Closed NeGomics closed 9 months ago
This is very much related to #652.
The command used for Bismark contains a lot of stuff, just mentioning a few things here:
--multicore "$num_cores"
: be a little careful... --non_directional
: Is the library really non directional? (most libraries aren't...)--phred33-quals
: is the default--no_overlap
: Is not a Bismark option (only for methylation extractor, and there it is the default)<(gunzip -c "$f")
before, it is also not necessary as Bismark reads gzipped filesGood to see that the files appear to be trimmed with Trim Galore!
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)
done