Comments (4)
wwood
commented on August 29, 2024
Hi,
I can't tell exactly since I don't have the command you used or the data, but the error message (found 446 reads when expected 223) suggests to me that the read sets are interleaved, since 223*2=446.
Does that help?
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steff1088
commented on August 29, 2024
Thank you very much for the quick response.
The command I used was:
graftM graft --threads 8 --evalue 0.000000001 --forward 11774.2.218915.CGAACTG-ACAGTTC.filter-METAGENOME.fastq --graftm_package 500PSI_mcrAs_refined.gpkg --output_directory GraftM_output_11774.2.218915.CGAACTG-ACAGTTC_500PSI_mcrAs_refined_package --force
If the reads are interleaved, what can I do to make them compatible with the graft command?
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wwood
commented on August 29, 2024
Hi,
You can either use the --interleaved flag instead of --forward. You can tell whether they are interleaved easily just by looking at the head of the file - they'll have 2 reads with the same name. Alternatively you can split the file up - there's plenty of tools out there for doing that out there.
ben
Ben WoodcroftMicrobial informatics group leader, ARC Future Fellow
(+617) 3443 7334
Centre for Microbiome Research, Level 3, Translational Research Institute, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology
https://research.qut.edu.au/cmr/team/ben-woodcroft
…On Apr 27 2022, at 11:26 am, steff1088 ***@***.***> wrote:
Thank you very much for the quick response.
The command I used was:
graftM graft --threads 8 --evalue 0.000000001 --forward 11774.2.218915.CGAACTG-ACAGTTC.filter-METAGENOME.fastq --graftm_package 500PSI_mcrAs_refined.gpkg --output_directory GraftM_output_11774.2.218915.CGAACTG-ACAGTTC_500PSI_mcrAs_refined_package --force
If the reads are interleaved, what can I do to make them compatible with the graft command?
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steff1088
commented on August 29, 2024
Thanks Ben, that did the trick!
-steffen
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