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#358 Unaligned File Request Triggers Bowtie2 to Fail

v0.9.0
open
nobody
None
5
2019-07-01
2019-06-24
Rodolfo.Aramayo
No
  • Bowtie Version:
Bowtie 2 version 2.3.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
  • The following command:
bowtie2 \
-t \
-p 20 \
-x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \
-q \
-U /data/fastq_file.fq \
--very-sensitive \
-un /data/requested_unaligned_fastq_file.fq
-S /data/requested_sam_file.sam;
  • Fails with the following error:
-u/--qupto arg must be at least 1
...
Error: Encountered internal Bowtie 2 exception (#1)
...
(ERR): bowtie2-align exited with value 1
  • However, the following command:
bowtie2 \
-t \
-p 20 \
-x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \
-q \
--very-sensitive \
-S /data/requested_sam_file.sam;
  • Works as expected
  • Failing behavior is observed every time an unaligned file is requested, regardless whether or not paired or unpaired files are provided as input
  • I was able to reproduce this behavior in two different linux architectures (Ubunt and CentOS)
  • I would be glad to provide files/index used if requested

Discussion

  • Rodolfo.Aramayo

    Rodolfo.Aramayo - 2019-06-24
    • Apologies, the second command should read:
    bowtie2 \
-t \
-p 20 \
-x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \
-q \
-U /data/fastq_file.fq \
--very-sensitive \
-S /data/requested_sam_file.sam;
     

  • Rodolfo.Aramayo

    Rodolfo.Aramayo - 2019-07-01
    • Please close this ticket
    • The command issued should have been:
    bowtie2 \
-t \
-p 20 \
-x /path/to/index/GCA_000001405.15_GRCh38_no_alt_analysis_set \
-q \
-U /data/fastq_file.fq \
--very-sensitive \
--un /data/requested_unaligned_fastq_file.fq
-S /data/requested_sam_file.sam;
    • This is "--un" and not "-un"
    • Small typo caused a lot of self-induced pain
    • Apologies for the disturbance...and cheers...
     

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