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Failed to extract primary alignments. #157
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Hi @anchizhang is this the same issue as #156 ? Apparently you pressed
Could you show me the error message in an uninterrupted execution? Thanks. |
Yunfei,
Thank you for your response.
No, it is not the same issue as #156.
…----------NOTICE----------
[ => SeqMule Execution Status: Running 18 of 20 steps: Generate variant stat, at Fri Apr 21 18:04:52 CDT 2017, Time Elapsed: 3 hr 58 min 9 s]
[ => SeqMule Execution Status: step 15 is finished at Fri Apr 21 18:04:52 CDT 2017, Extract consensus calls]
examine: TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf
count: <<12611>>
Generating variant stats
NOTICE: Output written to TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_var_stat.txt
[ => SeqMule Execution Status: step 18 is finished at Fri Apr 21 18:04:58 CDT 2017, Generate variant stat]
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...
----------ERROR----------
[ => SeqMule Execution Status: step 17 FAILED at Fri Apr 21 19:57:04 CDT 2017, Generate alignment and coverage stat]
ERROR: command failed
/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 "
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /home/lili/TCRBOA7-N-WEX' and 'seqmule run TCRBOA7-N-WEX.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
From: Yunfei Guo [mailto:[email protected]]
Sent: Saturday, April 22, 2017 10:03 PM
To: WGLab/SeqMule
Cc: anchizhang; Mention
Subject: Re: [WGLab/SeqMule] Failed to extract primary alignments. (#157)
Hi @anchizhang <https://github.com/anchizhang>
is this the same issue as #156 <#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.
—
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Reply to this email directly, view it on GitHub <#157 (comment)> , or mute the thread <https://github.com/notifications/unsubscribe-auth/AXTkEq_BRuxlArA4559fw_kasL_SJvOGks5ryr92gaJpZM4NFMDV> .Image removed by sender.
|
Could you show me the error message in an uninterrupted execution, i.e. do not press |
On Ctrl-c to this run:
[lili@pgm-serv2 TCRBOA7-N-WEX]$ tail -50 nohup.out
INFO 18:01:30,985 HelpFormatter - For support and documentation go to
http://www.broadinstitute.org/gatk
INFO 18:01:30,994 HelpFormatter - Program Args: -T SelectVariants -R
/vol/SeqMule/bin/secondary/../../database/human_g1k_v37.fasta -sn
TCRBOA7-N-WEX -V /tmp/129827429.38205636591_nofiltered.vcf -o
/tmp/TCRBOA7-N-WEX129828130.66132580357.129827429.38205636591_nofiltered.vcf
-U LENIENT_VCF_PROCESSING -l INFO
INFO 18:01:30,994 HelpFormatter - Date/Time: 2017/04/21 18:01:30
INFO 18:01:30,995 HelpFormatter -
--------------------------------------------------------------------------------
INFO 18:01:30,995 HelpFormatter -
--------------------------------------------------------------------------------
INFO 18:01:31,019 ArgumentTypeDescriptor - Dynamically determined type of
/tmp/129827429.38205636591_nofiltered.vcf to be VCF
INFO 18:01:31,055 GenomeAnalysisEngine - Strictness is SILENT
INFO 18:01:31,367 GenomeAnalysisEngine - Downsampling Settings: Method:
BY_SAMPLE, Target Coverage: 1000, Using the new downsampling implementation
INFO 18:01:31,396 RMDTrackBuilder - Creating Tribble index in memory for
file /tmp/129827429.38205636591_nofiltered.vcf
INFO 18:01:32,404 RMDTrackBuilder - Writing Tribble index to disk for file
/tmp/129827429.38205636591_nofiltered.vcf.idx
INFO 18:01:33,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING
PROCESSING]
INFO 18:01:33,190 ProgressMeter - Location processed.sites runtime
per.1M.sites completed total.runtime remaining
INFO 18:01:33,341 SelectVariants - Including sample 'TCRBOA7-N-WEX'
INFO 18:01:37,947 SelectVariants - 8615 records processed.
