You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hello,
I'm using gatk 4.2.2.0 with PathSeqPipelineSpark but I'm having some problems.
For some samples I have the generation of the outuput.bam file while for others no.
The path to the related file are correct so I was wondering if someone can help me.
This is the error
A USER ERROR has occurred: Couldn't write file pathseq.complete0.8.bam because writing failed with exception No FileSystem for scheme "null"
Best,
Martina
The text was updated successfully, but these errors were encountered:
Hello,
I'm using gatk 4.2.2.0 with PathSeqPipelineSpark but I'm having some problems.
For some samples I have the generation of the outuput.bam file while for others no.
gatk --java-options "-Xmx750G" PathSeqPipelineSpark
--input output.bam
--filter-bwa-image ${imagehuman}
--kmer-file ${pathseqdb}/host.hss
--min-clipped-read-length 60
--microbe-dict ${bactdict}
--microbe-bwa-image ${pathseqdb}/bacteria_only.fa.img
--taxonomy-file $taxdb
--output ${outpath}pathseq.complete0.8.bam
--scores-output ${outpath}/pathseq.complete0.8.csv
--is-host-aligned false
--filter-duplicates false
--min-score-identity .8
The path to the related file are correct so I was wondering if someone can help me.
This is the error
A USER ERROR has occurred: Couldn't write file pathseq.complete0.8.bam because writing failed with exception No FileSystem for scheme "null"
Best,
Martina
The text was updated successfully, but these errors were encountered: