Process egapx:rnaseq_short_plane:bam_bin_and_sort:bam_bin (2) terminated with an error exit status (3) #155
Description
Hi,
I'm finding an error of:
"Process egapx:rnaseq_short_plane:bam_bin_and_sort:bam_bin (2) terminated with an error exit status (3)"
It was accusing a malformed BAM, so I even tried to modified the regex option in the source code, and I keep having the same error.
I am using some RNA-seq libs that are locally on my machine, and I changed their names to have the _R1 and _R2 like you suggest on the GitHub page. I ran EGAPx for other species and it worked fine, in the same server, with same configs, but now I can't seen to get past this error.
Appreciate any help!!
Here is the log:
[11/d95453] NOTE: Process `egapx:rnaseq_short_plane:bam_bin_and_sort:bam_bin (1)` terminated with an error exit status (3) -- Execution is retried (3)
ERROR ~ Error executing process > 'egapx:rnaseq_short_plane:bam_bin_and_sort:bam_bin (2)'
Caused by:
Process `egapx:rnaseq_short_plane:bam_bin_and_sort:bam_bin (2)` terminated with an error exit status (3)
Command executed:
#!/usr/bin/env bash
mkdir -p output
echo "bam file : mTriSen1-SRR29188502_R1-Aligned.out.Sorted.bam, index file : mTriSen1-SRR29188502_R1-Aligned.out.Sorted.bam.csi"
s=$(basename mTriSen1-SRR29188502_R1-Aligned.out.Sorted.bam)
regex="^([^-]+)-(.+)-Aligned[.]out[.]Sorted[.]bam$"
#regex="^(.+)-([^-]+)-Aligned[.]out[.]Sorted[.]bam$"
if [[ $s =~ $regex ]]; then
assembly="${BASH_REMATCH[1]}"
run="${BASH_REMATCH[2]}"
else
echo "Malformed BAM name, mTriSen1-SRR29188502_R1-Aligned.out.Sorted.bam"
exit 1
fi
source assembly_sizes.hash
total_size=${assembly_sizes[$assembly]}
echo "Assembly $assembly, run $run, total size $total_size"
echo "genome mTriSen1.fasta"
head -5 mTriSen1.fasta
echo "organelle "
head -5
echo "mTriSen1.fasta" > genome.mft
echo "" > organelle.mft
samtools=`which samtools`
bam_bin -file-pattern 'bin#.bam' -avg-size-per-bin 200000000 -exclude-organelle -bam mTriSen1-SRR29188502_R1-Aligned.out.Sorted.bam -o output/$assembly-$run.bins -total-bam-size $total_size -fasta-manifest genome.mft -organelle-manifest organelle.mft -samtools-path $samtools
Command exit status:
3