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QIAGEN CLC Genomics Server 22.0.3

Release date: 2023-02-01

Shared with workbenches

Improvements

  • When exporting images to bitmap-based formats, the Screen resolution and High resolution options are now bounded so the maximum supported number of pixels will not be exceeded.
  • Various minor improvements

Bug fixes

  • Fixed an issue causing Map Reads to Reference to fail if a masking track covering a whole chromosome was provided as input.
  • Fixed an issue in RNA-Seq Analysis that could lead to an IndexOutOfBounds error when the option “Calculate expression for genes without transcripts” was selected, and two or more genes had the same name, and at least one of these has no transcripts, and the Region column of the table view of the gene track contains the text “join”, “>”, or “<” (i.e., the genes have splice structure, or uncertain end positions).
  • Fixed an issue affecting Extract Consensus Sequence where annotations transferred from the reference sequence to the consensus sequence could be wrongly positioned if the read mapping had an insertion in a region that was removed due to low coverage.
  • Amino Acid Changes
    • Fixed an issue causing the output from to be named after the reference data instead of the input data.
    • Fixed an issue that caused the transcripts and proteins listed in the Coding region change and Amino acid change columns in the annotated variant track output to be inconsistently ordered.
  • Fixed issues with Quantify miRNA where:
    • It would fail on paired reads if using spike-ins.
    • Opening a sequence list to view it would cause this tool to fail if that same sequence list had been used as input.
  • Fixed an issue causing Standard Import of GenBank format to stall if qualifier names spanned more than one line.
  • Fixed an issue where text in installer screens was not visible when installing the software in ‘dark mode’ on Linux.

Changes

  • The Java version bundled with CLC Genomics Server 22.0.3 is 11.0.17, where we use the JRE from the Azul Zulu Builds of OpenJDK.

Compatibility

The following are the corresponding clients for the QIAGEN CLC Genomics Server 22.0.3.

  • QIAGEN CLC Genomics Workbench 22.0.3
  • QIAGEN CLC Main Workbench 22.0.3
  • QIAGEN CLC Command Line Tools 22.0.3

We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 22.0, 22.0.1 and 22.0.2, QIAGEN CLC Main Workbench 22.0. 22.0.1 and 22.0.2 and QIAGEN CLC Command Line Tools 22.0, 22.0.1 and 22.0.2 can also connect to QIAGEN CLC Genomics Server 22.0.3.

CLC Server Command Line Tools

Bug fixes

  • Fixed an issue where text in installer screens was not visible when installing the software in ‘dark mode’ on Linux.

Compatibility

CLC Command Line Tools 22.0.3 is the corresponding client for QIAGEN CLC Genomics Server 22.0.3.

CLC Command Line Tools 22.0.3 can also act as a client for the QIAGEN CLC Genomics Server 22.0, 22.0.1 and 22.0.2. However, we recommend running the corresponding version.



QIAGEN CLC Genomics Server 22.0.2

Release date: 2022-06-09

Shared with workbenches

Bug fixes

  • Fixed an issue affecting Local Realignment where false positive insertions and deletions could be introduced in read mappings when a guidance variant was provided that had a sequence similar to the reference sequence immediately after the variant. See Important QIAGEN CLC software notifications for further details.
  • Fixed an issue affecting the naming of outputs when Local Realignment was provided with multiple read mappings as input. When the tool was not run in Batch mode, a read mapping was generated per input, as expected, but all the realigned read mappings were named after the first read mapping in the set of inputs. Now each is named after the corresponding input.
  • Fixed an issue that could result in an error like “no zstd-jni in java.library.path” when importing files or undertaking other activities involving the compression of CLC data elements.

Plugin notes

After upgrading the CLC Genomics Server:

The results from these tools may be slightly altered as a result of the underlying improvement.

Compatibility

The following are the corresponding clients for the QIAGEN CLC Genomics Server 22.0.2.

  • QIAGEN CLC Genomics Workbench 22.0.2
  • QIAGEN CLC Main Workbench 22.0.2
  • QIAGEN CLC Command Line Tools 22.0.2

We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 22.0 and 22.0.1, QIAGEN CLC Main Workbench 22.0 and 22.0.1 and QIAGEN CLC Command Line Tools 22.0 and 22.0.1 can also connect to QIAGEN CLC Genomics Server 22.0.2.

