imported mappings. This should be taken into account when looking for variations.)
  • Going from step 2 to 3 in SNP detection wizard took a long time when using data with many references/contigs
  • Various minor bug fixes


CLC Genomics Server 2.5.3

Release date: 2010-08-25

Bug fixes

  • Fixed error when importing 454 SFF files
  • Fixed error when importing SOLiD data with quality scores when the reads had “.”
  • Fixed error mapping large data sets on Windows 64-bit systems
  • Genbank export of annotations on the negative strand were not in the right order
  • Fixed memory and performance issues related to import of many sequences, eg. from ACE files.
  • Fixed problem with SNP detection on large data sets suddenly running very slow.
  • Better support for html when exporting tables to Excel.
  • Various minor bug fixes
 


CLC Genomics Server 2.5.2

Release date: 2010-07-05

Bug-fixes

  • Fixed a problem resulting in a “node communication error” when using built-in authentication and job nodes
  • Fixed a problem using initial bind credentials with LDAP authentication


CLC Genomics Server 2.5.1

Release date: 2010-06-30

Bug-fixes

  • Resolves problem with SAM/BAM import
  • Resolves problem with import of tabular mapping files
  • Missing FastQ export included
  • Scalability improvements in mapping and de-novo assembly with drastic improvements in performance


CLC Genomics Server 2.5

Release date: 2010-06-15

New features

  • New de novo assembly algorithm. Read more 
  • Small RNA Analysis 
    • Brand new tool for analyzing small RNA (including miRNA) data sets
    • Adapter trimming
    • Counting of tags
    • Annotation using miRBase and other resources
    • Visualization of miRNA variants
    • Expression analysis
  • Server-side import of High-throughput Sequencing Data. Read more
  • Trim sequences is now available on the server. Read more 
  • Renaming and redefining concepts
    • Reference assembly -> Read mapping. We adjust to the common term used today for aligning sequencing reads to a reference sequence.
    • Contig -> Read mapping. The result of read mapping was previously called a contig (i.e. the alignment of reads to a reference sequence). Now, the term “contig” is used exclusively for results from de novo assembly. The result of mapping reads is called a “read mapping”.
    • Paired-end -> Paired. We now distinguish during import between Paired-end and Mate pair data. Once imported, there is no difference, and they are both called “Paired”.
  • Improved SAM/BAM import :
    • BAM format now supported, both import and export
    • More robust implementation
    • Better performance
    • Preview panel making it easier to match reference and SAM/BAM file
    • Reference sequence name spaces automatically converted to underscores when comparing with SAM/BAM file
  • High-throughput Sequence Data Import
    • Gzip support
    • SOLiD fastq format supported (when downloading SOLiD data from Sequence Read Archive, SRA). Read more 
    • 454 paired data: Support for both FLX and Titanium linkers (also the possibility to add custom non-palindromic linkers). Read more 
    • Improved support for SOLiD paired-end data. Read more 
    • Support for data from Illumina Pipeline 1.5. Read more 
    • Import of tabular alignment files: it is now possible to specify a read name from the file to be imported with the read. Read more 
  • Better compression of reference sequences (lower memory footprint and disk space usage)
  • Performance improvement of read mapping algorithm
  • Improved memory management in general: lower memory footprint and shorter management overhead pauses.
  • Improved memory handling of large tabular data sets.
  • RNA-Seq:
    • Directional RNA-Seq. Read more 
    • Exon-intron reads are now counted under Total exon reads. When comparing new and old samples, please re-run the analysis on the old samples to ensure consistency. Read more .
  • SNP and DIP detection :
    • Dialog usability improved by adding an advanced panel for advanced users
    • Minimum counts have been made more clear by creating a Minimum and Sufficient count
  • Performance of ACE export improved, especially for long reference sequences or read mapping tables.
  • It is now possible to pause and restart processes involving read mapping and de novo assembly (except the accelerated mapping part of the analyses). Read more 
  • When searching data from the Workbench, the results did not list the custom attributes of the data. Read more .
  • Copy operations on server locations are now performed completely on the server side, eliminating client processing and network traffic
  • A number of import and export formats have been included on the server, including csv, ace and excel.
  • Progress when downloading files from the server using the web interface is shown in browser
  • External applications:
    • Added option to allow external application processes to run as master processes (no blocking of the queue). Read more
    • Command line call is now part of error message when an external application fails. Read more
  • Performance of export of data via the Workbench from a server location has been improved
  • Index server status added under User Statistics in the Admin tab of the web interface.
  • Possibility to report server-side bugs from both web interface and Workbench, including log and configuration files. Read more
  • Improved usability of user interface for adding locations in the web interface. Read more
  • Server home path has been removed from configuration panel in the web interface (it now resides in a properties file in the settings directory). This makes it easier to deploy a job node installation in a mixed environment.

