Error running the pipeline

[vrennie]

Hi @kristyhoran,

When running the pipeline, it seems to run into an error but it is unclear what the error is. This is what the log says

Command Failed:
set -u pipefail; bedtools makewindows -g /home/magmauser/mambaforge/envs/tbtamr/lib/python3.10/site-packages/tbtamr/db/tbtamr.fasta.fai -n 1 | awk '{print $1":"$2+1"-"$3" "$1""$2+1""$3}' | parallel -j 1 --col-sep " " "freebayes -f /home/magmauser/mambaforge/envs/tbtamr/lib/python3.10/site-packages/tbtamr/db/tbtamr.fasta -r {1} --haplotype-length -1 FD124/a78ae44f-44ce-404e-832a-10564e134ea2.{2}.tmp.bam > FD124/a78ae44f-44ce-404e-832a-10564e134ea2.{2}.tmp.vcf"
stderr:
WARNING: Interval :0-0 is smaller than the number of windows requested. Skipping.

Any ideas?

Thanks,

Vincent

[kristyhoran]

@vrennie in order for me to be more helpful can you please provide me with the series of commands you ran (the input files would be great too)? so i can see if i can replicate the issue? It looks like maybe bedtools and freebayes have choked on the input.. I have only ever seen this type of behviour on sequences where there was very little alignment to the reference or where there were lots of very very very large deletions...

[vrennie]

@kristyhoran I followed the wiki and ran this command:

tbtamr run -I tbtamr_FD124_146_test.tsv

With respect to the input files, I would have to check if we I can share them, but for these two samples, MAGMA found mapped percentages of 90% and 71% for FD124 and FD146.

Are these mapped percentages that would cause tbtamr to trip up?

Vincent