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paired end mode not working? #36
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Sounds like it could be a bug. What is the error message you get from the
It could be helpful for me it you show me the |
Error message with option -e: Input: Output: No error message with option -e and 1 file biobloomcategorizer --fq -e -p test -f /mnt/data/klif/svermeulen/Scripts_test/BioBloomTools/database/test_db.bf S70_R1.fastq.gz Output: --version output: |
To add, it works with interleaved files (although the reverse read of the pair gets placed in the forward (_1) file and the forward read gets placed in the reverse (_2) file |
Thanks for the report. I've found the bug and it will be fixed soon. |
The bug should be fixed in the lastest version of the master branch 8a47ccb. Sorry for the problem, turns out the new smart pairing code was the cause of the issue. When only one file is listed there should indeed be no error. Thanks again. |
It works pefectly! Thank you very much. We can now screen our metagenomics for contaminating ( in our case non-human) host DNA in minutes. |
Great I'll make sure the fix is present in the release version of 2.1.2. |
Sorry I didn't realize this until now but the files should have extensions on them for .fq or .fa. I've pushed a fix for this on the main branch. Minor issue, the output should still have been .fq by default if you used the output options. |
Hi,
I'm trying to use your software as described in the example with paired end fq reads:
biobloomcategorizer --fq -e -p test123 -f "mg1655.bf" 18072D-01-03_S71_L006_R1_001_val_1.fq.gz 18072D-01-03_S71_L006_R2_001_val_2.fq.gz -t 16
However then the program just tells me I'm doing something wrong. Without -e option it works, however then I get the matching/non-matching reads in one file, non-interleaved, which is not what I want. I assume paired end information is not used. Is there a bug somewhere that keeps biobloomcategorizer from recognizing 2 files as paired end reads when using the -e option?
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