mopline create_cov error

[jingydz]

Hi, thank you for developing this wonderful pipeline.

When I run the mopline create_cov module, I have a question. command: mopline create_cov -b sample.bam -r hg38.fasta -rl 150 -n 2

on the terminal, I got: command: create_cov Args: -b sample.bam -r hg38.fasta -rl 150 -n 2 mopline create_cov: /xxx/software/MOPline/scripts/create_coverage_file_bam.pl -b sample.bam -r hg38.fasta -rl 150 -n 2 sample: chr1 finished: sample: chr2 finished: sample: chr3 finished: sample: chr4 finished: sample: chr5 finished: sample: chr6 finished: sample: chr7 finished: sample: chr8 finished: sample: chr9 finished: sample: chr10 finished: sample: chr11 finished: sample: chr12 finished: sample: chr13 finished: sample: chr14 finished: sample: chr15 finished: sample: chr16 finished: sample: chr17 finished: sample: chr18 finished: sample: chr19 finished: sample: chr20 finished: sample: chr21 finished: sample: chr22 finished: sample: chrX finished: sample: chrY finished: Coverage calculation completed:

then I got nothing, and this command was finished.

Do you know why?

thanks in advance.

[stat-lab]

Do you find Cov directories in each sample directory? If Cov directories have no files, show the content of a command.log file (which may be .command.log if -p option has not been specified).

[jingydz]

Thank you very much!! when I used the "sample.cov.input", I got the Cov directories.

$ cat sample.cov.input /path/sample sample.bam

mopline create_cov -b sample.cov.input -r hg38.fasta -rl 150 -n 4

$ ls sample/Cov/ sample.chr10.cov.gz sample.chr12.cov.gz sample.chr14.cov.gz sample.chr16.cov.gz sample.chr18.cov.gz sample.chr1.cov.gz sample.chr21.cov.gz sample.chr2.cov.gz sample.chr4.cov.gz sample.chr6.cov.gz sample.chr8.cov.gz sample.chrX.cov.gz sample.chr11.cov.gz sample.chr13.cov.gz sample.chr15.cov.gz sample.chr17.cov.gz sample.chr19.cov.gz sample.chr20.cov.gz sample.chr22.cov.gz sample.chr3.cov.gz sample.chr5.cov.gz sample.chr7.cov.gz sample.chr9.cov.gz sample.chrY.cov.gz