biomedswe

Hi again! I have seen now that bwa-mem2 doesn't seem to follow any standard convention with neiter stdout, stderr or returncode. Is is possible for you to fix this issue?...

Thanks for having a look at it!

Hi! Unfortunatelly it doesn't seem to work still. Just to make sure I did it right, I did like this: git clone https://github.com/bwa-mem2/bwa-mem2 cd bwa-mem2 git submodule init git submodule...

Hi! I have discovered what causes this issue now! Apparently, I can't use | samtools view in the command: bwa-mem2/bwa-mem2 mem -R \'@RG\\tID:2064-01\\tSM:2064-01\\tLB:2064-01\\tPL:ILLUMINA\\tPU:2064-01\' reference_genome/human_g1k_v37.fasta BHYHT7CCXY.RJ-1967-987-02.2_1.fastq BHYHT7CCXY.RJ-1967-987-02.2_2.fastq -t 14 **| samtools...

Hi! how exactly do I have to write? I tried this: `"| samtools view -bS -o dna_seq/aligned/2064-01/2064-01.6.bam -"` but it doesn't work, still rc 0. best / Jonas

Hi! I was just reading about set -e and -o, but i don't know where to put it. I tried you example above but i says "/bin/sh: 1: set: Illegal...

thx i solved it with changing to bin/bash :) It works for now but I should maybe try to see if I can use two subprosses.popen() instead with process1.stdout as...

No worries, thx for your reply! It worked fine😊 could you pls make it more clear in the help section of CMplot? Best Jonas Jonas Andersson PhD student Lund University...