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NCI-CCR-GB / ClinomicsScripts

Dumping ground for (commented) scripts related to the Clinomics project. We do not support these scripts beyond our own work.
MIT License
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Problem running QC_stats_Final.py on Biowulf #1

Closed seandavi closed 8 years ago

seandavi commented 8 years ago

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 commented 8 years ago

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

seandavi commented 8 years ago

Who was the original author, @sentisci?

sentisci commented 8 years ago

Script is from Manoj .

zhujack commented 8 years ago

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 commented 8 years ago

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.