Illegal seek

[avrajit]

gridss conda installation
jar file 2.13.2-gridss-jar-with-dependencies.jar
platform : Ubuntu 22

The code I ran
gridss -t 20 -r ./reference/Ref/GRCh38.p14.genome.fa -j ~/tools/gridss-2.13.2-gridss-jar-with-dependencies.jar -o ./BAP19_SV.vcf -b ./reference/Ref/ENCFF356LFX.bed ./pancreatic_data/BPAN19_S29_bqsr.bam ./pancreatic_data/BPAT19_S23_bqsr.bam

After running a bit it is stopped with this error[

Fri Sep 06 22:05:51 IST 2024] gridss.ComputeSamTags done. Elapsed time: 13.10 minutes.
Runtime.totalMemory()=1852833792
[bam_sort_core] merging from 3 files and 20 in-memory blocks...
samtools sort: failed writing to "./BPAT19_S23_bqsr.bam.gridss.working/tmp.BPAT19_S23_bqsr.bam.coordinate.bam": Illegal seek

Is it the error related to memeory. Samtools not able to work on large amout of temp files? how to overcome this issue? using more RAM? please help

[d-cameron]

That's an unusual error especially since it's coming from samtools. Did you run out of disk space?

…

On Mon, Sep 9, 2024 at 3:22 PM avrajit ***@***.***> wrote: gridss conda installation jar file 2.13.2-gridss-jar-with-dependencies.jar platform : Ubuntu 22 The code I ran gridss -t 20 -r ./reference/Ref/GRCh38.p14.genome.fa -j ~/tools/gridss-2.13.2-gridss-jar-with-dependencies.jar -o ./BAP19_SV.vcf -b ./reference/Ref/ENCFF356LFX.bed ./pancreatic_data/BPAN19_S29_bqsr.bam ./pancreatic_data/BPAT19_S23_bqsr.bam After running a bit it is stopped with this error[ Fri Sep 06 22:05:51 IST 2024] gridss.ComputeSamTags done. Elapsed time: 13.10 minutes. Runtime.totalMemory()=1852833792 [bam_sort_core] merging from 3 files and 20 in-memory blocks... samtools sort: failed writing to "./BPAT19_S23_bqsr.bam.gridss.working/tmp.BPAT19_S23_bqsr.bam.coordinate.bam": Illegal seek Is it the error related to memeory. Samtools not able to work on large amout of temp files? how to overcome this issue? using more RAM? please help — Reply to this email directly, view it on GitHub <#677>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABOBYOFY5VMMPWRH6FRAFK3ZVUWBPAVCNFSM6AAAAABN3XO5YWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUYTEOJTGM4TSNQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[avrajit]

HI Cameron

Thanks for your response. Yes, This is a hardware issue with my HDD. I replaced it and checked with same command and found working well.
Please close the issue. Thanks