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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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Segmentation fault with Slurm exit code 139 #213

Closed biowackysci closed 4 years ago

biowackysci commented 4 years ago

Hello I am trying to run an assembly job with the following script wtdbg2 -x ont -g 2.8g -t 100 -p 19 -AS 2 -s 0.05 -L 30000 -i /group/pasture/Saila/wtdg2_L20KB_readlength/2020_newassembly/HSandSVreads/30kbplusreads/30kbplus_HSandSV_allreads_combine.fastq -fo HSandSVII_30kbabove_reads wtpoa-cns -t 100 -i HSandSVII_30kbabove_reads.ctg.lay.gz -fo HSandSVII_30kbabove_reads.ctg.fa

I get the following error messages each time I try

-- total memory 790881552.0 kB -- available 756311976.0 kB -- 48 cores -- Starting program: wtdbg2 -x ont -g 2.8g -t 100 -p 19 -AS 2 -s 0.05 -L 30000 -i /group/pasture/Saila/wtdg2_L20KB_readlength/2020_newassembly/HSandSVreads/30kbplusreads/30kbplus_HSandSV_allreads_combine.fastq -fo HSandSVII_30kbabove_reads -- pid 326481 -- date Wed Aug 12 21:23:08 2020

(Then it starts to load the reads) and does everything until it fails at 232 contigs 18200 edges 41541150 bases/var/spool/slurm/d/job2581635/slurm_script: line 51: 420083 Segmentation fault (core dumped) wtpoa-cns -t 100 -i HSandSVII_30kbabove_reads.ctg.lay.gz -fo HSandSVII_30kbabove_reads.ctg.fa

Is there somehow I can solve this segmentation fault

Thanks S

ruanjue commented 4 years ago

It was the error of wtpoa-cns. If you can separate the very small number of contigs's layout around 232'th from the big total lay file that will produce the segmentation fault, I will debug on the samll file to find what' wrong.

biowackysci commented 4 years ago

Hello Ruanjue, I could not 232 as it was empty, so I have sent you 231 contig. test.txt

ruanjue commented 4 years ago

I meant the minimal part of input file that repeat the seqfault.

biowackysci commented 4 years ago

Sorry, I am not entirely sure of what file you are after. Are you after the source input fastq file? Sorry I new to the assembly world.

Thanks S

ruanjue commented 4 years ago

HSandSVII_30kbabove_reads.ctg.lay.gz

biowackysci commented 4 years ago

Hello, The previous file I sent you was an extract from the .lay file. Do you require more contigs or something else? Sorry for this Thanks again S

ruanjue commented 4 years ago

Hi,

When you are sure of the minimal part that repeat the error on your computer, please compress the file and send to me (ruanjue.big AT qq.com)

Jue

biowackysci commented 4 years ago

Hello Ruanjue,

I have sorted the issue out. I had some bad fastq reads and I cleaned them and resubmitted the job. its all good now Thanks for your input though S PS you may close the issue