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stat-lab / MOPline

Detection and genotyping of structural variants
MIT License
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run_single.pl script error #14

Open lovelycatZ opened 8 months ago

lovelycatZ commented 8 months ago

Hi, when I run the script run_CNVnator.pl for one sample named XH1006.bam, there were some errors in the XH1006.histgram.log file processing data by CNVnator. But when I provided the same parameters as before and run CNVnator alone against the same sample, it worked very well. I really struggled with this problem. Below is the error file and running code: /data/xiangxd/project/software/callers/MOPline_1.8.2/scripts/run_SVcallers/run_CNVnator.pl -b XH1006.sort.mkdup.realign.bam -p XH1006 -rd root -build 38 -g MOPline-1.8.2/Data/gap.b38.bed -cp cnvnator -nh 0. XH1006.histgram.log

stat-lab commented 8 months ago

You seem to miss a reference file. Please specify reference fasta with the -r option.

lovelycatZ commented 8 months ago

Hi, thanks for the quick response! The -r option doesn't seem matter, the problem is that I have changed the script run_CNVnator.pl to provide an interface for the bin size of CNVnator, but I forgot to set the type for it. Now I have solved.

lovelycatZ commented 8 months ago

For CNVnator, it works with or without the reference genome for the BAM file.