Error: value too large to convert to int16_t

[catsargent]

Hi,

I have run talon successfully on a human single cell dataset - thanks for the great pipeline! As part of that experiment we also have a chimp sample. I am running the talon annotator on the chimp sample as follows:

python ${talonDir}/talon \
  --f config.csv \
  --cb \
  --db talon_chimp.db \
  --threads 4 \
  --build pt3 \
  --o chimp

I get the following output after submitting the job:

[ 2023-01-07 10:26:28 ] Started TALON run
[ 2023-01-07 10:26:31 ] Merged input SAM/BAM files
value too large to convert to int16_t

With the error as follows:

Traceback (most recent call last):
  File "/projects/b1177/pythonenvs/talon-env/lib/python3.9/site-packages/talon/process_sams.py", line 118, in partition_reads
    gr = pr.read_bam(merged_bam)
  File "/projects/b1177/pythonenvs/talon-env/lib/python3.9/site-packages/pyranges/readers.py", line 196, in read_bam
    df = bamread.read_bam(f, mapq, required_flag, filter_flag)
  File "/projects/b1177/pythonenvs/talon-env/lib/python3.9/site-packages/bamread/read.py", line 8, in read_bam
    chromosomes, starts, ends, strands, flags, chrmap = _bamread(
  File "bamread/src/bamread.pyx", line 17, in bamread.src.bamread._bamread
  File "bamread/src/bamread.pyx", line 76, in bamread.src.bamread._bamread
OverflowError: value too large to convert to int16_t

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/projects/b1177/pythonenvs/talon-env/bin/talon", line 8, in <module>
    sys.exit(main())
  File "/projects/b1177/pythonenvs/talon-env/lib/python3.9/site-packages/talon/talon.py", line 2620, in main
    read_groups, intervals, header_file = procsams.partition_reads(sam_files,
  File "/projects/b1177/pythonenvs/talon-env/lib/python3.9/site-packages/talon/process_sams.py", line 121, in partition_reads
    raise RuntimeError("Problem opening sam file %s" % (merged_bam))
RuntimeError: Problem opening sam file talon_tmp/merged_sorted.bam

Do you have any ideas about what could be causing this issue and/or how to fix it? I tried searching for previous issues relating to int16_t but did not come across anything.

Many thanks! Am excited to explore the results generated by talon!

Catherine

[catsargent]

This error is due to an issue with bamread:

pyranges/bamread#10