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alekseyzimin / masurca

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Disk space #46

Open ipavanellisouza opened 6 years ago

ipavanellisouza commented 6 years ago

Hi,

I am running a de novo hybrid assembly with illumina PE and pacbio long reads, and i'm facing a disk space issue. The intermediate files that MaSuRCA writes is consuming all my disk space and the assembly have failed several times because of it. At this point, my assembly running the following script: /usr/local/MaSuRCA-3.2.4/bin/translateReduceFile.perl work1_mr1/superReadNames.txt work1_mr1/reduce.tmp > work1_mr1/reduce.tmp.renamed I would like to know if there is any files that are safe to delete from the output files.

Thanks a lot,

Isabela

alekseyzimin commented 6 years ago

At this stage I would not recommend to remove anything because then if anything fails, it would be impossible to restart the assembly. In general I would recommend getting more disk space.

ipavanellisouza commented 6 years ago

Hi,

Thanks a lot for you reply.

After posted my issue i came across another problem. My assembly failed again, for the third time at the same point with the same error message. My advisor and i could not solve the problem. I will post the log file.

--> CA.mr.41.15.17.0.029.log `ENV: SGE_TASK_ID needs to be unset, done. ----------------------------------------START Fri Jul 20 10:54:35 2018 /usr/local/MaSuRCA-3.2.4/CA8/Linux-amd64/bin/gatekeeper -o /home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15.17.0.029/genome.gkpStore.BUILDING -T -F /home/isabela/assembly_masurcaHibrido/hibrido_new/mr.41.15.17.0.029.1.frg /home/isabela/assembly_masurcaHibrido/hibrido_new/mr.41.15.17.0.029.1.mates.frg > /home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15.17.0.029/genome.gkpStore.err 2>&1 ----------------------------------------END Fri Jul 20 10:57:29 2018 (174 seconds) ERROR: Failed with signal HUP (1)

runCA failed.

Stack trace:

at /usr/local/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 1613. main::caFailure("gatekeeper failed", "/home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15"...) called at /usr/local/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 1942 main::preoverlap("/home/isabela/assembly_masurcaHibrido/hibrido_new/mr.41.15.17"..., "/home/isabela/assembly_masurcaHibrido/hibrido_new/mr.41.15.17"...) called at /usr/local/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 6520

Last few lines of the relevant log file (/home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15.17.0.029/genome.gkpStore.err):

Starting file '/home/isabela/assembly_masurcaHibrido/hibrido_new/mr.41.15.17.0.029.1.frg'. ERROR: AS_MSG_pmesg.c::ReadLine()-- Premature end of input at line 23801986 (FRG) 'XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX'

Failure message:

gatekeeper failed

ENV: SGE_TASK_ID needs to be unset, done. ----------------------------------------START Fri Jul 20 10:57:29 2018 /usr/local/MaSuRCA-3.2.4/CA8/Linux-amd64/bin/gatekeeper -o /home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15.17.0.029/genome.gkpStore.BUILDING -T -F /home/isabela/assembly_masurcaHibrido/hibrido_new/mr.41.15.17.0.029.1.frg > /home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15.17.0.029/genome.gkpStore.err 2>&1 ----------------------------------------END Fri Jul 20 10:57:29 2018 (0 seconds) ERROR: Failed with signal HUP (1)

runCA failed.

Stack trace:

at /usr/local/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 1613. main::caFailure("gatekeeper failed", "/home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15"...) called at /usr/local/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 1942 main::preoverlap("/home/isabela/assembly_masurcaHibrido/hibrido_new/mr.41.15.17"...) called at /usr/local/MaSuRCA-3.2.4/bin/../CA8/Linux-amd64/bin/runCA line 6520

Last few lines of the relevant log file (/home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15.17.0.029/genome.gkpStore.err):

GateKeeper Store '/home/isabela/assembly_masurcaHibrido/hibrido_new/CA.mr.41.15.17.0.029/genome.gkpStore.BUILDING' exists; will not create a new one on top of it.

Failure message:

gatekeeper failed`

Anything it would help a lot! Thanks!