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1.17. Failure and incomplete imports for gzip and bzip2 compressed Illumina and Ion Torrent files
The issue described below has been fixed for CLC Genomics Workbench 9.5.1, Biomedical Genomics Workbench 3.5.1 and CLC Genomics Server 8.5.1. If you are running the CLC Genomics Workbench 9.5, Biomedical Genomics Workbench 3.5 or CLC Genomics Server 8.5, please update your installation.
Description of the issue
The problems in the list below can arise when using the tools Import | Illumina and Import | Ion Torrent to import fastq files compressed with gzip (.gzip) or bzip2 (.bz2). The problems are expected to be seen most frequently on Windows systems, but can sometimes also arise on Mac or Linux. The software affected is CLC Genomics Workbench 9.5, Biomedical Genomics Workbench 3.5 and CLC Genomics Server 8.5.
- Import can fail with an error message "Errors occurred: see log". No sequences are imported. The failure is sporadic: sometimes an import will succeed, but other times it will not.
- Import may seem to succeed, when in fact only a subset of the sequences in the fastq file(s) are imported.
Workaround if upgrading immediately is not an option
If you are running one of the affected software versions, we recommend that you upgrade your software as soon as possible. However, if you cannot do that immediately, a work-around to this issue is to decompress the sequence files before importing them.
Software affected by this problem
- Biomedical Genomics Workbench 3.5
- CLC Genomics Workbench 9.5
- CLC Genomics Server 8.5
Other versions of these products are not affected.