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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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base1 = r1_seq[i] IndexError: list index out of range #48

Closed antonkulaga closed 7 years ago

antonkulaga commented 7 years ago

I have the following later with latest master:

atropos.AtroposError: An error occurred at record 569 of batch 1237
2017-10-07 12:47:03,522 ERROR: Unexpected error in Worker process 0
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/atropos-1.1.14+10.g3060182-py3.6-linux-x86_64.egg/atropos/commands/base.py", line 74, in handle_records
    self.handle_record(context, record)
  File "/usr/local/lib/python3.6/site-packages/atropos-1.1.14+10.g3060182-py3.6-linux-x86_64.egg/atropos/commands/base.py", line 127, in handle_record
    return self.handle_reads(context, read1, read2)
  File "/usr/local/lib/python3.6/site-packages/atropos-1.1.14+10.g3060182-py3.6-linux-x86_64.egg/atropos/commands/trim/__init__.py", line 52, in handle_reads
    return self.record_handler.handle_record(context, read1, read2)
  File "/usr/local/lib/python3.6/site-packages/atropos-1.1.14+10.g3060182-py3.6-linux-x86_64.egg/atropos/commands/trim/__init__.py", line 70, in handle_record
    reads = self.modifiers.modify(read1, read2)
  File "/usr/local/lib/python3.6/site-packages/atropos-1.1.14+10.g3060182-py3.6-linux-x86_64.egg/atropos/commands/trim/modifiers.py", line 1054, in modify
    read1, read2 = mods(read1, read2)
  File "/usr/local/lib/python3.6/site-packages/atropos-1.1.14+10.g3060182-py3.6-linux-x86_64.egg/atropos/commands/trim/modifiers.py", line 401, in __call__
    self.correct_errors(read1, read2, insert_match)
  File "/usr/local/lib/python3.6/site-packages/atropos-1.1.14+10.g3060182-py3.6-linux-x86_64.egg/atropos/commands/trim/modifiers.py", line 252, in correct_errors

Here is the command that I run:

atropos trim \
  --aligner insert \
  -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG \
  -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT \
  -pe1 /cromwell-executions/quality_de_novo/2ce90b41-c1a7-4f7e-b31e-c0ae76ec1cb5/call-atropos_illumina_pe/inputs/pipelines/whales/graywhale/GWliver_S1_L001_R1_001.fastq.gz \
  -pe2 /cromwell-executions/quality_de_novo/2ce90b41-c1a7-4f7e-b31e-c0ae76ec1cb5/call-atropos_illumina_pe/inputs/pipelines/whales/graywhale/GWliver_S1_L001_R2_001.fastq.gz \
  -o GWliver_S1_L001_R1_001_trimmed.fastq.gz \
  -p GWliver_S1_L001_R2_001_trimmed.fastq.gz \
  --threads 8 \
  --correct-mismatches liberal \
  --trim-n

Here are the files: 1 and 2

antonkulaga commented 7 years ago

I also have this bug on other files, so it is more likely that it is not a file problem

jdidion commented 7 years ago

This is fixed in master and will be in the next release (1.1.15). The problem had to do with an assumption that the reads would be of equal length during error correction, but that is not always the case.

A bug still remains where error correction is not always performed on reads of unequal size - I am opening that separately.