Hello! I am using the fibertools pipeline (using pixi, like pixi run fire --configfile config.yaml ) to ultimately call accessible peaks on m6A-treated DNA. My sample was sequenced using ONT.
I have rerun this code a few times and it always stalled at the same step - 'exclude_from_shuffle' or step 71. Before running this pipeline, I filtered my BAM for highly confident modifications (with an accuracy filter of 0.9) and used fibertools add-nucleosomes.
Using fibertools 0.1.2 with linux-64.
My config file looks like:
> ref: /home/ubuntu/work/mm9/Sequence/WholeGenomeFasta/genome.fa
> ref_name: mm9
> manifest: config.tbl
> ont: True
Any guidance on how to get the pipeline to work would be helpful. Thank you so much!
Below is the relevant piece of the log file indicating the error:
[Wed Dec 3 21:57:07 2025]
Finished job 5.
71 of 202 steps (35%) done
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr1.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr10.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr11.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr12.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr13.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr14.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr15.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr16.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr17.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr18.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr19.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr2.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr3.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr4.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr5.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr6.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr7.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr8.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chr9.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chrM.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chrX.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-chrY.fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/GMP_KO_Hia5_mm9-v0.1.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-fiber-locations.bed.gz.
Removing temporary output temp/GMP_KO_Hia5_mm9/coverage/v0.1-fiber-locations.bed.gz.tbi.
Select jobs to execute...
Execute 1 jobs...
[Wed Dec 3 21:57:08 2025]
localrule exclude_from_shuffle:
input: temp/GMP_KO_Hia5_mm9/coverage/filtered-for-coverage/v0.1-fiber-locations.bed.gz, /home/ubuntu/work/mm9/Sequence/WholeGenomeFasta/genome.fa.fai
output: results/GMP_KO_Hia5_mm9/additional-outputs-v0.1/coverage/exclude-from-shuffles.bed.gz
jobid: 4
reason: Missing output files: results/GMP_KO_Hia5_mm9/additional-outputs-v0.1/coverage/exclude-from-shuffles.bed.gz; Input files updated by another job: temp/GMP_KO_Hia5_mm9/coverage/filtered-for-coverage/v0.1-fiber-locations.bed.gz
wildcards: sm=GMP_KO_Hia5_mm9, v=v0.1
threads: 4
resources: tmpdir=/tmp
Activating conda environment: .snakemake/conda/7c596f604f23a453e334598e67001a40_
It looks as though you have less than 3 columns at line 305 in file stdin. Are you sure your files are tab-delimited?
[Wed Dec 3 21:58:20 2025]
Error in rule exclude_from_shuffle:
jobid: 4
input: temp/GMP_KO_Hia5_mm9/coverage/filtered-for-coverage/v0.1-fiber-locations.bed.gz, /home/ubuntu/work/mm9/Sequence/WholeGenomeFasta/genome.fa.fai
output: results/GMP_KO_Hia5_mm9/additional-outputs-v0.1/coverage/exclude-from-shuffles.bed.gz
conda-env: /home/ubuntu/FIRE/.snakemake/conda/7c596f604f23a453e334598e67001a40_
shell:
( bedtools genomecov -bga -i temp/GMP_KO_Hia5_mm9/coverage/filtered-for-coverage/v0.1-fiber-locations.bed.gz -g /home/ubuntu/work/mm9/Sequence/WholeGenomeFasta/genome.fa.fai | awk '$4 == 0'; less ) | cut -f 1-3 | bedtools sort | bedtools merge | bgzip -@ 4 > results/GMP_KO_Hia5_mm9/additional-outputs-v0.1/coverage/exclude-from-shuffles.bed.gz
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job exclude_from_shuffle since they might be corrupted:
results/GMP_KO_Hia5_mm9/additional-outputs-v0.1/coverage/exclude-from-shuffles.bed.gz
Hello! I am using the fibertools pipeline (using pixi, like
pixi run fire --configfile config.yaml) to ultimately call accessible peaks on m6A-treated DNA. My sample was sequenced using ONT.I have rerun this code a few times and it always stalled at the same step - 'exclude_from_shuffle' or step 71. Before running this pipeline, I filtered my BAM for highly confident modifications (with an accuracy filter of 0.9) and used fibertools add-nucleosomes.
Using fibertools 0.1.2 with linux-64.
My config file looks like:
Any guidance on how to get the pipeline to work would be helpful. Thank you so much!
Below is the relevant piece of the log file indicating the error: