Problem running QC_stats_Final.py on Biowulf

[seandavi]

Sivasish might have fixed this, but it seems the python version problem:

$ which python
/usr/local/Anaconda/envs/py3.4.3/bin/python

$ python /data/Clinomics/Tools/QC_stats_Final.py SUBJECT/HD753/CL0015_T_P/ucsc.hg19.bwamem/bam/CL0015_T_P.final.bam > test
File "/data/Clinomics/Tools/QC_stats_Final.py", line 76
if (depth >= 1000):

[sentisci]

can a valid output file/s and readme for script be included. ?

[seandavi]

Who was the original author, @sentisci?

[sentisci]

Script is from Manoj .

[zhujack]

Script location: /data/Clinomics/Tools/

QC Script: QC_stats_Final.py
Panel Example: python QC_stats_Final.py CL0015_T_P.final.bam /data/Clinomics/Ref/serpentine_resources/design/Agilent_SureSelect_Killian_Version4.target.hg19.merged.bed > outputfile
Exome Example: python QC_stats_Final.py CL0012_T_E.final.bam /data/Clinomics/Ref/serpentine_resources/design/Agilent_SureSelect_Clinical_Research_Exome.design.hg19.merged.bed > outputfile

Note: Please change line #31, 32, 151, & 156 accordingly to include it in Snakemake rules.

Failed Exon list Script: failed_Exon_Final.pl
Example: perl failed_Exon_Final.pl <.../SUBJECT/HD753/CL0015_T_P/ucsc.hg19.bwamem/qc/CL0015_T_P.final.bam.depth_per_base> THRES

For Panel Tumor: THRES is 50
For Panel Normal: THRES is 20

[seandavi]

So, I looked at the script. It is written to conform to python 2, not python 3. Jack, you'll need to

module load python/2.7.9

for this script to work. I checked and after doing so, this appears to work. I opened issue #2 to address the hard-coded paths.