INFO 18:01:38,561 ProgressMeter - done 1.32e+04 5.4 s
6.8 m 30.8% 17.5 s 12.1 s
INFO 18:01:38,561 ProgressMeter - Total runtime 5.37 secs, 0.09 min, 0.00
hours
WARN 18:01:42,452 RestStorageService - Error Response: PUT
'/GATK_Run_Reports/BlTlDWkhRJS5oY5JmTX4M8ZRnWIDEqD5.report.xml.gz' --
ResponseCode: 403, ResponseStatus: Forbidden, Request Headers:
[Content-Length: 388, Content-MD5: 3dqei6aQeE1Oqzb3pNfhNQ==, Content-Type:
application/octet-stream, x-amz-meta-md5-hash:
ddda9e8ba690784d4eab36f7a4d7e135, Date: Fri, 21 Apr 2017 23:01:41 GMT,
Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:hbd8gP4az8zBviNgwxM0p0FfH8A=,
User-Agent: JetS3t/0.8.1 (Linux/2.6.32-696.1.1.el6.x86_64; amd64; en; JVM
1.7.0_131), Host: s3.amazonaws.com, Expect: 100-continue], Response
Headers: [x-amz-request-id: 0B9D54E53EF588F0, x-amz-id-2:
W3ISrl2kEMnG8erWNWUQLk0YaBL+Wxpk2RodJ5l8TQbc0xjACUwAJw+Fkd6EvtMVFlBz9GtRcJc=,
Content-Type: application/xml, Transfer-Encoding: chunked, Date: Fri, 21
Apr 2017 23:01:41 GMT, Connection: close, Server: AmazonS3]
NOTICE: normalzing VCF with Vt...
NOTICE: done normalzing.
NOTICE: keep variants if they are unfiltered in any one of the input files.
NOTICE: extracting variants shared by at least 2 input files.
NOTICE: 8655 variants written to
TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.extract_consensus.vcf.
NOTICE: Cleaning...
…----------NOTICE----------
[ => SeqMule Execution Status: Running 18 of 20 steps: Generate variant
stat, at Fri Apr 21 18:04:52 CDT 2017, Time Elapsed: 3 hr 58 min 9 s]
[ => SeqMule Execution Status: step 15 is finished at Fri Apr 21 18:04:52
CDT 2017, Extract consensus calls]
examine:
TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf
count: <<12611>>
Generating variant stats
NOTICE: Output written to TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_var_stat.txt
[ => SeqMule Execution Status: step 18 is finished at Fri Apr 21 18:04:58
CDT 2017, Generate variant stat]
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...
----------ERROR----------
[ => SeqMule Execution Status: step 17 FAILED at Fri Apr 21 19:57:04 CDT
2017, Generate alignment and coverage stat]
ERROR: command failed
/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 "
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
After fixing the problem, please execute 'cd /home/lili/TCRBOA7-N-WEX' and
'seqmule run TCRBOA7-N-WEX.script' to resume analysis.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
On Fri, Apr 28, 2017 at 9:50 AM, Yunfei Guo ***@***.***> wrote:
Could you show me the error message in an uninterrupted execution, i.e. do
not press Ctrl-C during running?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#157 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/AXTkEgIjv0mtAImVDa_VMCSekAssbHlZks5r0fyygaJpZM4NFMDV>
.
|
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 |
[lili@pgm-serv2 ~]$ cd TCRBOA7-N-WEX
[lili@pgm-serv2 TCRBOA7-N-WEX]$
/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
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...
…On Mon, May 1, 2017 at 5:22 PM, Yunfei Guo ***@***.***> wrote:
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.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#157 (comment)>, or mute
the thread
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.
|
did you check |
The coverage seems low:
[lili@pgm-serv2 TCRBOA7-N-WEX]$ cat
TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_cov_stat.txt
TCRBOA7-N-WEX_result/TCRBOA7-N-WEX.0_bwamem.sort.rmdup.readfiltered.bam=Coverage
stats
total length (defined by
/vol/SeqMule/misc/hg19_exonPlus5bp_UCSCrefGene.bed) = 78.54Mb
Fraction of reads mapped to target region = 28.07%
Average coverage in target region = 12.08
Percentage above 30=12.53%
Percentage above 20=13.68%
Percentage above 10=14.71%
Percentage above 5=16.23%
…On Thu, May 4, 2017 at 9:28 AM, Yunfei Guo ***@***.***> wrote:
did you check TCRBOA7-N-WEX_result/TCRBOA7-N-WEX_cov_stat.txt? Is the
coverage expected?
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<#157 (comment)>, or mute
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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
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