Bismark Version: v0.24.2 Issue

[NeGomics]

I am executing the bismark on paired end data using the command: bismark --multicore 12 path/genome_dir --output_dir path/alignment -1 <(gunzip -c "filename_R1.fq.gz") -2 <(gunzip -c "filename_R2.fq.gz")

Error: Child process terminated with exit signal: '65280'

Child process terminated with exit signal: '65280'

Child process terminated with exit signal: '65280'

Child process terminated with exit signal: '3072'

Child process terminated with exit signal: '3072'

Child process terminated with exit signal: '3072'

Child process terminated with exit signal: '3072'

Terminating. Not all child processes successfully finished. at /home/cloud-user/anaconda3/bin/bismark line 602, line 106663392.

I request for the help to resolve the issue. I have 32 core processor. I am heartily thankful to you.

When I am running in shell script then it is not reading R2 the script is:

#!/bin/bash

Define the number of CPU cores to use

num_cores=12 # Adjust accordingly based on your system's specifications

Define the path to the genome directory

genome_dir="/mount/raw_data/goel/wgbs_methylation/methylation_new/genome_T2T_Y_2023"

Define the path to the output directory for alignment results

alignment_results_dir="/mount/raw_data/goel/wgbs_methylation/methylation_new/alignment_result_T2T"

Define the path to the temporary directory

temp_dir="/mount/raw_data/goel/wgbs_methylation/methylation_new/temp_t2t"

Loop through each pair of forward and reverse reads files in the folder

for f in /mount/raw_data/goel/wgbs_methylation/methylation_new/trimmed_data/_R1_001_val_1.fq.gz; do
# Extract the file name (without extension)
filename=$(basename -- "$f")
filename_no_ext="${filename%.}"

# Extract the sample ID from the filename
sample_id="${filename_no_ext%%_*}"

# Perform Bismark alignment
bismark --multicore "$num_cores" --non_directional --phred33-quals --no_overlap --temp_dir "$temp_dir" "$genome_dir" --output_dir "$alignment_results_dir/$sample_id" -1 <(gunzip -c "$f") -2 <(gunzip -c "/mount/raw_data/goel/wgbs_methylation/methylation_new/trimmed_data/${filename_no_ext}_R2_001_val_2.fq.gz")

done

[FelixKrueger]

This is very much related to #652.

The command used for Bismark contains a lot of stuff, just mentioning a few things here:

• --multicore "$num_cores": be a little careful...
• --non_directional: Is the library really non directional? (most libraries aren't...)
• --phred33-quals: is the default
• --no_overlap: Is not a Bismark option (only for methylation extractor, and there it is the default)
• I have never seen the <(gunzip -c "$f") before, it is also not necessary as Bismark reads gzipped files

Good to see that the files appear to be trimmed with Trim Galore!