CLC Server Command Line Tools

Compatibility

CLC Command Line Tools 22.0.2 is the corresponding client for QIAGEN CLC Genomics Server 22.0.2.

CLC Command Line Tools 22.0.1 can also act as a client for the QIAGEN CLC Genomics Server 22.0 and 22.0.1. However, we recommend running the corresponding version.



QIAGEN CLC Genomics Server 22.0.1

Release date: 2022-03-28

Server specific

Bug fixes

  • Fixed an issue where the presence of a file without a file name extension under an import/export directory caused null errors when browsing that area.

Shared with Workbenches

Improvements

  • The RNA-Seq Analysis Report has been updated to include new text in the “Adapter read-through” section. The additional text explains that trimming the start of paired-end reads (5′ trim) can lead to spurious detection of adapter read-through.
  • When two or more reports produced by the same tool are used as input to Create Sample Report, and they contain conflicting values, the tool now fails. Previously, the results from the first report were used.
  • When reports that contain identical tables and values are input to Create Sample Report, the values are included once in the report. Previously, a row per input report was included, even when the values were identical.
  • Update Sequence Attributes in Lists now accepts attribute information from comma separated (.csv) and tab separated (.tsv) format files.
  • Various minor improvements

Bug fixes

  • Fixed an issue in Copy Number Variant Detection (CNVs), where a subset of region CNVs were not correctly calculated on chromosomes with low coverage target regions in the control samples. The issue led to overly large region CNVs. As gene-level CNVs are calculated from region-level CNVs, these were also affected. When only few target regions had low coverage in control samples, results were likely not affected.
  • Fixed an issue in Maximum Likelihood Phylogeny that in rare situations led to tree construction never completing.
  • Fixed an issue with Create BLAST Database, which could fail if the underlying native BLAST tool reported warnings.
  • Fixed an issue with Split Sequence List when splitting based on attribute values, where an error resulted if the sequence list had more than 1000 distinct values for the selected attribute.
  • Fixed an issue where a workflow could fail or produce an incorrect folder structure for outputs when it contained Split Sequence List, with splitting based on attribute values, and the name of at least one of the groups contained a forward slash “/” character.
  • Fixed an issue affecting the naming of workflow outputs defined using a naming pattern of the form {input:N} or its equivalent {2:N}, e.g. {input:1} or {2:1}. The intended input name was not the one used to form the output element names when the workflow included an Iterate element, and import was done on the fly, and the batch units were defined based on the organization data, and:
    • Each batch unit was a set of paired reads, or
    • Each batch unit was a folder.
  • Fixed an issue where the median read length in the supplementary report produced by QC for Sequencing Reads could be incorrect when the number of reads was very low. The median reported in the graphical report was correct.
  • Fixed an issue with Create Sample Report affecting samples where reads mapped to only one chromosome. For such samples, the QC metric “% reads mapped in target region” was not included in the Quality Control table, even when that option had been selected when launching the tool.
  • Various  minor bug fixes

Changes

The Java version bundled with CLC Genomics Server 22.0.1 is Java 11.0.14.1, where we use the JRE from the Azul OpenJDK builds.

Compatibility

The following are the corresponding clients for the QIAGEN CLC Genomics Server 22.0.1.

  • QIAGEN CLC Genomics Workbench 22.0.1
  • QIAGEN CLC Main Workbench 22.0.1
  • QIAGEN CLC Command Line Tools 22.0.1

We recommend running the corresponding versions of clients for QIAGEN CLC Genomics Server. However, QIAGEN CLC Genomics Workbench 22.0, QIAGEN CLC Main Workbench 22.0, and QIAGEN CLC Command Line Tools 22.0 can also connect to QIAGEN CLC Genomics Server 22.0.1.

CLC Server Command Line Tools

CLC Command Line Tools 22.0.1 is the corresponding client for QIAGEN CLC Genomics Server 22.0.1.

Compatibility

CLC Command Line Tools 22.0.1 is the corresponding client for QIAGEN CLC Genomics Server 22.0.1.

