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SorenKarst / longread_umi

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centroids.fa #50

Open thierryjanssens opened 2 years ago

thierryjanssens commented 2 years ago

Hi,

I have a problem with running the test data.

the centroids.fa that is cat by variants.sh script (line 553) is not produced.

cat: test_r941/variants/centroids.fa: No such file or directory

The part of the script that generates this files (from line 482) is commented out.

I am making use of the vsearch coomand, but everything is working fine, except the variants analysis. So this is probably not the cause.

kind regards,

Thierry

ziels commented 2 years ago

Hi Thierry,

Do you mind providing the output from source <path-to-longread_umi>/scripts/dependencies.sh ; longread_umi_version_dump ?

I am actually experiencing something similar with the variants step on a HPC where I was forced to do a manual install due to lack of conda support. On a different machine where I have longread_umi installed via conda, the variants.sh command is working fine. So, thanks for raising your issue, as it appears to be a reproducible problem,.

Thanks, Ryan

thierryjanssens commented 2 years ago

$ conda activate longread_umi $ source /home/minion/anaconda3/envs/longread_umi/longread_umi/scripts/dependencies.sh $ longread_umi_version_dump fatal: not a git repository: '/.git' vsearch v2.19.0_linux_x86_64, 46.7GB RAM, 8