Missing output files

[scontcast]

Describe the bug Hi,

I've been trying to run mgatk on the test files provided here but the output files are not quite right on the logs folder. This is the output in filterlogs: barcodes.1.filter.log barcodes.2.filter.log barcodes.3.filter.log and in rmdupslogs barcodes.1.rmdups.log barcodes.2.rmdups.log barcodes.3.rmdups.log

The code I've run is this:

mgatk tenx -i test_barcode.bam -n test -o out -bt CB -b test_barcodes.txt

A summary of .log files Here is the log file, I can see a problem with numpy and . I don't know if that's what's causing this behavior. cat log.txt

Post an ls -lRh of mgatk_output_folder

out:
total 1.5K
drwxr-xr-x 2 scontre_m hpc-ag-ludwig 4.0K Apr  9 09:11 final
drwxr-xr-x 4 scontre_m hpc-ag-ludwig 4.0K Apr  9 09:16 logs
drwxr-xr-x 4 scontre_m hpc-ag-ludwig 4.0K Apr  9 09:10 qc

out/final:
total 2.8M
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 119K Apr  9 09:10 chrM_refAllele.txt
-rw-r--r-- 1 scontre_m hpc-ag-ludwig  96K Apr  9 09:10 test.A.txt.gz
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 194K Apr  9 09:10 test.coverage.txt.gz
-rw-r--r-- 1 scontre_m hpc-ag-ludwig  96K Apr  9 09:10 test.C.txt.gz
-rw-r--r-- 1 scontre_m hpc-ag-ludwig   76 Apr  9 09:10 test.depthTable.txt
-rw-r--r-- 1 scontre_m hpc-ag-ludwig  50K Apr  9 09:10 test.G.txt.gz
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 537K Apr  9 09:11 test.rds
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 477K Apr  9 09:11 test.signac.rds
-rw-r--r-- 1 scontre_m hpc-ag-ludwig  77K Apr  9 09:10 test.T.txt.gz

out/logs:
total 258K
-rw-r--r-- 1 scontre_m hpc-ag-ludwig  353 Apr  9 09:11 base.mgatk.log
drwxr-xr-x 2 scontre_m hpc-ag-ludwig 4.0K Apr  9 09:10 filterlogs
drwxr-xr-x 2 scontre_m hpc-ag-ludwig 4.0K Apr  9 09:10 rmdupslogs
-rw-r--r-- 1 scontre_m hpc-ag-ludwig  489 Apr  9 09:10 test.parameters.txt
-rw-r--r-- 1 scontre_m hpc-ag-ludwig  13K Apr  9 09:11 test.snakemake_tenx.log

out/logs/filterlogs:
total 1.5K
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 21 Apr  9 09:10 barcodes.1.filter.log
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 21 Apr  9 09:10 barcodes.2.filter.log
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 21 Apr  9 09:10 barcodes.3.filter.log

out/logs/rmdupslogs:
total 1.5K
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 1.4K Apr  9 09:10 barcodes.1.rmdups.log
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 1.4K Apr  9 09:10 barcodes.2.rmdups.log
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 1.4K Apr  9 09:10 barcodes.3.rmdups.log

out/qc:
total 1.0K
drwxr-xr-x 2 scontre_m hpc-ag-ludwig 4.0K Apr  9 09:10 depth
drwxr-xr-x 2 scontre_m hpc-ag-ludwig 4.0K Apr  9 09:10 quality

out/qc/depth:
total 1.5K
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 25 Apr  9 09:10 barcodes.1.depth.txt
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 25 Apr  9 09:10 barcodes.2.depth.txt
-rw-r--r-- 1 scontre_m hpc-ag-ludwig 26 Apr  9 09:10 barcodes.3.depth.txt

out/qc/quality:
total 0

Describe the sequencing assay being analyzed Test barcodes

Additional context This is the java version in my environment

openjdk version "1.8.0_112"
OpenJDK Runtime Environment (Zulu 8.19.0.1-linux64) (build 1.8.0_112-b16)
OpenJDK 64-Bit Server VM (Zulu 8.19.0.1-linux64) (build 25.112-b16, mixed mode)

dependencies:
  - r-base
  - r-matrix
  - r-data.table
  - bioconductor-summarizedexperiment
  - bioconductor-genomicranges
  - ruamel.yaml=0.17.21
  - java-jdk
  - python=3.8
  - pulp=2.7
  - pip
encoding-tools            0.0.3 
click                     8.1.7 
dataclasses               0.6
pyyaml                    6.0.1
matplotlib                3.7.3
mgatk                     0.7.0 

I hope you can help me, thanks! Steph