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Published 20 hours ago • verified publisher icon ablab

err code: 255, bwa failed, skipping sublib

Open hjsbio opened this issue 5 years ago • 9 comments

Dear developer,

Thank you for sharing the wonderfull software!Recently I am trying to assembly a kind of bat using it's whole genome resequencing data. I had the issue as said above, the params.txt and spades.log were attached. params.txt spades.log

If you have any problem about my issue, please let me know!

Hjsun

hjsbio avatar Aug 14 '18 01:08 hjsbio

Hello

Thank you for your interest in SPAdes.

Well, looks like bwa crashed while aligning your reads. Does the problem reproduce if you're restart SPAdes via --continue option

asl avatar Aug 14 '18 07:08 asl

Thank you for your answere. I will follow your suggestion and see what happens.

hjsbio avatar Aug 14 '18 09:08 hjsbio

Hello, Below is my new log file with continue option, it seems that there are still problems with bwa. params.txt spades.log

hjsbio avatar Aug 14 '18 10:08 hjsbio

Hello,

I have been having the same "bwa failed, skipping sublib" issue. It persists if I try spades with the --continue option. I trimmed these data with Trimmomatic and here are what the FASTQ headers look like:

==> 7263-1_1P.fastq <== @MG01HX01:804:HK7GLCCXY:7:1101:3285:2012

==> 7263-1_1U.fastq <== @MG01HX01:804:HK7GLCCXY:7:1101:3315:2030

==> 7263-1_2P.fastq <== @MG01HX01:804:HK7GLCCXY:7:1101:3285:2012

==> 7263-1_2U.fastq <== @MG01HX01:804:HK7GLCCXY:7:1101:13464:2030

Below are my log files and the slurm script I used to run the job: params.txt spades.log

Any advice would be greatly appreciated. sbatch-spades.txt

Best, Kevin Kocot

kmkocot avatar May 10 '19 16:05 kmkocot

Thanks for referencing this issue - I previously assumed that was my problem but my .fastq PE headers now match and I'm still getting the same error.

kmkocot avatar May 20 '19 21:05 kmkocot

If your assembly is larger than 2Gb, then the error is likely. It will be fixed in the next SPAdes release. The only workaround is not to use --careful

asl avatar May 21 '19 00:05 asl

Thanks @asl. That is almost certainly my problem. I'll try again without --careful.

kmkocot avatar May 21 '19 17:05 kmkocot

I got the same error, it was because I had a '(' in the path of the input files.

Piplopp avatar Jul 25 '19 12:07 Piplopp

Just to follow up - my assemblies completed normally when I removed the --careful flag.

kmkocot avatar Jul 25 '19 13:07 kmkocot