Atropos does not output read 2 fastq provided by `-p` argument in paired end mode
jessrosenfield opened this issue · comments
When running this I
atropos -T 8 \
-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
-o "out.1.fastq" \
-p "out.2.fastq" \
-pe1 "R1.fastq.gz" -pe2 "R2.fastq.gz" \
--bisulfite truseq \
--nextseq-trim 5 \
--aligner insert \
--no-default-adapters --no-cache-adapters \
--report-file summary.txt --report-formats txt
When running I get output:
2019-06-27 18:38:57,483 INFO: This is Atropos 1.1.22 with Python 3.7.3
2019-06-27 18:38:57,486 INFO: Trimming 2 adapters with at most 10.0% errors in paired-end mode ...
Also, I think it's a bit misleading that it outputs --error_rate when running in insert mode instead of --insert-match-adapter-error-rate.
The output out.1.fastq only contains read 1 reads. However, the summary file includes read 1 and read 2 stats.
Can you please generate a minimal pair of fastq files that reproduces the issue? Thanks!
Whoops this issue was submitted prematurely. The there was an issue in with the paths the caller was passing in causing the directories for the -o and -p to be different. Thank you so much for the prompt response, it's very appreciated.