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Nextomics / NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads
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memory allocation failed #8

Closed Ne0tea closed 5 months ago

Ne0tea commented 1 year ago

Hi！ I was tring to polish a genome with 1.3g at a node with 2T memory, but constantly got the error of "memory allocation of xxx bytes failed". According to your previous recommendation, I decraesed -t to 1, and it failed. Then, I split my genome and bam file, while it turns out the same error. Could you please your comments?

moold commented 1 year ago

Can you download the latest version and try again? If still have this error? Can you paste the full error message here?

Ne0tea commented 1 year ago

Thanks for your comment! The error message is Starting Wed Aug 2 21:37:35 CST 2023 node21 memory allocation of 835916608 bytes failed /opt/gridview//pbs/dispatcher/mom_priv/jobs/42661.tc6000.SC: line 19: 371102 Aborted (core dumped) ~/software/next_polish2/target/release/next_polish2 -t 20 -r $bam $asm ${yak1} $yak2 > ${asm%.*}_gfa_chr_np2.fa Finished Starting Wed Aug 2 13:49:00 CST 2023 node21 memory allocation of 835916608 bytes failed /opt/gridview//pbs/dispatcher/mom_priv/jobs/42634.tc6000.SC: line 19: 373261 Aborted (core dumped) ~/software/next_polish2/target/release/next_polish2 -t 1 -r $bam $asm ${yak1} $yak2 > ${asm%.*}_gfa_chr_np2.fa Finished and nextpolish2 version is 1691075451128

moold commented 1 year ago

Did you run the test data successfully?

Ne0tea commented 1 year ago

image yeah, it is successful with test data.

Marison-1 commented 5 months ago

Thanks for your comment! The error message is Starting Wed Aug 2 21:37:35 CST 2023 node21 memory allocation of 835916608 bytes failed /opt/gridview//pbs/dispatcher/mom_priv/jobs/42661.tc6000.SC: line 19: 371102 Aborted (core dumped) ~/software/next_polish2/target/release/next_polish2 -t 20 -r $bam $asm ${yak1} $yak2 > ${asm%.*}_gfa_chr_np2.fa Finished Starting Wed Aug 2 13:49:00 CST 2023 node21 memory allocation of 835916608 bytes failed /opt/gridview//pbs/dispatcher/mom_priv/jobs/42634.tc6000.SC: line 19: 373261 Aborted (core dumped) ~/software/next_polish2/target/release/next_polish2 -t 1 -r $bam $asm ${yak1} $yak2 > ${asm%.*}_gfa_chr_np2.fa Finished and nextpolish2 version is 1691075451128

this tools may has a high resource consumption, I met the same problem as you, so I separate the Chr into different file and run them again in a separate way, it worked well