exitcode1 by slurm about sns

[ptoru001]

All Good!
thanks for your support!

[igordot]

Can you share the full log file? There is usually more information about the error right before the actual error message.

[ptoru001]

Good Morning Igor,

Thank you for your time

Here is the error message:

Error from 17778705.out
cat: write error: Disk quota exceeded
Wed Jul 6 17:20:28 EDT 2022

gzip: /gpfs/home/torunp01/234518/bed/FASTQ-CLEAN/ptm1__214518_R1.fastq.gz: unexpected end of file
FASTQ R1: /gpfs/home/torunp01/234518/bed/FASTQ-CLEAN/ptm1__214518_R1.fastq.gz
FASTQ R2: /gpfs/home/torunp01/234518/bed/FASTQ-CLEAN/ptm1__214518_R2.fastq.gz
READS R1: 237334916
READS R2: 193358378

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’
removed ‘/gpfs/home/torunp01/234518/bed/FASTQ-CLEAN/ptm1__214518_R2.fastq.gz’
grep: /gpfs/home/torunp01/234518/bed/samples.fastq-clean.csv: No such file or directory
grep: /gpfs/home/torunp01/234518/bed/samples.fastq-clean.csv: No such file or directory

wes.sh ERROR: SEGMENT fastq-clean DID NOT FINISH

[igordot]

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.

[ptoru001]

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. — Reply to this email directly, view it on GitHub<#8 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APEULTUWBTKNPN4BWATIH5DVS3SGZANCNFSM52XG3VQQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[ptoru001]

Good Evening Igor,

Hope you are well...
after running the data for a couple of hours I ended up with these error messages.
How may i resolve this?

thanks
pedro

CMD:
java -Xms8G -Xmx8G -jar /gpfs/data/igorlab/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar -T RealignerTargetCreator -dt NONE --logging_level ERROR -nt 8 --reference_sequence /gpfs/data/igorlab/ref/hg38/genome.fa -known /gpfs/data/igorlab/ref/hg38/gatk-bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --intervals /gpfs/data/hackerlab/TruSeq_Exome_TargetedRegions_v1.2.bed --interval_padding 10 --input_file /gpfs/data/hackerlab/BAM-DD/ptm1__214518.dd.bam --out /gpfs/data/hackerlab/logs-bam-ra-rc-gatk/ptm1__214518.intervals

ERROR --

ERROR stack trace

java.lang.NullPointerException
at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
at java.util.Arrays.sort(Arrays.java:1312)
at java.util.Arrays.sort(Arrays.java:1506)
at java.util.ArrayList.sort(ArrayList.java:1462)

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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.

ERROR

ERROR If the problem is an invalid argument, please check the online documentation guide

ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.

ERROR

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.

ERROR

ERROR 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]$

[igordot]

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 /gpfs/data/hackerlab now. Maybe you had some permissions issues there. Also, you should create a project-specific sub-directory.

[ptoru001]

Thanks Igor,

Will do as you recommend and yes this was for only one file. Should I run one more time?
Also it took 9 hours for the data to run...is that normal?

Thank you for your time and recommendations!

[igordot]

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.

[ptoru001]

Hello again Igor,
I did as you instructed but still to no avail....this is the error message I am getting out of los-sbatch:

MESSAGE: Could not read file /gpfs/data/hackerlab/logs-bam-ra-rc-gatk/ptm1__214518.intervals because The interval file does not exist.

[igordot]

It looks like you are still running it from the same directory. Please create a project-specific sub-directory.

[ptoru001]

Good Morning,

Here is the current lab path directory with the required files:

NUMBER OF SAMPLES : 1
NUMBER OF SINGLE FILES : 0
NUMBER OF PAIRED FILES : 4
[torunp01@bigpurple-ln3 07_12_2022]$ pwd
/gpfs/data/hackerlab/07_12_2022
[torunp01@bigpurple-ln3 07_12_2022]$ ll
total 11074
-rw------- 1 torunp01 hackerlab 796 Jul 12 13:45 samples.fastq-raw.csv
-rw------- 1 torunp01 hackerlab 87 Jul 12 13:41 settings.txt
drwx--S--- 6 torunp01 hackerlab 4096 Jul 12 13:39 sns
-rwx------ 1 torunp01 hackerlab 11302942 Jul 12 13:40 TruSeq_Exome_TargetedRegions_v1.2.bed

And I am getting the same error message:

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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 to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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.

ERROR

ERROR If the problem is an invalid argument, please check the online documentation guide

ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.

ERROR

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.

ERROR

ERROR MESSAGE: Badly formed genome location: Parameters to GenomeLocParser are incorrect:The stop position 248956422 is less than start 249106097 in contig chr1

I apologize for the trouble.

[igordot]

This is a different error now. I did not see "Badly formed genome location" before. Can you share the entire log file?

[ptoru001]

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 trace

java.lang.NullPointerException
at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
at java.util.Arrays.sort(Arrays.java:1312)
at java.util.Arrays.sort(Arrays.java:1506)
at java.util.ArrayList.sort(ArrayList.java:1464)
at java.util.Collections.sort(Collections.java:143)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:256)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:873)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.loadIntervals(IntervalUtils.java:680)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalBindingsPair(IntervalUtils.java:657)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:617)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:801)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:297)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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 to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Code exception (see stack trace for error itself)

ERROR ------------------------------------------------------------------------------------------

CMD:
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 100 --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.pad100

ERROR --

ERROR stack trace

java.lang.NullPointerException
at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
at java.util.Arrays.sort(Arrays.java:1312)
at java.util.Arrays.sort(Arrays.java:1506)
at java.util.ArrayList.sort(ArrayList.java:1464)
at java.util.Collections.sort(Collections.java:143)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:256)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:873)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.loadIntervals(IntervalUtils.java:680)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalBindingsPair(IntervalUtils.java:657)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:617)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:801)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:297)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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 to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Code exception (see stack trace for error itself)

ERROR ------------------------------------------------------------------------------------------

CMD:
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 --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.bed

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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.

