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Failed to extract primary alignments. #157

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anchizhang opened this issue Apr 22, 2017 · 8 comments
Open

Failed to extract primary alignments. #157

anchizhang opened this issue Apr 22, 2017 · 8 comments
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@anchizhang
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Your help would be very much appreciated.

SeqMule running nicely until:

[ => SeqMule Execution Status: step 16 is finished at Sat Apr 22 13:39:11 CDT 2017, Generate Venn digram]

Current version: 1.2.6
Check for upgrade ...
NOTICE: This is the latest version!

----------NOTICE----------
[ => SeqMule Execution Status: Running 18 of 20 steps: Generate variant stat, at Sat Apr 22 13:39:12 CDT 2017, Time Elapsed: 0 hr 0 min 2 s]
examine: TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf
count: <<12611>>
Generating variant stats

----------NOTICE----------
[ => SeqMule Execution Status: Running 19 of 20 steps: Remove intermediate files, at Sat Apr 22 13:39:13 CDT 2017, Time Elapsed: 0 hr 0 min 3 s]
NOTICE: Calculating coverage for TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam. This takes a while
NOTICE: checking contig(chromosome) name consistency in /vol/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed and TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam.
[ => SeqMule Execution Status: step 19 is finished at Sat Apr 22 13:39:15 CDT 2017, Remove intermediate files]

NOTICE: Output written to TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_var_stat.txt
[ => SeqMule Execution Status: step 18 is finished at Sat Apr 22 13:39:16 CDT 2017, Generate variant stat]

NOTICE: all chromosome names in BED can be found in BAM header.
NOTICE: Calculating coverage ...
NOTICE: Start reading from SAMTools depth command ...
^CFailed to caculate coverage stat for TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam

WARNING: (PID:27151) Ctrl-C signal received, dying...
[lili@seqmule TCRBOA7-N-WEX]$ /vol/SeqMule/bin/secondary/../../bin/secondary/worker /home/lili/TCRBOA7-N-WEX/seqmule.04212017.15825.logs 17 "/vol/SeqMule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -bam TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam -aln -prefix TCRBOA7-N-WEX_result/TCRBOA7-N-WEX -capture /vol/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed "
Current version: 1.2.6
Check for upgrade ...
NOTICE: This is the latest version!
NOTICE: Calculating coverage for TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam. This takes a while
NOTICE: checking contig(chromosome) name consistency in /vol/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed and TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam.
NOTICE: all chromosome names in BED can be found in BAM header.
NOTICE: Calculating coverage ...
NOTICE: Start reading from SAMTools depth command ...
NOTICE: /vol/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed contains 78541243 base pairs
NOTICE: /vol/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed contains 78541243 base pairs
Statistics written to TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_cov_stat.txt and TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_cov_stat_detail.txt
NOTICE: coverage plot <<TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_cov.jpg>> generated
NOTICE: Extracting primary alignments
[main_samview] truncated file.
Failed to extract primary alignments.
NOTICE: Cleaning...

[lili@pgm-serv2 TCRBOA7-N-WEX]$ grep status TCRBOA7-N-WEX.script
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=finished
status=error
status=finished
status=finished
status=waiting

@yunfeiguo
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Hi @anchizhang

is this the same issue as #156 ? Apparently you pressed Ctrl-C to kill seqmule

WARNING: (PID:27151) Ctrl-C signal received, dying...

Could you show me the error message in an uninterrupted execution? Thanks.

@yunfeiguo yunfeiguo self-assigned this Apr 23, 2017
@anchizhang
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anchizhang commented Apr 26, 2017 via email

@yunfeiguo
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Could you show me the error message in an uninterrupted execution, i.e. do not press Ctrl-C during running?

@anchizhang
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anchizhang commented Apr 28, 2017 via email

@yunfeiguo
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from the posted output, I did not see the cause of the problem, could you go to the directory where you started seqmule and run /vol/SeqMule/bin/secondary/../../bin/seqmule stats -tmpdir /tmp -bam TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam -aln -prefix TCRBOA7-N-WEX_result/TCRBOA7-N-WEX -capture /vol/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed and post the error msg? Thanks.

@anchizhang
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anchizhang commented May 2, 2017 via email

@yunfeiguo
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did you check TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_cov_stat.txt? Is the coverage expected?

@anchizhang
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anchizhang commented May 8, 2017 via email

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