methratio.py OverflowError

[rmvpaeme]

I get this error when running methratio.py, samples was mapped to GRCh37. It seems that the error usually occurs when chr2 is being read.

methratio.py -d GRCh37.fa -o output.txt -x CG -N 18 sample.bam

Things I've tried:

• Different sample (doesn't work)
• Removing all tmp files before running methratio.py (doesn't work)
• Using the python 3 branch in this repository (no error but it just stops doing anything after 2 minutes)
• Setting -N to 1 and setting -N to 25 (doesn't work)
• BSMAPz has 76 GB memory available. I tried limiting this to 25GB with -M (doesn't work)

[methratio] @Thu May 14 14:22:53 2020   Using 90% of available memory (38621 MB) as limit
[methratio] @Thu May 14 14:22:53 2020   Presorting inputs
[methratio] @Thu May 14 14:22:53 2020   Calling samtools sort on mapped_reads/GRCh37.CFD1900266-NBL_R1_trimmed_BSMAP.bam and using 38621 MB of memory
[methratio] @Thu May 14 14:23:06 2020   Processing 1 chromosomes at a time
[part of log cut]
[methratio] @Thu May 14 14:27:48 2020   Reading 2 from mapped_reads/GRCh37.CFD1900266-NBL_R1_trimmed_BSMAP.tmpSrt.bam with samtools
Traceback (most recent call last):
  File "/apps/gent/CO7/skylake-ib/software/BSMAPz/1.1.1-intel-2019b-Python-2.7.16/bin/methratio.py", line 571, in <module>
    main()
  File "/apps/gent/CO7/skylake-ib/software/BSMAPz/1.1.1-intel-2019b-Python-2.7.16/bin/methratio.py", line 138, in main
    ret = map(chromWorker, argList)
  File "/apps/gent/CO7/skylake-ib/software/BSMAPz/1.1.1-intel-2019b-Python-2.7.16/bin/methratio.py", line 287, in chromWorker
    searchFunc(refseq, seq, depth, meth, convert, match, pos)
  File "/apps/gent/CO7/skylake-ib/software/BSMAPz/1.1.1-intel-2019b-Python-2.7.16/bin/methratio.py", line 529, in searchFunc
    depth[ip] += 1
OverflowError: unsigned short is greater than maximum

[zyndagj]

It looks like you're aligning a huge sample with very deep coverage. I'll get a fix in for you.

[rmvpaeme]

Is that commit 244ca43? If so, then I'm still getting the same error with methratio.py (on the same bamfiles, havent done realignment).

[zyndagj]

I added the -I flag to use unsigned integers instead of shorts for counting read depth in version 1.1.2. Try pulling it from conda or github and let me know if it solves your error.

[rmvpaeme]

problem is fixed, thanks

[zyndagj]

No problem, thanks for being patient!