skchronicles
commented
5 years ago Update
After closer inspection, it looks that pysam is not actively being used. The function call to normalize_bam_file_chromosomes, which was using pysam, has been commented out. For the time being, I will move the import statement inside of the function normalize_bam_file_chromosomes.
def normalize_bam_file_chromosomes(bamfns, obamfns=[], suffix='.common_chrom.bam'):
from pysam import Samfile, FastaFile
counts = []
for bamfn1 in bamfns :
bam1 = Samfile(bamfn1)
cnt1 = Counter()
for aread1 in bam1 :
if aread1.is_unmapped :
continue
cnt1[aread1.reference_name] += 1
bam1.close()
counts.append(cnt1)
common = None
for cnt in counts :
if common != None :
common = common.intersection(cnt)
else :
common = set(cnt)Changes will be made in the following locations:
- module load ccbrpipeliner/3.0
- master branch
- activeDev branch
Permanent solution:
Remove the snakemake run for the rule PePr, and make a script. This will allow us to submit a job with the exact version of python that should be used.
Secondary Issue related to HPC Snakemake Upgrade #371
Dry-running the second half of the ChIP-seq pipeline causes a python
ImportError. This error is related to recent changes HPC has made to thepython/3.5module on Biowulf (see issue #371 for more information).module load python/3.5. It was changed from snakemake version 5.1.3 to snakemake version 5.3.0. There are a few incompatibility issues with these two versions of snakemake due to changes in command-line arguements. To overcome these issues, snakemake/5.1.3 is loaded after module loading python 3.5.The import error is due to the version of python that is bundled with snakemake (see:
/usr/local/Anaconda/envs_app/snakemake/5.1.3/bin/). This version of python only includes the standard libraries that come standard with python 3.6, and does not include pysam.