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ParkinsonLab / MetaPro

GNU General Public License v3.0
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BWA output empty #8

Closed Jeltje closed 1 year ago

Jeltje commented 3 years ago

I looked up a single command: >cat /mydata/testout/GA_BWA/BWA_singletons_50_chocophlan_h3_chunk.sh

>&2 echo 2021-11-05 18:55:16.623196 BWA on singletons_50 | /pipeline_tools/BWA/bwa mem -t 55 /mydata/indices/chocophlan_h3_chunks/chocophlan_h3_chunks.fasta /mydata/testout/GA_BWA/data/0_read_split/singletons/singletons_50.fastq | /pipeline_tools/samtools/samtools view > /mydata/testout/GA_BWA/data/1_bwa/singletons_50_chocophlan_h3_chunk.sam && touch /mydata/testout/GA_BWA/data/jobs/singletons_50_chocophlan_h3_chunk_bwa

When running without the pipe, I get an error: > /pipeline_tools/BWA/bwa mem -t 55 /mydata/indices/chocophlan_h3_chunks/chocophlan_h3_chunks.fasta /mydata/testout/GA_BWA/data/0_read_split/singletons/singletons_50.fastq [E::bwa_idx_load_from_disk] fail to locate the index files

So BWA does not recognize the indexed chocophlan chunks

Adrian-Zet commented 2 years ago

I got a similar error running the pipeline today:

FileNotFoundError: [Errno 2] No such file or directory: '/media/database/ChocoPhlAn/ChocoPhlAn_split/'

Any help? Is it probably due to a problem with the database script ?

Edit: It seems the library_dowloader script didn't download the ChocoPhlAn.fasta and the /ChocoPhl_split/ either. I took them from the curated libraries and pointed the Config.ini to them and now the pipeline is working again. I'm not sure my comment is in the right threat though.

billytaj commented 1 year ago

issue no longer present.