CLC Command Line Tools 22.0.1 can also act as a client for the QIAGEN CLC Genomics Server 22.0. However, we recommend running the corresponding version.



QIAGEN CLC Genomics Server 22.0

Release date: 2022-01-11

Server specific

New features and improvements

Reorganization of web administrative interface

The top level tabs in the CLC Genomics Server web administrative interface have been renamed and the contents under them re-organized. From left to right in the interface:

  • Element info  – Functionality for working with with data stored in CLC Server Locations, including for setting group-level permissions on folders.
  • Configuration – Configuration functionality, including for setting up CLC Server Locations, configuring the server setup, configuring settings for external data, configuring user authentication, etc.
  • Management – Functionality for managing the CLC Server, including downloading licenses, stopping, restarting and putting the server in maintenance mode, as well as access to the queue, audit log, etc.
  • Extensions – Configuration relating to extending the functionality of the CLC Server, such as downloading and managing plugins, and configuring External Applications.
New functionality in the web administrative interface
  • Group-level permissions on CLC Server File System Locations and their contents can be configured via the web administrative interface. Previously, configuration could be done only using a CLC Workbench client.
  • Recycle bins can be emptied via the web interface. When logged in as an administrative user, any individual recycle bin can be emptied, or all recycle bins in a FIle System Location can be emptied in a single action.
Other new features

  • Access to Amazon S3 and BaseSpace

  • Admin level access can be granted to specified groups for installing and configuring workflows, and configuring and enabling external applications via the web administrative interface.
External applications improvements
  • External Applications can now be configured with a failure strategy.
  • The audit log entries for external applications now include the native process command line and the exit value.
  • Improvements to error handling when external applications fail, when run directly as a tool or within a workflow context, including that any results files produced despite the job failure will be posted. In such cases, the std out and error files can contain valuable troubleshooting information.
  • For external applications in workflows, the final, substituted command line executed by the external application and the native process exit code are posted to the workflow log. In addition, every error contained in the server result (thus also all failures triggered), is posted to the workflow log. Previously, only the first error thrown to stop the process was posted.
  • History information can optionally be added to CLC data elements created by external applications.
Other improvements
  • Tomcat has been updated to version 9.0.46. Custom port and SSL settings will need to be reconfigured after this upgrade
  • Improvements to the display of history information for data elements. The History tab is now under the top level Element info tab.
  • The contents of tool and workflow logs, generated when an analysis are run, can be viewed directly under the Element info tab.
  • The audit log shows the XML serialized version of any exception.
  • Various minor improvements

Bug fixes

  • Fixed an issue that could cause the Main configuration tab of the web administrative interface to occasionally be blank after logging in.
  • Fixed an issue where the maintenance mode banner, expected in the top right hand corner, was sometimes not shown when it should have been.
  • Fixed an issue with the maintenance mode banner message where the reason for maintenance mode/restart was not correctly displayed.
  • Fixed an issue where Find and Model Structure could not be run on a CLC Genomics Server.
  • Various minor bugfixes

Functionality removal

The Genomics Analysis Portal client is no longer provided in the CLC Genomics Server distribution.

Changes

Shared with CLC Workbenches

New features and improvements

Tools for annotating and manipulating sequence lists

The new Sequence Lists folder under Toolbox | Utility Tools contains tools for working with sequence lists. This includes existing tools, with new names and expanded functionality, as well as new tools:

  • Split Sequence List New tool: Splits up nucleotide or peptide sequence lists. The output can be a specified number of lists, lists containing a specified number of sequences, or lists containing sequences with particular attribute values, such as terms in the description.
  • Update Sequence Attributes in Lists New tool: Updates and adds information about the sequences in a list. For example, descriptions can be updated, or new information types can be added based on information  provided in an Excel file.
  • Create Sequence List Existing tool. Create new sequence lists from sequence elements and/or sequence list elements. Previously available only from the File | New menu.
Other new functionality
  • MGI/BGI importer An importer for MGI/BGI fastq format files.
  • Rename Sequences in Lists Rename sequences within sequence lists by adding or removing characters, or replacing parts of names, optionally using regular expressions.
  • Rename Elements  Rename elements by adding or removing characters, or replacing parts of names, optionally using regular expressions.
  • A Heat map graphics exporter has been introduced for exporting heat maps to graphics file formats.
  • Files containing tab separated values (.tsv) can be imported as tables using Standard Import.
  • Export VDJ tools Exports T-Cell VDJ repertoire in txt format.
RNA-Seq and Expression Analysis improvements
Demultiplex Reads
  • Demultiplex Reads now supports setting barcodes from table elements in addition to importing barcodes from local files.
  • The barcode import table format has been extended to support additional columns.
  • When multiple elements are provided as input, the information in the Preview pane includes information obtained from across these. Previously, only the first input element was used for this.

