maybe this is related:
I go the following error that never had using the pipeline and doing peak calling.
As a note I am running the developmental version
Error in rule MACS2_peak_qc:
jobid: 33
input: filtered_bam/A006200387_220458_S15.filtered.bam, MACS2/A006200387_220458_S15.filtered.BAM_peaks.xls
output: MACS2/A006200387_220458_S15.filtered.BAM_peaks.qc.txt
conda-env: /home/tgeorgom/CHN01/bam/None/264d54d86c09dd2633f7597f5b77ab09_
shell:
# get the number of peaks
peak_count=`wc -l < MACS2/A006200387_220458_S15.filtered.BAM_peaks.narrowPeak`
# get the number of mapped reads
mapped_reads=`samtools view -c -F 4 filtered_bam/A006200387_220458_S15.filtered.bam`
# calculate the number of alignments overlapping the peaks
# exclude reads flagged as unmapped (unmapped reads will be reported when using -L)
reads_in_peaks=`samtools view -c -F 4 -L MACS2/A006200387_220458_S15.filtered.BAM_peaks.narrowPeak filtered_bam/A006200387_220458_S15.filtered.bam`
# calculate Fraction of Reads In Peaks
frip=`bc -l <<< "$reads_in_peaks/$mapped_reads"`
# compute peak genome coverage
peak_len=`awk '{total+=$3-$2}END{print total}' MACS2/A006200387_220458_S15.filtered.BAM_peaks.narrowPeak`
genome_size=`awk '{total+=$3-$2}END{print total}' /home/tgeorgom/GRCm38_gencode_release19/genome_fasta/genome.fa.fai`
genomecov=`bc -l <<< "$peak_len/$genome_size"`
# write peak-based QC metrics to output file
printf "peak_count FRiP peak_genome_coverage
%d %5.3f %6.4f
" $peak_count $frip $genomecov > MACS2/A006200387_220458_S15.filtered.BAM_peaks.qc.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-04-02T163604.681904.snakemake.log
maybe this is related: I go the following error that never had using the pipeline and doing peak calling. As a note I am running the developmental version