TypeError: 'NoneType' object is not subscriptable

[Tianran1]

Error message:

Traceback (most recent call last):
File "/opt/conda/bin/scAllele", line 8, in
sys.exit(main())
File "/opt/conda/lib/python3.9/site-packages/scAllele/scAllele.py", line 388, in main
RCs = gqv_bam_utils.find_read_clusters(bam_file, options, chrom, fetch_start, fetch_end)
File "/opt/conda/lib/python3.9/site-packages/scAllele/gqv_bam_utils.py", line 196, in find_read_clusters
new_read = remove_homopolymer_ends(read, r_blocks)
File "/opt/conda/lib/python3.9/site-packages/scAllele/gqv_bam_utils.py", line 397, in remove_homopolymer_ends
aligned_qual = read.query_alignment_qualities[prefix : sufix]
TypeError: 'NoneType' object is not subscriptable

[giovanniquinones]

It seems some reads in your bam file don't have a base quality string.
You will need to remove such reads as scAllele needs the base quality information to score variants.

[Tianran1]

Thanks. But I think all of my reads are without the quality score since they are converted from the bam file. Are there any solutions?

[giovanniquinones]

You can try adding a dummy string i.e. "JJJJJJ..." using pysam

[Tianran1]

Thanks. I also noticed that there are some without sequence in the bam file, do I need to remove them?