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Type:
Bug
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Status: Closed
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Priority:
Major
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Resolution: Won't Fix
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Affects Version/s: 1.16.2
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Fix Version/s: None
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Labels:None
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Story Points:2
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Tests Type:GUI automatic
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Sprint:DEV-24/06/2015, DEV-24-2, DEV-25-1, DEV-25-2, DEV-26-1, DEV-26-2, DEV-26-3, DEV-26-4
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Affect Type:Userdefined
Run "Raw RNA-Seq data processing" with next non-default settings:
- input FASTQ file: "_common_data/NGS_tutorials/RNA-Seq_Analysis/Prepare_Raw_Data/lymph.fastq"
- bowtie index for tophat: "_common_data/NIAID_pipelines/tuxedo_pipeline/data/index/chr6"
Workflow finishes successfully, but cutadapt tool writes some messages to the error log:
[DETAILS][12:42] Launching cutadapt tool: /Users/atiunov/root/projects/clear/clear_clear/installer/macosx/debug_bundle/ugeneuid.app/Contents/MacOS/tools/python/bin/python2.7 /Users/atiunov/root/projects/clear/clear_clear/installer/macosx/debug_bundle/ugeneuid.app/Contents/MacOS/tools/cutadapt-1.7.1/cutadapt.py -a file:/Users/atiunov/root/projects/clear/clear_clear/installer/macosx/debug_bundle/ugeneuid.app/Contents/MacOS/data/adapters/adapters.fasta -f fastq /Users/atiunov/workflow_output/2015.05.19_12-41/run/lymph.fastq.filtered.fastq
[ERROR][12:45] NGS: Maximum error rate: 10.00%
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[ERROR][12:45] NGS: No. of allowed errors:
[ERROR][12:45] NGS: length count expect max.err error counts
[DETAILS][12:45] Tool cutadapt finished successfully
I suppose that these messages are not errors, they are logged because they contain word "error".
If they are not errors, they shouldn't be on the error log.
Also, ensure that cutadapt can show errors on the dashboard.
- relates to
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- Closed
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