You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I have been having intermittent issues with runs failing at the map_sort step. This seems to be due to a formatting error in the ema align output that results in samtools sort failing. The formatting error is usually related to the cigar, see my issue arshajii/ema#39.
To solve this I have so far mapped manually with ema and the parsed the SAM output with this script found below. This simply skips any entries that are wrongly formatted. The I manually sort the output using samtools and name is initialmapping.bam to integrate it to the workflow again.
"""
Parse filter BAM/SAM
"""
import argparse
import pysam
from tqdm import tqdm
def main(args):
in_mode = "rb" if args.input.endswith(".bam") else "r"
out_mode = "wb" if args.output.endswith(".bam") else "w"
with pysam.AlignmentFile(args.input, mode=in_mode) as infile:
with pysam.AlignmentFile(args.output, mode=out_mode, template=infile) as outfile:
progress = tqdm()
parser = infile.fetch(until_eof=True)
while True:
try:
read = next(parser)
except StopIteration:
break
except OSError:
continue
progress.update()
outfile.write(read)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument("input", help="Input SAM/BAM")
parser.add_argument("output", help="Output SAM/BAM")
main(parser.parse_args())
I have been having intermittent issues with runs failing at the map_sort step. This seems to be due to a formatting error in the
ema align
output that results insamtools sort
failing. The formatting error is usually related to the cigar, see my issue arshajii/ema#39.To solve this I have so far mapped manually with ema and the parsed the SAM output with this script found below. This simply skips any entries that are wrongly formatted. The I manually sort the output using samtools and name is
initialmapping.bam
to integrate it to the workflow again.Issue copied from FrickTobias/BLR#235
The text was updated successfully, but these errors were encountered: