error in samtools sort

[sunta3iouxos]

Hi all, I got an interesting and unexpected error.
Unfortunately, I can not retrieve the bam file to see what it is about:

samtools sort: failed to read header from "-"

the log:

---- This analysis has been done using snakePipes version 2.8.0 ----
Building DAG of jobs...
Falling back to greedy scheduler because no default solver is found for pulp (you have to install either coincbc or glpk).
Using shell: /bin/bash
Provided cores: 24
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=1000, disk_mb=1000
Select jobs to execute...

[Mon Jul 22 20:09:09 2024]
rule bwa:
    input: FASTQ_fastp/A006200402_224949_S7_L000_R1_001.fastq.gz, FASTQ_fastp/A006200402_224949_S7_L000_R2_001.fastq.gz
    output: bwa/A006200402_224949_S7_L000.bwa_summary.txt, bwa/A006200402_224949_S7_L000.sorted.bam
    log: bwa/logs/A006200402_224949_S7_L000.sort.log
    jobid: 0
    reason: Missing output files: bwa/A006200402_224949_S7_L000.bwa_summary.txt, bwa/A006200402_224949_S7_L000.sorted.bam
    wildcards: sample=A006200402_224949_S7_L000
    threads: 8
    resources: mem_mb=1000, disk_mb=1000, tmpdir=/scratch/tgeorgom_temp


            TMPDIR=/scratch/tgeorgom/temp/
            MYTEMP=$(mktemp -d ${TMPDIR:-/tmp}/snakepipes.XXXXXXXXXX);
            bwa mem             -t 8             -R '@RG\tID:A006200402_224949_S7_L000\tDS:A006200402_224949_S7_L000\tPL:ILLUMINA\tSM:A006200402_224949_S7_L000'               FASTQ_fastp/A006200402_224949_S7_L000_R1_001.fastq.gz FASTQ_fastp/A006200402_224949_S7_L000_R2_001.fastq.gz |             samtools view -Sb - |             samtools sort -m 2G -@ 2 -O bam - > bwa/A006200402_224949_S7_L000.sorted.bam 2> bwa/logs/A006200402_224949_S7_L000.sort.log;
            rm -rf $MYTEMP
            samtools flagstat bwa/A006200402_224949_S7_L000.sorted.bam

and this is the command

nohup DNA-mapping -i /scratch/tgeorgom/bastet2.ccg.uni-koeln.de/downloads/NGS_CHN02_cnikopoulou_A006200402/ -o /scratch/tgeorgom/CH02/mm10_gencodeM19 --fastqc --trim --trimmer fastp --trimmerOptions "--trim_poly_g --trim_poly_x -Q -L --correction" --dedup --plotFormat "pdf" --mapq 2 -j 50 --dedup --aligner bwa --verbose --snakemakeOptions='--rerun-incomplete' --insertSizeMax 5000 mm10_gencodeM19_spikesTEST > nohup_CH02.txt &

[sunta3iouxos]

I tested the same but using the bowtie2 and it seems that it does not through this error anymore.
So, it is a bwa specific issue, that migh be related to -R '@RG\tID:A006200402_224949_S7_L000\tDS:A006200402_224949_S7_L000\tPL:ILLUMINA\tSM:A006200402_224949_S7_L000'

[katsikora]

Hi,

this error message from samtools means that the alignment has failed e.g. no proper bam was produced (and piped into samtools).
Do you mean that running the workflow with --aligner bowtie2 didn't reproduce the error?

Best wishes,

Katarzyna

[sunta3iouxos]

Exactly, I used the same DNA-mapping command, and only changed the --al8gner entry to bowtie.
Then the whole thing worked.