Error in rule Bowtie2

[sunta3iouxos]

Could you help me overcome the following issue? the command I am running is:

DNA-mapping -i AP04/fastq/ -o /scratch/tmp/DNAseq/AP04 --fastqc --trim --trimmer fastp --trimmerOptions "--trim_poly_g --trim_poly_x -Q -L --correction" --dedup --plotFormat "pdf" --mapq 2 -j 14 --alignerOpts " --end-to-end --very-sensitive-local --no-mixed --no-discordant --dovetail -I 10 -X 1000" --insertSizeMax 1000 mm10_gencodeM19

Error in rule Bowtie2:
    jobid: 178
    output: Bowtie2/A006850324_209972_S8_L000.Bowtie2_summary.txt, Bowtie2/A006850324_209972_S8_L000.sorted.bam
    log: Bowtie2/logs/A006850324_209972_S8_L000.sort.log (check log file(s) for error message)
    conda-env: /projects-raptor/ccg-ngs/production/sw/miniconda3/envs/4094a9892df79329972dc6079b5814b5
    shell:

            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 2> Bowtie2/logs/A006850324_209972_S8_L000.sort.log;
            rm -rf $MYTEMP

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: Submitted batch job 1444270

Error executing rule Bowtie2 on cluster (jobid: 178, external: Submitted batch job 1444270, jobscript: /scratch/tmp/DNAseq/AP04/.snakemake/tmp.otsudz_m/snakejob.Bowtie2.178.sh). For error details see the cluster log and the log files of the involved rule(s).
Job failed, going on with independent jobs.

[roddypr]

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

[sunta3iouxos]

@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)

[katsikora]

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

[sunta3iouxos]

Unfortunately it is empty:

(base) [tgeorgom@cheops1:~]$ 07:54:33$ls /scratch/tgeorgom/AP04/Bowtie2/logs/
(base) [tgeorgom@cheops1:~]$ 07:54:38$

[katsikora]

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

[sunta3iouxos]

I am closing this one I figured it out, but do not really remember how I solved it.