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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
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Can not open k141.final.contigs.fa. Now exit to system...' #811

Closed mingxues2024 closed 2 months ago

mingxues2024 commented 3 months ago

Dear sir, I have probloms like that Error running command: /lustre/BIF/nobackup/sun091/miniforge3/envs/SqueezeMeta/SqueezeMeta/bin/megahit/megahit -1 /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/data/raw_fastq/par1.fastq.gz -2 /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/data/raw_fastq/par2.fastq.gz -t 12 -o /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/data/megahit >> /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/syslog 2>&1 at /lustre/BIF/nobackup/sun091/miniforge3/envs/SqueezeMeta/SqueezeMeta/lib/SqueezeMeta/assembly_megahit.pl line 36. Assembly not present in /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/results/01.A17.fasta, exiting Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

If you don't know what went wrong or want further advice, please look for similar issues in https://github.com/jtamames/SqueezeMeta/issues Feel free to open a new issue if you don't find the answer there. Please add a brief description of the problem and upload the /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/syslog file (zip it first) Died at /lustre/BIF/nobackup/sun091/miniforge3/envs/SqueezeMeta/bin/SqueezeMeta.pl line 941. syslog.zip

fpusan commented 3 months ago

Can you check the log in /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/data/megahit/log and share it with us?

mingxues2024 commented 3 months ago

From: Fernando Puente-Sánchez @.> Sent: Monday, March 11, 2024 5:00 PM To: jtamames/SqueezeMeta @.> Cc: Sun, Mingxue @.>; Author @.> Subject: Re: [jtamames/SqueezeMeta] Can not open k141.final.contigs.fa. Now exit to system...' (Issue #811)

Can you check the log in /lustre/BIF/nobackup/sun091/metagenome/6_others_squeeze/A17/data/megahit/log and share it with us?

- Reply to this email directly, view it on GitHubhttps://github.com/jtamames/SqueezeMeta/issues/811#issuecomment-1988789311, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFTDQ6NYP6PNKGBN7FRBEOTYXXIJRAVCNFSM6AAAAABEQSUHHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBYG44DSMZRGE. You are receiving this because you authored the thread.Message ID: @.***>

fpusan commented 3 months ago

Seems related to this previously described MEGAHIT error (https://github.com/voutcn/megahit/issues/219). Maybe this is a memory issue, and your dataset is too large for the resources you have. Is this also happening with our test dataset?

mingxues2024 commented 3 months ago

Thanks, it doesn't happen in test file. Is there necessary I need to expand my memory?

From: Fernando Puente-Sánchez @.> Sent: Monday, March 11, 2024 5:06 PM To: jtamames/SqueezeMeta @.> Cc: Sun, Mingxue @.>; Author @.> Subject: Re: [jtamames/SqueezeMeta] Can not open k141.final.contigs.fa. Now exit to system...' (Issue #811)

Seems related to this previously described MEGAHIT error (voutcn/megahit#219https://github.com/voutcn/megahit/issues/219). Maybe this is a memory issue, and your dataset is too large for the resources you have. Is this also happening with our test dataset?

- Reply to this email directly, view it on GitHubhttps://github.com/jtamames/SqueezeMeta/issues/811#issuecomment-1988800641, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFTDQ6N63WTOWB2IYJ6AC73YXXI4ZAVCNFSM6AAAAABEQSUHHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBYHAYDANRUGE. You are receiving this because you authored the thread.Message ID: @.***>

fpusan commented 3 months ago

Then this may be the issue. Can you try running it in sequential mode instead to make sure there is not a problem with your individual fastq files?

mingxues2024 commented 3 months ago

Then this may be the issue. Can you try running it in sequential mode instead to make sure there is not a problem with your individual fastq files?

I first used code sequencial mode and occurred questions like that

mingxues2024 commented 3 months ago

Then this may be the issue. Can you try running it in sequential mode instead to make sure there is not a problem with your individual fastq files?

I first used code sequencial mode and occurred questions like that SqueezeMeta.pl -m sequential -s samples2.txt -f /lustre/BIF/nobackup/sun091/metagenome/4_assembly

fpusan commented 3 months ago

Ah, you are right, I didn't realize this was already a run on the sequential mode. Then it's unlikely that the problem is a memory issue. Can you try excluding the sample that fails and see if it works for the rest? Also is this a computing cluster or your own computer/workstation? How much RAM do you have available?

mingxues2024 commented 3 months ago

Ah, you are right, I didn't realize this was already a run on the sequential mode. Then it's unlikely that the problem is a memory issue. Can you try excluding the sample that fails and see if it works for the rest? Also is this a computing cluster or your own computer/workstation? How much RAM do you have available?

I have successfully run 5 samples and this was the sixth. I think I have 2T memory

fpusan commented 3 months ago

Then the issue seems related to this sample in particular, and since it happens inside MEGAHIT it's difficult for me to help you. What happens if you just run that samples using SPAdes instead as the assembler? (adding -a spades to the SqueezeMeta call). 2Tb RAM should be more than enough (as long as you actually have access to all of it, which is not always the case when e.g. working in a computing cluster)

fpusan commented 2 months ago

Closing due to lack of activity, feel free to reopen