BLAST related updates

  • BLAST has been upgraded to BLAST+ 2.12.0 that includes a number of improvements and bug fixes. A full list of BLAST+ 2.12.0 changes can be viewed at http://www.ncbi.nlm.nih.gov/books/NBK131777.
  • The list of databases available using BLAST at NCBI has been expanded, including the addition of ‘16S ribosomal RNA sequences (Bacteria and Archea)’ and ‘28S ribosomal RNA sequences from Fungi type and reference material (LSU)’.
  • When BLAST at NCBI is used with multiple query sequences, the job will continue even if particular sequences fail due to a problem. Results for successful searches (including those with no hits) are returned. Sequences missing from the results due to problems are recorded in the job log.
  • Searches against the Patented protein sequences database using BLAST at NCBI work once again. Previously, these searches always failed, with a dialog message saying only that no hits were found even though an error was returned by the NCBI. For affected searches, the error was reported in the job log.
  • Fixed an issue affecting BLAST HSP Tables where the calculation of percent overlap between blast hits in reverse direction and query sequence was based on a sequence length that was 2 base pairs two short leading to incorrect values.
  • Improvements have been made to make it less likely that a “CPU usage limit was exceeded” error will be returned when running blastp, blastx, tblastn or tblastx using BLAST at NCBI.
Importer and exporter improvements
  • Multiple tables can be exported to a single file when using the following exporters: Tab delimited text, Annotation tab delimited text, Table CSV, Annotation CSV.
  • A new custom reads option was added to the Illumina importer. The extended options for fastq file import has been added to support 10X data, it is e.g. now possible to import three fastq files with R1, R2, and I1 as paired reads where I1 is added in front of R1.
  • When exporting variant tracks to VCF format, variants that fall under thresholds to be exported can now optionally be excluded entirely from the resulting VCF file.
  • When using the VCF export setting for complex variant representation “Reference overlap and depth estimate”, complex overlapping reference alleles are now exported with a homozygous reference genotype.
  • The list of supported GVF attributes in column 9 has been expanded when importing GVF files using the GFF2/GTF/GVF track importer.
  • 1000 Genomes annotations are now better supported by the GFF2/GTF/GVF track importer.
  • The Zygosity field is now included when exporting to GVF format.
  • A subset of columns to export can be specified when exporting Mapping Coverage data.
Other improvements
  • Copy Number Variant Detection (CNVs) can use coverage tables generated by QC for Targeted Sequencing as control mappings. Read mappings can still be used as control mappings.
  • Copy Number Variant Detection (CNVs) allows different fold-change thresholds for deletions and amplifications.
  • When working with paired reads, Trim Reads allows the trimming of a fixed number of bases to apply to only read 1, only read 2, or both reads of each pair.
  • An option has been added to Extract Reads or Create Reads Track from Selection to allow just one member of a pair to be extracted when only one meets the extraction criteria.
  • Extract Reads accepts stand alone read mappings in addition to reads tracks as input.
  • Create Sample Report can take both the Graphical and the Supplementary Report created by QC for Sequencing Reads as input.
  • An option has been added to Amino Acid Changes for using one letter amino acid codes in HGVS annotations.
  • Filter on Custom Criteria now accepts expression tracks as input.
  • In Quantify miRNA the option to select strand-specific analysis has been removed. The analysis is now always strand-specific.
  • Remove Duplicate Mapped Reads considers if reads are duplicates based on the start position of reads instead of both start and end. This allows reads that have undergone quality trimming to be recognised as duplicates.
  • The distance to consider around an intron-exon boundary when using Predict Splice Site Effect can be specified. Previously a length of 2 was always used.
  • Create Mapping Graph can now generate graphs for forward read coverage and reverse read coverage.
  • The Sample Reads tool is now named Subsample Sequence List. Peptide sequence lists are now accepted by this tool, in addition to nucleotide sequence lists.
  • When a Track List and the tracks it refers to are copied in a single operation, the new copy of the Track List will refer to the the new copies of the tracks. Previously, the new Track List continued to refer to the original tracks.
  • For workflows with paired read import as part of the workflow run, and when the workflow is launched in batch mode, or contains Iterate elements, paired read handling is now the same as for the relevant NGS importer tools (Illumina, Fasta, Sanger) themselves, irrespective of how batch units are defined or organized. Previously when batch units were based on data organization and all files were in the same folder, each file was treated as a separate batch unit, irrespective of whether the Paired option was checked.
  • Memory usage when launching workflows in batch mode has been improved.
  • Trim Sequences specifies which version of the UniVec database was used, both in the report and in the history of the trimmed sequences output.
  • The few tools that directly manipulate input elements, instead of generating a new element containing the changes as output, now generate a new element as output when used within a workflow. This allows them to be handled like any other tool in a workflow context.
  • In addition to sequence elements, Add attB Sites accepts sequence lists with fewer than 10,000 sequences as input.
  • Internal compression of CLC data has been improved.  Elements created with this version of the software, with compression enabled, can be opened in version 21.0.5 and higher. Data must be exported or saved as uncompressed if sharing data with earlier versions of the software.
  • Various minor improvements

