ERROR: Unknown error

[joonlee3]

Hi John,

As you suggested, I attach the error log along with my command line and mini fastq files.

2017-08-05 01:06:56,535 INFO: This is Atropos 1.1.9 with Python 3.6.2 2017-08-05 01:06:56,539 INFO: Loading list of known contaminants from https://raw.githubusercontent.com/jdidion/atropos/master/atropos/adapters/sequencing_adapters.fa 2017-08-05 01:06:56,810 INFO: Trimming 2 adapters with at most 10.0% errors in paired-end mode ... 2017-08-05 01:07:10,720 ERROR: Unknown error Traceback (most recent call last): File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/util/init.py", line 673, in run_interruptible func(*args, **kwargs) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/base.py", line 23, in call self.process_batch(batch) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/base.py", line 58, in process_batch self.handle_records(context, records) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/trim/init.py", line 48, in handle_records super().handle_records(context, records) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/base.py", line 73, in handle_records self.handle_record(context, record) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/base.py", line 122, in handle_record return self.handle_reads(context, read1, read2) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/trim/init.py", line 52, in handle_reads return self.record_handler.handle_record(context, read1, read2) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/trim/init.py", line 70, in handle_record reads = self.modifiers.modify(read1, read2) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/trim/modifiers.py", line 1054, in modify read1, read2 = mods(read1, read2) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/trim/modifiers.py", line 401, in call self.correct_errors(read1, read2, insert_match) File "/site/ne/home/i0180769/apps/python/v3.6.2/lib/python3.6/site-packages/atropos/commands/trim/modifiers.py", line 253, in correct_errors base2 = BASE_COMPLEMENTS[r2_seq[j]] IndexError: list index out of range 2017-08-05 01:07:10,731 DEBUG: Not generating report file

Here is my command line ADAPTER_FWD="AGATCGGAAGAGCACACGTCTGAACTCCAGTCA" ADAPTER_REV="AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" atropos --aligner insert -a ${ADAPTER_FWD} -A ${ADAPTER_REV} \ --correct-mismatches liberal -q 20 -m 30 --log-file atropos.log --log-level DEBUG \ -o ${fastq_R1_name}.fq.gz -p ${fastq_R2_name}.fq.gz \ -pe1 ${fastq_R1} -pe2 ${fastq_R2}

temp_1.fastq.gz temp_2.fastq.gz

[jdidion]

That command works for me on your temporary input files.

I thought that the DEBUG output would show what line in the fastq is causing the error, but that's not the case. I'm going to push a new version that has better debugging. Once that's done, I'd appreciate if you could run it again on the complete file so we can pinpoint which line is causing the error.

[jdidion]

Version 1.1.10 is now in pypi. Please try again on the full input files and upload the logs. Thanks

[joonlee3]

Thanks. I will try it again.

[jdidion]

Closing this. Please reopen if the error persists.