Comments (8)
Sounds like it could be a bug. What is the error message you get from the -e
option? What happens when you try inputting 1 file with the -e
option? If it is working correctly it should output an error message in that case, but not when 2 files are listed.
-e
should produce 2 files (with a _1.fq and _2.fq suffix) (non-interleaved). You are right about how paired end information is not used when -e
is not used.
It could be helpful for me it you show me the --version
output as well.
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Error message with option -e:
Input:
biobloomcategorizer --fq -e -p test -f /mnt/data/klif/svermeulen/Scripts_test/BioBloomTools/database/test_db.bf S70_R1.fastq.gz S70_R2.fastq.gz
Output:
Usage of paired end mode:
BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [FILEPAIR1] [FILEPAIR2]
or BioBloomCategorizer [OPTION]... -f "[FILTER1]..." [SMARTPAIR]
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:
Starting to Load Filters.
Loaded Filter: test_db
Filter Loading Complete.
Filtering Start
File written to: test_test_db_1.
File written to: test_test_db_2.
File written to: test_noMatch_1.
File written to: test_noMatch_2.
File written to: test_multiMatch_1.
File written to: test_multiMatch_2.
Total Reads:121994
Writing file: test_summary.tsv
--version output:
biobloomcategorizer (BIOBLOOMTOOLS) 2.1.2-2-g0703
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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
from biobloom.
Thanks for the report. I've found the bug and it will be fixed soon.
The smart pairing option is assigning the (_1) and (_2) arititrarally based on which it sees first. I agree that the order should be changed though and I will change that as well.
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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.
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It works pefectly! Thank you very much. We can now screen our metagenomics for contaminating ( in our case non-human) host DNA in minutes.
from biobloom.
Great I'll make sure the fix is present in the release version of 2.1.2.
from biobloom.
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.
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Related Issues (20)
- Create indexable output
- Add check for identical headers use multiple times
- Project page link does not link to latest release HOT 1
- Issue compiling release 2.3.2 HOT 2
- Segfault triggered by using multiple threads with -e option on a single file using multiple threads HOT 1
- Run ntcard automatically before creating filter
- During miBF construction automatically adjust occupancy to ensure minimum match length
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- Missing header file "Common/Uncompress.h" HOT 13
- Add recipe to conda HOT 1
- Check virus from human fastq HOT 12
- configure: error: Requires sdsl HOT 5
- False positive HOT 3
- Reproducible outputs HOT 3
- Biobloom categorizer dies in a misterious way HOT 5
- Need Filter File HOT 15
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