ERROR

ERROR If the problem is an invalid argument, please check the online documentation guide

ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.

ERROR

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.

ERROR

ERROR MESSAGE: Badly formed genome location: Parameters to GenomeLocParser are incorrect:The stop position 248956422 is less than start 249106097 in contig chr1

ERROR ------------------------------------------------------------------------------------------

genome total coverage: 32839088570
cat: /gpfs/data/hackerlab/07_12_2022/QC-target-reads/ptm1__214518.pad500.sample_summary: No such file or directory
bed +/- 500bp total coverage:
(standard_in) 1: syntax error
bed +/- 500bp %: %
cat: /gpfs/data/hackerlab/07_12_2022/QC-target-reads/ptm1__214518.pad100.sample_summary: No such file or directory
bed +/- 100bp total coverage:
(standard_in) 1: syntax error
bed +/- 100bp %: %
bed total coverage:
(standard_in) 1: syntax error
bed %: %

========== SEGMENT: bam-ra-rc-gatk ==========

• R: /gpfs/share/apps/R/3.6.1/bin/R
• R version: R version 3.6.1 (2019-07-05) -- "Action of the Toes"
• Rscript: /gpfs/share/apps/R/3.6.1/bin/Rscript
• Rscript version: R scripting front-end version 3.6.1 (2019-07-05)

checking R package: getopt
loading package: getopt
checking R package: optparse
loading package: optparse
checking R package: gsalib
loading package: gsalib
installing package: gsalib
Bioconductor version 3.10 (BiocManager 1.30.15), R 3.6.1 (2019-07-05)
Installing package(s) 'gsalib'
package not available on CRAN or Bioconductor: gsalib
Error in library(p, character.only = TRUE) :
there is no package called ‘gsalib’
Calls: load_install_packages ... suppressPackageStartupMessages -> withCallingHandlers -> library
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘gsalib’
2: In .inet_warning(msg) :
package ‘gsalib’ is not available (for R version 3.6.1)
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘gsalib’
Execution halted
checking R package: reshape
loading package: reshape
checking R package: gplots
loading package: gplots
checking R package: ggplot2
loading package: ggplot2
checking R package: data.table
loading package: data.table
checking R package: naturalsort
loading package: naturalsort

• GATK: /gpfs/data/igorlab/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar
• GATK version: 3.8-1-0-gf15c1c3ef
• BAM IN: /gpfs/data/hackerlab/07_12_2022/BAM-DD/ptm1__214518.dd.bam
• BAM RA: /gpfs/data/hackerlab/07_12_2022/BAM-GATK-RA/ptm1__214518.dd.ra.bam

CMD:
java -Xms8G -Xmx8G -jar /gpfs/data/igorlab/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar -T RealignerTargetCreator -dt NONE --logging_level ERROR -nt 8 --reference_sequence /gpfs/data/igorlab/ref/hg38/genome.fa -known /gpfs/data/igorlab/ref/hg38/gatk-bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --intervals /gpfs/data/hackerlab/07_12_2022/TruSeq_Exome_TargetedRegions_v1.2.bed --interval_padding 10 --input_file /gpfs/data/hackerlab/07_12_2022/BAM-DD/ptm1__214518.dd.bam --out /gpfs/data/hackerlab/07_12_2022/logs-bam-ra-rc-gatk/ptm1__214518.intervals

ERROR --

ERROR stack trace

java.lang.NullPointerException
at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:325)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:202)
at java.util.Arrays.sort(Arrays.java:1312)
at java.util.Arrays.sort(Arrays.java:1506)
at java.util.ArrayList.sort(ArrayList.java:1462)
at java.util.Collections.sort(Collections.java:143)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:256)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:873)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.loadIntervals(IntervalUtils.java:680)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalBindingsPair(IntervalUtils.java:657)
at org.broadinstitute.gatk.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:617)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:801)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:297)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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 to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Code exception (see stack trace for error itself)

ERROR ------------------------------------------------------------------------------------------

CMD:
java -Xms8G -Xmx8G -jar /gpfs/data/igorlab/software/GenomeAnalysisTK/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar -T IndelRealigner -dt NONE --logging_level ERROR --reference_sequence /gpfs/data/igorlab/ref/hg38/genome.fa --maxReadsForRealignment 50000 -known /gpfs/data/igorlab/ref/hg38/gatk-bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -targetIntervals /gpfs/data/hackerlab/07_12_2022/logs-bam-ra-rc-gatk/ptm1__214518.intervals --input_file /gpfs/data/hackerlab/07_12_2022/BAM-DD/ptm1__214518.dd.bam --out /gpfs/data/hackerlab/07_12_2022/BAM-GATK-RA/ptm1__214518.dd.ra.bam

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 3.8-1-0-gf15c1c3ef):

ERROR

ERROR 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.

ERROR

ERROR If the problem is an invalid argument, please check the online documentation guide

ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.

ERROR

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions https://software.broadinstitute.org/gatk

ERROR

ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.

ERROR

ERROR 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]$

[igordot]

Your reference genome is hg38, but your BED file is likely hg19. Are you able to check?

[ptoru001]

I will check once I am in the lab. Thanks for your input. Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ 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? — Reply to this email directly, view it on GitHub<#8 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APEULTVWWHQVYT5HGZSPJOTVT3PYTANCNFSM52XG3VQQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>