“Error in checkGrep(grep(".A.txt", files))

[Cesco16]

Hi! I ran into this error:

“Error in checkGrep(grep(".A.txt", files)) :

Improper folder specification; file missing / extra file present. See documentation

Calls: importMito -> checkGrep

Execution halted”

To Reproduce
Steps to reproduce the behavior:

mgatk tenx -i possorted_bam.bam -n atac-08 -o atac-08 -c 30 -bt CB -b cellranger/atac-08/filtered_peak_bc_matrix/barcodes.tsv --keep-temp-files

The same if I use scRNA data:

mgatk tenx -i possorted_bam.bam -n scRNA-09 -o scRNA-09 -c 30 -ub UB -bt CB -b cellranger/scRNA-09/filtered_feature_bc_matrix/barcodes.tsv --keep-temp-files

Thank you very much for your help!

[Eomesodermin]

I have the same issue, any work arounds?

[yirenshao]

Hello there! I ran into the same error. After checked the output folder, I found that a few of subfolders that should be created as in line ~302-308 in cli.py were missing. what I did is I changed '/.internal' to /internal' and in OneSample.py, I changed line ~17 config = yaml.load(stream, Loader=yaml.Loader) to from ruamel.yaml import YAML; d = YAML(typ='rt'); config = d.load(stream). Leave --keep-temp-files in the command so that u can know whether all the folders were made.

HTHs!!!

[mencian]

Pinning ruamel.yaml to 0.16.12 did the trick for me. I've updated the Bioconda recipe for mgatk here.

[AbhinavSoni20191995]

Hello, I tried doing both the above option, but keep getting the same error. Below is the code I used:

mgatk tenx -i possorted_bam.bam -n ASAP_Seq_young -o mgatk_young -b barcodes.tsv -bt CB -g mm10

Output:
Mon Sep 30 15:37:36 CEST 2024: mgatk v0.7.0
Mon Sep 30 15:37:37 CEST 2024: Found bam file: possorted_bam.bam for genotyping.
Mon Sep 30 15:37:37 CEST 2024: Found file of barcodes to be parsed: barcodes.tsv
Mon Sep 30 15:37:37 CEST 2024: User specified mitochondrial genome matches .bam file
Mon Sep 30 15:40:18 CEST 2024: Finished determining/splitting barcodes for genotyping.
Mon Sep 30 15:40:19 CEST 2024: Genotyping samples with 8 threads
Fehler in checkGrep(grep(".A.txt", files)) :
Improper folder specification; file missing / extra file present. See documentation
Ruft auf: importMito -> checkGrep
Ausführung angehalten

Is there a workaround for this? or I am doing something weird. Any help will be appreciated. Thank you!

[AbhinavSoni20191995]

I figured it out, in the end troubleshooting using the log file "ASAP_Seq_young.snakemake_tenx.log" was quite helpful.

For my particular case first it showed some error in pulp package, and downgrading with pip3 install --force-reinstall -v "pulp==2.7" did the trick as mentioned in issue #93

There were some other issues post this, however they could be easily resolved by following the log files.