Comments (3)
from adapterremoval.
Hi Mikkel,
Thank you for your help previously. I followed your steps checking for error messages and doing a re-install of AdapterRemoval, but I am still experiencing the same issue.
AdapterRemoval runs to completion - and for instance, when I run one sample, I get this information:
(base) qiime@qiime-190-virtual-box:~/DecompTX/Fastq$ AdapterRemoval --file1 D61.16.R1.fastq.gz --file2 D61.16.R2.fastq.gz --basename output_paired --trimns --trimqualities --collapse
Trimming paired end reads ...
Opening FASTQ file 'D61.16.R1.fastq.gz'
Opening FASTQ file 'D61.16.R2.fastq.gz'
Processed a total of 42,396 reads in 0.5s; 91,000 reads per second on average ...
When I do a seqs count on each individual extracted file, R1 and R2 both show:
21198 : D61.16.R1.fastq (Sequence lengths (mean +/- std): 200.0000 +/- 0.0000)
21198 : Total
However, of the files written, only output_paired.collapsed (12.1MB), output_paired.pair1.truncated (138.7kB), output_paired.pair2.truncated (138.7kB), and output_paired.settings (8.3kB) have any information. No information was written to output_paired.collapsed.truncated.
I am having this issue with almost every file, except for several where no information was written to either output_paired.collapsed or collapsed.truncated. My collaborator is not having this issue, which makes me think it's something to do with my computing setup rather than the data.
I'm not sure what my next step is except to maybe reinstall everything all the way down to VirtualBox.
If you have any insight, that would be much appreciated! Thank you for your time.
Sarah
from adapterremoval.
from adapterremoval.
Related Issues (20)
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from adapterremoval.