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Swart-lab / bleties

IES retention analysis from PacBio CCS reads
https://swart-lab.github.io/bleties
MIT License
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Milraa failed in subread mode #17

Closed kbseah closed 4 years ago

kbseah commented 4 years ago

Error message:

Traceback (most recent call last):
  File "/ebio/abt2_projects/ag-swart-blepharisma/data/bleties/envs/bleties_env/bin/bleties", line 349, in <module>
    args.func(args)
  File "/ebio/abt2_projects/ag-swart-blepharisma/data/bleties/envs/bleties_env/lib/python3.7/site-packages/bleties/main.py", line 114, in milraa
    args.min_break_coverage, args.min_del_coverage)
  File "/ebio/abt2_projects/ag-swart-blepharisma/data/bleties/envs/bleties_env/lib/python3.7/site-packages/bleties/Milraa.py", line 1425, in reportPutativeIesInsertSubreads
    rname, gffpos, gffpos, consseq, breakpointid)
  File "/ebio/abt2_projects/ag-swart-blepharisma/data/bleties/envs/bleties_env/lib/python3.7/site-packages/bleties/Milraa.py", line 895, in reportAdjustPointers
    self._refgenome[ctg], ins_start, ins_end, consseq, breakpointid)
  File "/ebio/abt2_projects/ag-swart-blepharisma/data/bleties/envs/bleties_env/lib/python3.7/site-packages/bleties/Milraa.py", line 263, in getPointers
    while iesseq[i] == seq[end+i]:
  File "/ebio/abt2_projects/ag-swart-blepharisma/data/bleties/envs/bleties_env/lib/python3.7/site-packages/Bio/Seq.py", line 323, in __getitem__
    return self._data[index]
IndexError: string index out of range

BleTIES v0.1.4 With Contig_9 and Contig_14 in test data

kbseah commented 4 years ago

This bug appears to be associated with telomeric regions on reference; repeat-rich regions are expected to cause problems for mapper and will not give biologically meaningful results.