No error message (34045 Aborted)

[sarah872]

Hi, I wanted to run w2rap-contigger, but it stops at step 2.

w2rap-contigger/bin/w2rap-contigger -t 48 -m 10000 -r /tmp/slurm-7878835/R1.fq,/tmp/slurm-7878835/R2.fq -o /tmp/slurm-7878835/w2rap -p w2rap --tmp_dir /tmp/slurm-7878835/temp --min_freq 10

Welcome to w2rap-contigger
--== Step 1: Reading input files ==--
Wed Dec 02 12:21:00 2020: finding input files
Wed Dec 02 12:21:00 2020: reading 2 files (which may take a while)

INPUT FILES:
[1a,type=frag,sample=C,lib=1,frac=1] /tmp/slurm-7878835/R1.fq
[1b,type=frag,sample=C,lib=1,frac=1] /tmp/slurm-7878835/R2.fq

Fri Dec 04 10:10:25 2020: found 1 samples
Fri Dec 04 10:10:25 2020: starts = 0
Fri Dec 04 10:10:25 2020: data extraction complete, peak = 244.52 GB
1.91 days used extracting reads
Reading input files DONE!

--== Step 2: Building first (small K) graph ==--
Fri Dec 04 10:10:25 2020: creating kmers from reads...
terminate called recursively
/var/spool/slurm/slurmd/job7878835/slurm_script: line 28: 34045 Aborted                 w2rap-contigger/bin/w2rap-contigger -t $SLURM_CPUS_PER_TASK -m 10000 -r $TMPDIR/R1.fq,$TMPDIR/R2.fq -o $TMPDIR/w2rap -p w2rap --tmp_dir $TMPDIR/temp --min_freq 10
[ERRO] /tmp/slurm-7878835/w2rap/*.fasta: fastx: open /tmp/slurm-7878835/w2rap/*.fasta: no such file or directory

[gonzalogacc]

Hi Sarah. Did you find the problem? Can you try running step 1 and 2 separately and check how the fastb and qualb files look like after step 1!? Best Gonzalo.-

[bjclavijo]

This is likely an out of memory... clsoing for now, please @sarah872 reopen if you still need a solution.