Bug fixes

  • Fixed an issue in Create Box Plot where percentiles reported in the history of a box plot element were off by one. For example, the “25%-ile” value was given the 24th percentile value. The correct values were used in the plots themselves.
  • Fixed an issue in Demultiplex Reads where dual barcodes were not allowed to have mismatches in both barcodes.
  • Fixed an issue in Demultiplex Reads where dual barcodes could previously be selected in random combinations. Dual barcodes are now handled in pairs.
  • When using the “Genome annotated with genes only” in RNA-Seq Analysis, the range of annotation track types that can be used has been expanded. This includes the use of CDS annotation tracks, among others.
  • Fixed an issue in Create Sample Report where, when QC thresholds had been specified for Trim Reads, wrong values from the Trim Reads report were shown in table 1.1 Quality Control of the sample report.
  • Fixed an issue that caused Create Sample Report to fail when input reports did not contain values for specified QC thresholds.
  • Fixed an issue in Combine Reports and Create Sample Report where the “Mean coverage per target” section would report coverages 10x too high when including a report from QC for Targeted Sequencing.
  • Fixed an issue in VCF export where, in rare cases, variants below a specified minimum allele fraction threshold were not removed.
  • Fixed an issue affecting Local Realignment where large indels upstream of a target region were sometimes not used when provided as guidance variants.
  • Fixed an issue that in rare cases could cause Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection to fail on very high coverage samples when the “Remove pyro-errors variants” option was enabled.
  • Fixed an issue where Remove Duplicate Mapped Reads did not always de-duplicate paired reads with read-through correctly.
  • Fixed an issue where Remove Duplicate Mapped Reads did not always de-duplicate reverse mapping single-end reads correctly.
  • Fixed an issue affecting QC for Targeted Sequencing, where it failed with an error when an RNA-Seq read mapping containing paired reads was provided as input.
  • Fixed an issue in Filter on Custom Criteria where numeric annotations were sometimes not allowed to be filtered using numerical operators such as “<“, “>”, “=”.
  • Fixed an issue in Trio Analysis where, in rare cases, inconsistent zygosity between mother and father could lead to a wrong annotation of inheritance. Trio Analysis now reports inheritance as ‘Inconsistent zygosity’ if zygosity or the number of alleles is inconsistent between child, mother or father.
  • Fixed an issue with VCF files exported from the CLC Genomics Workbench, where fusions that had one breakpoint in common were represented in a way that prevented QIAGEN Clinical Insight Interpret from displaying the counts.
  • Fixed an issue causing Quantify miRNA to fail when there were empty entries in the Accession column of miRbase
  • Fixed an issue where the names of outputs from Output elements attached directly to an Iterate element in workflows were not as intended when the metadata ({3} placeholder was used. We generally recommend that the specific input number(s) to include in output names are specified when configuring workflows that contain control flow elements.
  • Fixed an issue where the content of the recycle bin was not shown correctly after the recycle bin had been emptied.
  • Various bug fixes

