Dear EGAPx Team,
I have recently been using EGAPx v0.5.2 for genome annotation with approximately 300 RNA-seq datasets. Most steps run well, but we consistently encounter an error during the rnaseq_collapse step.
I am not sure what is causing this issue and would appreciate your advice on how to troubleshoot or resolve it.
Could you please let me know:
what the possible reasons for this error might be,
whether this could be related to the large number of RNA-seq samples,
and what information or log files would be most useful for debugging?
Thank you very much for your help.
Erro like this:
76063dc00000-76063dc04000 r-xp 00000000 00:73 357133357 /img/root/lib/libSegFault.so
76063dc04000-76063de03000 ---p 00004000 00:73 357133357 /img/root/lib/libSegFault.so
76063de03000-76063de04000 r--p 00003000 00:73 357133357 /img/root/lib/libSegFault.so
76063de04000-76063de05000 rw-p 00004000 00:73 357133357 /img/root/lib/libSegFault.so
76063de05000-76063de06000 rw-p 00005000 00:73 357133357 /img/root/lib/libSegFault.so
76063de07000-76063de11000 rw-p 00000000 00:00 0
76063de11000-76063de12000 r--p 00000000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de12000-76063de13000 r-xp 00001000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de13000-76063de14000 r--p 00002000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de14000-76063de15000 r--p 00002000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de15000-76063de16000 rw-p 00003000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de16000-76063de18000 rw-p 00000000 00:00 0
76063de18000-76063de19000 r--p 00000000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de19000-76063de1a000 r-xp 00001000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1a000-76063de1b000 r--p 00002000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1b000-76063de1c000 r--p 00002000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1c000-76063de1d000 rw-p 00003000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1d000-76063de1e000 r--p 00000000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de1e000-76063de1f000 r-xp 00001000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de1f000-76063de20000 r--p 00002000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de20000-76063de21000 r--p 00002000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de21000-76063de22000 rw-p 00003000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de23000-76063de50000 rw-p 00000000 00:00 0
76063de50000-76063de52000 r--p 00000000 00:00 0 [vvar]
76063de52000-76063de54000 r--p 00000000 00:00 0 [vvar_vclock]
76063de54000-76063de56000 r-xp 00000000 00:00 0 [vdso]
76063de56000-76063de57000 r--p 00000000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de57000-76063de82000 r-xp 00001000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de82000-76063de8c000 r--p 0002c000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de8c000-76063de8e000 r--p 00036000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de8e000-76063de90000 rw-p 00038000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
7ffce5f4b000-7ffce5f6c000 rw-p 00000000 00:00 0 [stack]
ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0 [vsyscall]
.command.sh: line 8100: 164 Segmentation fault (core dumped) rnaseq_collapse -backlog 1 -max-jobs 1 -support-non-sra -O tmp/interim -nogenbank -lds2 tmp/genome_lds -sorted-vols align.mft -scaffold-list scaffold_list.mft -sra-metadata-manifest metadata.mft -start-job-id $start_job_id -input-jobs job.003 -workers 32
++ kill 28
Work dir:
/data/lidong/81.egapx/workdir/03/41743b9ff99534979b8d214fe16c72
Container:
ncbi/egapx:0.5.2
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
-- Check '/data/lidong/81.egapx/TJ.300sample/nextflow/nextflow.log' file for details
Dear EGAPx Team,
I have recently been using EGAPx v0.5.2 for genome annotation with approximately 300 RNA-seq datasets. Most steps run well, but we consistently encounter an error during the rnaseq_collapse step.
I am not sure what is causing this issue and would appreciate your advice on how to troubleshoot or resolve it.
Could you please let me know:
what the possible reasons for this error might be,
whether this could be related to the large number of RNA-seq samples,
and what information or log files would be most useful for debugging?
Thank you very much for your help.
Erro like this:
76063dc00000-76063dc04000 r-xp 00000000 00:73 357133357 /img/root/lib/libSegFault.so
76063dc04000-76063de03000 ---p 00004000 00:73 357133357 /img/root/lib/libSegFault.so
76063de03000-76063de04000 r--p 00003000 00:73 357133357 /img/root/lib/libSegFault.so
76063de04000-76063de05000 rw-p 00004000 00:73 357133357 /img/root/lib/libSegFault.so
76063de05000-76063de06000 rw-p 00005000 00:73 357133357 /img/root/lib/libSegFault.so
76063de07000-76063de11000 rw-p 00000000 00:00 0
76063de11000-76063de12000 r--p 00000000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de12000-76063de13000 r-xp 00001000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de13000-76063de14000 r--p 00002000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de14000-76063de15000 r--p 00002000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de15000-76063de16000 rw-p 00003000 00:73 356079471 /usr/lib/x86_64-linux-gnu/libpthread.so.0
76063de16000-76063de18000 rw-p 00000000 00:00 0
76063de18000-76063de19000 r--p 00000000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de19000-76063de1a000 r-xp 00001000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1a000-76063de1b000 r--p 00002000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1b000-76063de1c000 r--p 00002000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1c000-76063de1d000 rw-p 00003000 00:73 356079473 /usr/lib/x86_64-linux-gnu/librt.so.1
76063de1d000-76063de1e000 r--p 00000000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de1e000-76063de1f000 r-xp 00001000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de1f000-76063de20000 r--p 00002000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de20000-76063de21000 r--p 00002000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de21000-76063de22000 rw-p 00003000 00:73 356079406 /usr/lib/x86_64-linux-gnu/libdl.so.2
76063de23000-76063de50000 rw-p 00000000 00:00 0
76063de50000-76063de52000 r--p 00000000 00:00 0 [vvar]
76063de52000-76063de54000 r--p 00000000 00:00 0 [vvar_vclock]
76063de54000-76063de56000 r-xp 00000000 00:00 0 [vdso]
76063de56000-76063de57000 r--p 00000000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de57000-76063de82000 r-xp 00001000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de82000-76063de8c000 r--p 0002c000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de8c000-76063de8e000 r--p 00036000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
76063de8e000-76063de90000 rw-p 00038000 00:73 356079372 /usr/lib/x86_64-linux-gnu/ld-linux-x86-64.so.2
7ffce5f4b000-7ffce5f6c000 rw-p 00000000 00:00 0 [stack]
ffffffffff600000-ffffffffff601000 --xp 00000000 00:00 0 [vsyscall]
.command.sh: line 8100: 164 Segmentation fault (core dumped) rnaseq_collapse -backlog 1 -max-jobs 1 -support-non-sra -O tmp/interim -nogenbank -lds2 tmp/genome_lds -sorted-vols align.mft -scaffold-list scaffold_list.mft -sra-metadata-manifest metadata.mft -start-job-id $start_job_id -input-jobs job.003 -workers 32
++ kill 28
Work dir:
/data/lidong/81.egapx/workdir/03/41743b9ff99534979b8d214fe16c72
Container:
ncbi/egapx:0.5.2
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.run-- Check '/data/lidong/81.egapx/TJ.300sample/nextflow/nextflow.log' file for details