Open cccnrc opened 4 years ago
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
Thanks for your reply @zeeev The .bam is actually sequenced with paired-end....any other idea?
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?
I am struggling having Whamg running for a WGS .bam file. I used GATKSV/Wham docker image and the following command:
Returns:
and nothing else. I also tried to reconvert the .bam to .fastq and realign with BWA-MEM:
but nothing works, keep getting the same output.
Thank you in advance for any help!