exitcode1 by slurm #8
Comments
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Can you share the full log file? There is usually more information about the error right before the actual error message. |
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Good Morning Igor, Thank you for your time Here is the error message: Error from 17778705.out gzip: /gpfs/home/torunp01/234518/bed/FASTQ-CLEAN/ptm1__214518_R1.fastq.gz: unexpected end of file fastq-clean.sh ERROR: FASTQ R1 AND R2 HAVE DIFFERENT NUMBER OF READS removed ‘/gpfs/home/torunp01/234518/bed/FASTQ-CLEAN/ptm1__214518_R1.fastq.gz’ wes.sh ERROR: SEGMENT fastq-clean DID NOT FINISH |
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Looks like you have multiple errors. The first one was from job 17749908 about the reference. The one you posted the second time is for 17778705 where you'll notice it says "Disk quota exceeded". It looks like you are doing analysis in your home directory ( |
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Excellent Thank you Igor!
From: igor ***@***.***>
Date: Thursday, July 7, 2022 at 10:25 AM
To: igordot/sns ***@***.***>
Cc: Pedro Toruno ***@***.***>, Author ***@***.***>
Subject: Re: [igordot/sns] exitcode1 by slurm (Issue #8)
Note: This message originated from outside the FIU Faculty/Staff email system.
Looks like you have multiple errors. The first one was from job 17749908 about the reference. The one you posted the second time is for 17778705 where you'll notice it says "Disk quota exceeded". It looks like you are doing analysis in your home directory (/gpfs/home/torunp01/) and you ran out of space there. You should be working out of a lab directory (/gpfs/data/[labname]/) which would have a have higher limit. You could request one for the lab.
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Good Evening Igor, Hope you are well... thanks CMD: ERROR --ERROR stack tracejava.lang.NullPointerException ERROR ------------------------------------------------------------------------------------------ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This means that one or more arguments or inputs in your command are incorrect.ERROR The error message below tells you what is the problem.ERRORERROR If the problem is an invalid argument, please check the online documentation guideERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.ERRORERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.ERRORERROR MESSAGE: Could not read file /gpfs/data/hackerlab/logs-bam-ra-rc-gatk/ptm1__214518.intervals because The interval file does not exist.ERROR ------------------------------------------------------------------------------------------bam-ra-rc-gatk.sh ERROR: BAM /gpfs/data/hackerlab/BAM-GATK-RA/ptm1__214518.dd.ra.bam NOT GENERATED grep: /gpfs/data/hackerlab/samples.bam-ra-rc-gatk.csv: No such file or directory wes.sh ERROR: SEGMENT bam-ra-rc-gatk DID NOT FINISH [torunp01@bigpurple-ln1 logs-sbatch]$ |
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It looks like there was a problem reading/writing certain files. Did this happen for one sample or all? It looks like you are running this in |
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Thanks Igor, Will do as you recommend and yes this was for only one file. Should I run one more time? Thank you for your time and recommendations! |
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Yes, I would do everything from scratch in a new directory. The runtime is going to largely depend on how many reads you have. 9 hours seems reasonable. |
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Hello again Igor, MESSAGE: Could not read file /gpfs/data/hackerlab/logs-bam-ra-rc-gatk/ptm1__214518.intervals because The interval file does not exist. |
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It looks like you are still running it from the same directory. Please create a project-specific sub-directory. |
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Good Morning, Here is the current lab path directory with the required files: NUMBER OF SAMPLES : 1 And I am getting the same error message: ERROR ------------------------------------------------------------------------------------------ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This might be a bug. Please check the documentation guide to see if this is a known problem.ERROR If not, please post the error message, with stack trace, to the GATK forum.ERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR ------------------------------------------------------------------------------------------ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This means that one or more arguments or inputs in your command are incorrect.ERROR The error message below tells you what is the problem.ERRORERROR If the problem is an invalid argument, please check the online documentation guideERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.ERRORERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.ERRORERROR MESSAGE: Badly formed genome location: Parameters to GenomeLocParser are incorrect:The stop position 248956422 is less than start 249106097 in contig chr1I apologize for the trouble. |
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This is a different error now. I did not see "Badly formed genome location" before. Can you share the entire log file? |
