Comments (6)
roddypr
commented on September 3, 2024
In my (very limited!) experience, if you are using Slurm, the error message in the cluster_logs directory is more helpful. And doing "seff 1444270" to check if you ran out of memory or time
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sunta3iouxos
commented on September 3, 2024
@roddypr
thsnk you, this is what I get:
seff 1444270
Job ID: 1444270
Cluster: raptor
User/Group: hthiele0/uniuser
State: FAILED (exit code 1)
Nodes: 1
Cores per node: 24
CPU Utilized: 00:00:02
CPU Efficiency: 2.08% of 00:01:36 core-walltime
Job Wall-clock time: 00:00:04
Memory Utilized: 0.00 MB (estimated maximum)
Memory Efficiency: 0.00% of 24.00 GB (1.00 GB/core)from snakepipes.
katsikora
commented on September 3, 2024
Hi Sunta3iouxos,
thanks for reporting your issue. Could you have a look in the Bowtie log file: Bowtie2/logs/A006850324_209972_S8_L000.sort.log ?
Best wishes,
Katarzyna
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sunta3iouxos
commented on September 3, 2024
Unfortunately it is empty:
(base) [tgeorgom@cheops1:~]$ 07:54:33$ls /scratch/tgeorgom/AP04/Bowtie2/logs/
(base) [tgeorgom@cheops1:~]$ 07:54:38$
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katsikora
commented on September 3, 2024
That's a pity. You can try to reproduce the error by rerunning the command manually like this:
cd $output_directory
conda activate /projects-raptor/ccg-ngs/production/sw/miniconda3/envs/4094a9892df79329972dc6079b5814b5
TMPDIR=/scratch/tmp/tmp/
MYTEMP=$(mktemp -d ${TMPDIR:-/tmp}/snakepipes.XXXXXXXXXX);
bowtie2 -X 1000 -x /data/repository/organisms/GRCm38_ensembl/BowtieIndex/genome -1 FASTQ_fastp/A006850324_209972_S8_L000_R1_001.fastq.gz -2 FASTQ_fastp/A006850324_209972_S8_L000_R2_001.fastq.gz --end-to-end --very-sensitive-local --no-mixed --no-discordant --dovetail -I 10 -X 1000 --fr --rg-id A006850324_209972_S8_L000 --rg DS:A006850324_209972_S8_L000 --rg PL:ILLUMINA --rg SM:A006850324_209972_S8_L000 -p 24 2> Bowtie2/A006850324_209972_S8_L000.Bowtie2_summary.txt | samtools view -Sb - | samtools sort -m 2G -T $MYTEMP/A006850324_209972_S8_L000 -@ 2 -O bam - > Bowtie2/A006850324_209972_S8_L000.sorted.bam
The error message should be printed to the screen then.
Hope this helps,
Katarzyna
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sunta3iouxos
commented on September 3, 2024
I am closing this one I figured it out, but do not really remember how I solved it.
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