search

NabaviLab / VarSimLab

A complete command-line pipeline to simulate genomic variations
MIT License
4 stars 1 forks source link

exome sequence case fails #3

Open snesic opened 5 years ago

snesic commented 5 years ago

Hi,

I would like to use your tool to create wes reads with CNVs but it fails with segmentation fault on $ref/SInC/SInC_simulate. After debugging a little bit, it looks like the reference file created in the python script (line 187) is not closed before art_run.sh is called so an empty file is passed. Still, when I close it, SInC_simulate finishes successfully but then it breaks on correct_error_file_faster as the input file has empty or 'non-structural' lines..

thomas-davis commented 5 years ago

Hello,

Thank you for helping to debug-- I have a few questions. Is there a file called "SIMULATION_IS_RUNNING.txt" or "SIMULATION_IS_COMPLETE.txt" in the output directory? If so, do you mind sharing it here? Also can you tell me a bit more about the input sequence and BED file you were using?

Thanks again,

snesic commented 5 years ago

Hi,

Thanks for your fast reply. SIMULATION_IS_RUNNING.txt is in the output dir. SIMULATION_IS_RUNNING.txt

I created a dummy test sequence in oder to test the tool. It has A ~1k times.

1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA and so on (copy-paste several times)..........

BED file: 1 10 200

CMD: python3 Exome_Script.py tesst genome.fa -bed genes.bed -l 100 -cnv 5 -cnv_min_size 4 -cnv_max_size 5 -c 2 -subclones 1 -ploidy 1 -indel 2 -s