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thanks for your feedback.. i will share everything from where it starts to say error: java -Xms8G -Xmx8G -jar /gpfs/data/igorlab/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar -T DepthOfCoverage -dt NONE -rf BadCigar -nt 8 --logging_level ERROR --omitIntervalStatistics --omitLocusTable --omitDepthOutputAtEachBase -ct 10 -ct 100 -mbq 20 -mmq 20 --reference_sequence /gpfs/data/igorlab/ref/hg38/genome.fa --intervals /gpfs/data/hackerlab/07_12_2022/TruSeq_Exome_TargetedRegions_v1.2.bed --interval_padding 500 --input_file /gpfs/data/hackerlab/07_12_2022/BAM-DD/ptm1__214518.dd.bam --outputFormat csv --out /gpfs/data/hackerlab/07_12_2022/QC-target-reads/ptm1__214518.pad500 ERROR --ERROR stack tracejava.lang.NullPointerException ERROR ------------------------------------------------------------------------------------------ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This might be a bug. Please check the documentation guide to see if this is a known problem.ERROR If not, please post the error message, with stack trace, to the GATK forum.ERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR MESSAGE: Code exception (see stack trace for error itself)ERROR ------------------------------------------------------------------------------------------CMD: ERROR --ERROR stack tracejava.lang.NullPointerException ERROR ------------------------------------------------------------------------------------------ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This might be a bug. Please check the documentation guide to see if this is a known problem.ERROR If not, please post the error message, with stack trace, to the GATK forum.ERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR MESSAGE: Code exception (see stack trace for error itself)ERROR ------------------------------------------------------------------------------------------CMD: ERROR ------------------------------------------------------------------------------------------ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This means that one or more arguments or inputs in your command are incorrect.ERROR The error message below tells you what is the problem.ERRORERROR If the problem is an invalid argument, please check the online documentation guideERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.ERRORERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.ERRORERROR MESSAGE: Badly formed genome location: Parameters to GenomeLocParser are incorrect:The stop position 248956422 is less than start 249106097 in contig chr1ERROR ------------------------------------------------------------------------------------------genome total coverage: 32839088570 ========== SEGMENT: bam-ra-rc-gatk ==========
checking R package: getopt
CMD: ERROR --ERROR stack tracejava.lang.NullPointerException ERROR ------------------------------------------------------------------------------------------ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This might be a bug. Please check the documentation guide to see if this is a known problem.ERROR If not, please post the error message, with stack trace, to the GATK forum.ERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR MESSAGE: Code exception (see stack trace for error itself)ERROR ------------------------------------------------------------------------------------------CMD: ERROR ------------------------------------------------------------------------------------------ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):ERRORERROR This means that one or more arguments or inputs in your command are incorrect.ERROR The error message below tells you what is the problem.ERRORERROR If the problem is an invalid argument, please check the online documentation guideERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.ERRORERROR Visit our website and forum for extensive documentation and answers toERROR commonly asked questions https://software.broadinstitute.org/gatkERRORERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.ERRORERROR MESSAGE: Could not read file /gpfs/data/hackerlab/07_12_2022/logs-bam-ra-rc-gatk/ptm1__214518.intervals because The interval file does not exist.ERROR ------------------------------------------------------------------------------------------bam-ra-rc-gatk.sh ERROR: BAM /gpfs/data/hackerlab/07_12_2022/BAM-GATK-RA/ptm1__214518.dd.ra.bam NOT GENERATED grep: /gpfs/data/hackerlab/07_12_2022/samples.bam-ra-rc-gatk.csv: No such file or directory wes.sh ERROR: SEGMENT bam-ra-rc-gatk DID NOT FINISH [torunp01@bigpurple-ln1 logs-sbatch]$ |
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Your reference genome is hg38, but your BED file is likely hg19. Are you able to check? |
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I will check once I am in the lab.
Thanks for your input.
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From: igor ***@***.***>
Sent: Wednesday, July 13, 2022 11:43:05 AM
To: igordot/sns ***@***.***>
Cc: Pedro Toruno ***@***.***>; Author ***@***.***>
Subject: Re: [igordot/sns] exitcode1 by slurm (Issue #8)
Note: This message originated from outside the FIU Faculty/Staff email system.
Your reference genome is hg38, but your BED file is likely hg19. Are you able to check?
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Reply to this email directly, view it on GitHub<#8 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APEULTVWWHQVYT5HGZSPJOTVT3PYTANCNFSM52XG3VQQ>.
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All Good! |
Good Afternoon,
I am getting this error:
Slurm Job_id=17749799 Name=sns.wes.ptm1__214518 Failed, Run time 00:00:02, FAILED, ExitCode 1
eventhough I have added the reference bed file for the sequence to run...
when I checked the progress or error for the file being run I got this error from terminal, eventhough the reference bed file was copied into the working folder.
align-bwa-mem.sh ERROR: REF DOES NOT EXIST
logs-sbatch/slurm-17749908.out: wes.sh ERROR: SEGMENT align-bwa-mem DID NOT FINISH
Any suggestions?
Thank you
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