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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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error while running the detect command #127

Open manasakaringula opened 3 years ago

manasakaringula commented 3 years ago

I get a random error while running the detect command. Although few runs are successful. We have ran near to 50 jobs with same inputs on local server to understand the root cause of the issue. Out of 50, 17 failed and others were successful.But a samll note is that it finds the adapters properly, but it generates an error. Could you please help us with the issue .Here is the error - 2021-06-29 13:29:42,110 INFO: This is Atropos 1.1.29 with Python 3.6.1 2021-06-29 13:29:42,114 INFO: Loading list of known contaminants from file:/data/Atropos_sequencing_adapters.fa 2021-06-29 13:29:42,120 INFO: Detecting adapters and other potential contaminant sequences based on 12-mers in 50000 reads 2021-06-29 13:33:59,145 ERROR: Error executing command: detect Traceback (most recent call last): File "/usr/local/lib/python3.6/site-packages/atropos-1.1.29-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 217, in execute_cli retcode, summary = command.execute(args) File "/usr/local/lib/python3.6/site-packages/atropos-1.1.29-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 74, in execute self.generate_reports(summary, options) File "/usr/local/lib/python3.6/site-packages/atropos-1.1.29-py3.6-linux-x86_64.egg/atropos/commands/__init__.py", line 154, in generate_reports generator.generate_reports(summary) File "/usr/local/lib/python3.6/site-packages/atropos-1.1.29-py3.6-linux-x86_64.egg/atropos/commands/reports.py", line 65, in generate_reports self.generate_text_report(fmt, summary, outfile, **kwargs) File "/usr/local/lib/python3.6/site-packages/atropos-1.1.29-py3.6-linux-x86_64.egg/atropos/commands/detect/reports.py", line 21, in generate_text_report generate_reports(out, summary, **kwargs) File "/usr/local/lib/python3.6/site-packages/atropos-1.1.29-py3.6-linux-x86_64.egg/atropos/commands/detect/reports.py", line 33, in generate_reports generate_detector_report(outstream, input_idx, n_reads, matches, name) File "/usr/local/lib/python3.6/site-packages/atropos-1.1.29-py3.6-linux-x86_64.egg/atropos/commands/detect/reports.py", line 66, in generate_detector_report ",\n{}".format(' ' * (pad_size + 11)).join(match['known_seqs']))) TypeError: sequence item 0: expected str instance, tuple found

jdidion commented 3 years ago

It would be helpful to be able to reproduce this error. Would you be able to share the first 50k reads from one of fastq files/pairs that caused an error?

manasakaringula commented 2 years ago

Hi @jdidion, we have used sample "ENCSR356KRQ" from ENCODE. Basically, its an ATAC-seq sample. The detect command fails randomly, when we setup multiple runs on the same sample. It works sometimes and it fails sometimes, although the input and parameter is same. Here I am attaching you the first 50k reads. Any help will be greatly appreciated. I have uploaded both the R1/R2 50k reads. ENCSR356KRQ.zip