Changes

  • The Sample Reads tool is now named Subsample Sequence List and is located under the Utility Tools | Sequence Lists subfolder of the Toolbox. The functionality of this tool has been expanded. See the Improvements listing above, or refer to the manual.
  • The Extract Annotations tool is now named Extract Annotated Regions.
  • The tool Set Up Experiment is now named Set Up Microarray Experiment.
  • The “Number of duplicates distribution” section has been removed from the report produced by Remove Duplicate Mapped Reads.
  • When exporting BAM files, file names are limited to a maximum of 254 characters.
  • Input modifying tools within workflows generate an output element instead of directly modifying the input provided. Workflows containing these tools may need to be edited.

Legacy tools

The following tools are now legacy tools and will be retired in a future version of the software:

Functionality retirement

The following tools have been retired:

  • Create Track from Experiment (legacy)
  • Extract and Count (legacy)
  • Download miRBase (legacy)
  • Annotate and Merge Counts (legacy)
  • Roche 454 NGxS import (legacy)
  • Create Combined RNA-Seq Report (legacy)
  • Remove Reference Variants (legacy)

Compatibility

The follow are the corresponding client applications for CLC Genomics Server 22.0

  • CLC Genomics Workbench 22.0
  • CLC Main Workbench 22.0
  • CLC Command Line Tools 22.0

CLC Genomics Server 22.0 is compatible with GCE version 22.0.

CLC Server Command Line Tools

Please see the CLC Genomics Server 22.0 listings above for the details about the new tools and features listed here.

New tools

Administrative tools
  • install_plugin_download_and_restart
  • list_plugins_download
  • list_installed_plugins
  • empty_recycle_bins
Utility tools
  • split_sequence_list
  • update_seq_attrs_in_list
  • rename_seqs_in_seq_list
  • rename_elements
Other tools
  • ngs_import_mgi_bgi
  • history_add

New and updated options for existing tools

Analysis related
  • amino_acid_changes
    • option added:  –one-letter-codon
  • cnv_detection
    • option added: –minimum-fold-change-amplification
    • option added: –minimum-fold-change-deletion
    • option removed: –minimum-fold-change-magnitude
  • create_sequence_statistics
    • option added: –extinction-coefficient
  • differential_expression_rna_seq
    • option added:  –metadata-table-tsv
  • extract_overlapping_reads
    • option added:  –only-matching-read-pair
  • mapping_graph_tracks
    • option added: –forward-read-coverage
    • option added: –reverse-read-coverage
  • ngs_import_illumina
    • option added: –reads-options
    • option added:  –use-reads-options
  • predict_splice_site
    • option added: –splice-window-size
  • process_tagged_sequences
    • option added: –barcode-table-element
  • quantify_small_rna
    • option removed: –strand-specific
  • rna_seq
    • option added: –count-paired-reads-as-two
    • option added: –ignore-broken-pairs
    • option removed: –broken-pair-countingscheme
  • changed: sample_reads
    • option added: –shuffle
  • trim
    • option added: –first-read-trim
    • option added: –second-read-trim
Other updates

Export options added:

  • heatmap_graphics
  • immune_rept_vdj_tools

Import option added

  • table_tsv

Improvements

  • If options with identical names are found within an element of a workflow, each of the corresponding CLC Server Command Line Tools parameters will have a number appended to ensure uniqueness.
  • Job status updates are now more frequent and the time needed for handling finished jobs has been reduced.

Commands removed

Administrative commands removed
  • empty_recycle_bin    Replaced by new command empty_recycle_bins
  • list_plugins                See new commands for several commands relating to plugin administration
Analysis related commands removed
  • create_combined_rnaseq_report
  • experiment_to_track
  • filter_reference_variants
  • ngs_import_roche454
  • small_rna_annotate
  • small_rna_sampling

Bugfixes

  • Fixed an issue where find_structure_algo was not listed as an available tool when it should have been.


Sample to Insight