samtools #54
Description
Many thanks to the author's team for developing a user-friendly analytical tool, unfortunately, a difficult problem has arisen during use.
Problem description: I have no problem running a single sample, and I have no problem running 5 samples together, but strangely, when I try to run 18 samples together, I have a problem converting sam to bam in samtools.
Error code:def convert_sam_to_sorted_bam(input_sam_file, num_threads):
# Open the SAM file in reading mode
samfile = pysam.AlignmentFile(input_sam_file, "r")
# Create a BAM file in writing mode
out_bam_file = input_sam_file.replace('.sam', '.bam', 1)
bamfile = pysam.AlignmentFile(out_bam_file, "wb", template=samfile)
# Iterate through the records in the SAM file and write them to the BAM file
for record in samfile:
bamfile.write(record)
# Close the files
samfile.close()
bamfile.close()
# Sort the BAM file
out_sorted_bam_file = input_sam_file.replace('.sam', '.sorted.sam', 1)
pysam.sort("-o", out_sorted_bam_file, out_bam_file)
I would appreciate your help in resolving the issue! Thanks again for all your hard work!!