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Structural variant detection and association testing

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error: INFO: processed 0 reads for BAM file

cccnrc opened this issue · comments

commented

I am struggling having Whamg running for a WGS .bam file. I used GATKSV/Wham docker image and the following command:

whamg \
    -c ${chr_list} \
    -x 30 \
    -a ${reference_fasta} \
    -f ${bam_file}

Returns:

Invoking whamg:
whamg -c /var/lib/cwl/stg5910348b-6df0-43de-baff-568ee78530fc/hg38.primary_contig.csv -x 30 -a /var/lib/cwl/stg85dd1661-e28a-42b5-a410-ee90e45240cc/Homo_sapiens_assembly38.fasta -f /var/lib/cwl/stg80c5a3ef-bc35-40ce-9482-f42a56486e04/DAKIKI.sorted.markup.bam

INFO: WHAM will analyze seqid: /var/lib/cwl/stg5910348b-6df0-43de-baff-568ee78530fc/hg38.primary_contig.csv
INFO: OpenMP will roughly use 30 threads
INFO: fasta file: /var/lib/cwl/stg85dd1661-e28a-42b5-a410-ee90e45240cc/Homo_sapiens_assembly38.fasta
INFO: target bams:
/var/lib/cwl/stg80c5a3ef-bc35-40ce-9482-f42a56486e04/DAKIKI.sorted.markup.bam
INFO: gathering stats (may take some time) for bam: /var/lib/cwl/stg80c5a3ef-bc35-40ce-9482-f42a56486e04/DAKIKI.sorted.markup.bam
INFO: processed 0 reads for: /var/lib/cwl/stg80c5a3ef-bc35-40ce-9482-f42a56486e04/DAKIKI.sorted.markup.bam

and nothing else. I also tried to reconvert the .bam to .fastq and realign with BWA-MEM:

bedtools bamtofastq -i DAKIKI.final.sorted.bam -fq DAKIKI.final.sorted.fq
bwa mem -t 30 -R "@RG\tID:DAKIKI\tSM:DAKIKI" \
          /media/kong/enrico/fasta_X01_hg38/Homo_sapiens_assembly38.fasta \
          /media/kong/enrico/wgs_cnv/DAKIKI.final.sorted.fq \
               > /media/kong/enrico/wgs_cnv/DAKIKI.sam
samtools view -@ 30 -F 4 -S -b -h /media/kong/enrico/wgs_cnv/DAKIKI.sam > /media/kong/enrico/wgs_cnv/DAKIKI.bam
samtools sort -@ 30 -n  /media/kong/enrico/wgs_cnv/DAKIKI.bam -o  /media/kong/enrico/wgs_cnv/DAKIKI.sorted.bam
samtools fixmate -@ 30 -m /media/kong/enrico/wgs_cnv/DAKIKI.sorted.bam /media/kong/enrico/wgs_cnv/DAKIKI.fixmate.bam > /media/kong/enrico/wgs_cnv/DAKIKI_fixmate.out 
samtools sort -@ 30 /media/kong/enrico/wgs_cnv/DAKIKI.fixmate.bam -o /media/kong/enrico/wgs_cnv/DAKIKI.fixmate.sorted.bam
samtools markdup -@ 30 -r -s /media/kong/enrico/wgs_cnv/DAKIKI.fixmate.sorted.bam /media/kong/enrico/wgs_cnv/DAKIKI.sorted.markup.bam 
samtools index -@ 30 /media/kong/enrico/wgs_cnv/DAKIKI.sorted.markup.bam

but nothing works, keep getting the same output.

Thank you in advance for any help!

commented

Hi @cccnrc, the wham suite of tools was designed for paired-end reads? Looking over the commands, above, I'm guessing you're using single-end reads?

Best,

Zev

commented

Thanks for your reply @zeeev
The .bam is actually sequenced with paired-end....any other idea?

commented

I had the same issue using whamg. I'm processing paired-end samples. whamg used to be working on this sample, the only change I made was using bbduk.sh to trim low quality bases from fastq file and then went through the same processes. When I used sickle to trim the same file, whamg just worked fine.

I looked into the .err file produced, and the content is as follows:

INFO: target bams:
../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: fasta file: ../../GCF_000195955.2_ASM19595v2_genomic.fna
INFO: OpenMP will roughly use 3 threads
INFO: gathering stats (may take some time) for bam: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam
INFO: processed 0 reads for: ../../bam_trimed_sorted/1_trimebbduk_sorted_addRG.bam

and then the program will hault here for ever. Any idea what's going on?