Bug-fixes

  • Added support for viewing data attributes in web browser for enzyme lists.
  • Job nodes failed to start when master server was not already running.
  • Display of folder structure was not right in special cases involving differentiated permission on folders
  • Changed order of custom attributes was not reflected in search drop-down menu
  • Searching for data entered as custom attributes required specification of which attribute to search in
  • Read mapping: fixed windows errors on large data sets, fixed color space errors
  • RNA-Seq: max number of mismatches when running color space data could be set to three in the dialog but did not take effect. Now the limit at 2 is enforced in the dialog.
  • Genbank import: sequence name (LOCUS) was truncated to 18 characters


CLC Genomics Server 2.0.1

Release date: 2010-02-04

Bug fixes

  • A few import formats was missing on the server (when importing using the API and the web interface)
  • RNA-seq: reads that extend over more than two exons are now shown correctly
  • Names of results from reference assemblies are now named according to the input data
  • Various bug fixes


CLC Genomics Server 2.0

Release date: 2009-12-15

New features

  • Support for Job Nodes. Parallelized Job Execution (on Command level) with flexible/scalable multi job node setup. Advanced configuration of job nodes on command level.
  • 3 tier data communication. Data communication/management is now based on communication through the Server middleware.
  • Option for File locations on server.
  • Index Server for stability/scalability.
  • Command Line Integration tool on server side for invocation through user friendly UI on Workbench. Includes example (ClustalW)
  • All High throughput sequencing data importers are now on the Server. That is “Roche 454″, “Illumina”, “SOLiD”, “Fasta/Helicos”, “Sanger”, “SAM Assembly Files”, “Tabular Assembly Files (ELAND format)”
  • RNA-Sequencing can now be run on the Server. Read more…
    • The analysis including mapping of reads, distributing non-specific matches and calculating expression values are done on the server
    • Visualization is done in the Workbench
    • Statistical analysis of the results are done in the Workbench (these are not heavy calculations)
  • Administrators can close user sessions. Read more…
  • Option to automatically log in to the server when the Workbench starts Read more…
  • The order of attributes can now be changed. Read more…
  • Finished server processes are removed when closing down the Workbench. Running processes will be shown next time the Workbench connects to the server.
  • Global alignment for long reads when running reference assembly algorithm
  • Gapped color-space alignment when running reference assembly
  • Significantly improved speed of all operations with large data sets
  • The unassembled reads from an assembly now preserves their paired-end status (this also means that you can get two lists – one with pairs and one with the remainder of the broken pairs
  • SNP detection output table now reports if multiple non-synonymous SNPs exist in same codon
  • SNP detection dialog: Quality filtering is no longer disabled when quality scores are missing. Due to performance issues it is not possible to check if quality scores are present. The SNP detection will just omit the quality score filtering if quality scores are not present.
  • SNP detection: possible to detect variants with frequency less than 1 percent.
  • General import and export
    • Export tables and reports in Excel format.
    • Import section of user manual re-structured to provide better overview Read more…. Expression data importers are now described in technical details in a separate section Read more….
    • You can now export multiple sequence lists in fasta format
    • Forced import of zip files is now supported (it will force import the contents of the zip file)
    • The standard import now accepts gzip and tar files as well as zip
    • Genbank importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: “product”, “locus_tag”, “protein_id” and “transcript_id”
    • When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.

Bug-fixes:

  • Fixed an error opening external files from a server location


CLC Genomics Server 1.6.1

Release date: 2009-08-21

New features

  • Export of annotations in GFF format (joined regions not supported)
  • Export of sequence data in fastq format

Bug-fixes:

  • Fixed problems importing expression annotation files
  • Various bug-fixes
This update is recommended for all users.


CLC Genomics Server 1.6

Release date: 2009-07-02

New features

  • ChIP-Seq analysis is now able to (optionally) use a control sample. Read more… 
  • Reference assembly of short reads: user can now choose between local and global alignment Read more… 
  • Reference and de novo assembly output options have been changed so that you no longer need to decide whether you want a contig table or single contigs. Whenever more than one contig is produced, the Workbench automatically creates a contig table Read more… 

Bug fixes

  • Assembly against many reference sequences could run out of memory. This is been significantly improved.
  • Integration with the Genomics Server: fixed an error when selecting contigs from a contig table for analysis. This is no longer possible (i.e. you have to save the contig first).
  • Various bug fixes


CLC Genomics Server 1.5

Release date: 2009-06-02

Data formats:

  • Data generated with version 3.5 cannot be read in earlier versions

New features:

  • ChIP Sequencing
  • DIP Detection
  • Wizard-based database initiation tool released
  • Peak detection and filtering on ChIP-seq data
  • New filter options in SNP and DIP  detection.
    • SNP and DIP detection: as supplement to minimum variant frequency in percent, you can also specify a minimum variant count.
    • SNP detection: just as DIP detection there is a maximum coverage filter
    • SNP detection: there is now a “ploidy” setting just as for DIPs. This is used to mark SNPs as “complex”. The “Genetic code” drop-down box has been moved to step 3.
  • SNP and DIP detection can now be performed directly on RNA-seq output contig tables
  • Much improved memory performance and processing time of NGS data
  • You can now specify minimum length of contigs to be reported in de novo assembly

Bug fixes:

  • Fixed stability issues regarding database connection.
  • Fixed issue that would make client unresponsive if network connection disappeared


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