tutorial to run from singularity is failing with this error:The following required tool(s) are not callable: macs2

[bioarpit1]

hi

I am trying to follow the tutorial for run from container. I am using latest docker image to make the sif image. but somehow its failing with the following required tools are not callable:macs2

•          Command:  `/home/amishra/pepatac_tutorial/tools/pepatac/pipelines/pepatac.py --single-or-paired paired --prealignment-index rCRSd= /home/amishra/pepatac_tutorial/tools/pepatac/genome_folder/alias/rCRSd/bowtie2_index/default/rCRSd. --genome hg38 --genome-index /home/amishra/pepatac_tutorial/tools/pepatac/genome_folder/alias/hg38/bowtie2_index/default/hg38. --chrom-sizes /home/amishra/pepatac_tutorial/tools/pepatac/genome_folder/alias/hg38/fasta/default/hg38.chrom.sizes --sample-name test1 --input /home/amishra/pepatac_tutorial/tools/pepatac/examples/data/test1_r1.fastq.gz --input2 /home/amishra/pepatac_tutorial/tools/pepatac/examples/data/test1_r2.fastq.gz --genome-siz hs -O /home/amishra/pepatac_tutorial/`
  

•     Compute host:  SRV-SINGLE-01.BRIVMRC.ORG
  

•      Working dir:  /home/amishra
  

•        Outfolder:  /home/amishra/pepatac_tutorial/test1/
  

• Pipeline started at: (03-04 23:54:57) elapsed: 0.0 TIME

Version log:

•   Python version:  3.10.6
  

•      Pypiper dir:  `/usr/local/lib/python3.10/dist-packages/pypiper`
  

•  Pypiper version:  0.12.3
  

•     Pipeline dir:  `/home/amishra/pepatac_tutorial/tools/pepatac/pipelines`
  

• Pipeline version:  0.10.4
  

•    Pipeline hash:  756632d1bd9aae182eab10e34b294f08744663cc
  

•  Pipeline branch:  * master
  

•    Pipeline date:  2023-02-22 10:19:16 -0500
  

•    Pipeline diff:  2 files changed, 2 insertions(+), 2 deletions(-)
  

Arguments passed to pipeline:

•       `TSS_name`:  `None`
  

•        `aligner`:  `bowtie2`
  

•      `anno_name`:  `None`
  

•      `blacklist`:  `None`
  

•    `chrom_sizes`:  `/home/amishra/pepatac_tutorial/tools/pepatac/genome_folder/alias/hg38/fasta/default/hg38.chrom.sizes`
  

•    `config_file`:  `pepatac.yaml`
  

•          `cores`:  `1`
  

•   `deduplicator`:  `samblaster`
  

•          `dirty`:  `False`
  

•         `extend`:  `250`
  

•          `fasta`:  `None`
  

•   `force_follow`:  `False`
  

• `frip_ref_peaks`:  `None`
  

• genome_assembly: hg38

•   `genome_index`:  `/home/amishra/pepatac_tutorial/tools/pepatac/genome_folder/alias/hg38/bowtie2_index/default/hg38.`
  

•    `genome_size`:  `hs`
  

•          `input`:  `['/home/amishra/pepatac_tutorial/tools/pepatac/examples/data/test1_r1.fastq.gz']`
  

•         `input2`:  `['/home/amishra/pepatac_tutorial/tools/pepatac/examples/data/test1_r2.fastq.gz']`
  

•           `keep`:  `False`
  

•           `lite`:  `False`
  

•         `logdev`:  `False`
  

•            `mem`:  `4000`
  

•          `motif`:  `False`
  

•      `new_start`:  `False`
  

•        `no_fifo`:  `False`
  

•       `no_scale`:  `False`
  

•  `output_parent`:  `/home/amishra/pepatac_tutorial/`
  

•     `paired_end`:  `True`
  

•    `peak_caller`:  `macs2`
  

•      `peak_type`:  `fixed`
  

• prealignment_index: ['rCRSd=', '/home/amishra/pepatac_tutorial/tools/pepatac/genome_folder/alias/rCRSd/bowtie2_index/default/rCRSd.']
• prealignment_names: []

•     `prioritize`:  `False`
  

•        `recover`:  `False`
  

•    `sample_name`:  `test1`
  

•    `search_file`:  `None`
  

•         `silent`:  `False`
  

• single_or_paired: paired

•         `skipqc`:  `False`
  

•            `sob`:  `False`
  

•       `testmode`:  `False`
  

•        `trimmer`:  `skewer`
  

•      `verbosity`:  `None`
  

---

The following required tool(s) are not callable: macs2

Pipeline failed at: (03-04 23:54:57) elapsed: 0.0 TIME

Total time: 0:00:00
Failure reason: Missing required tools. See message above.
Traceback (most recent call last):
File "/home/amishra/pepatac_tutorial/tools/pepatac/pipelines/pepatac.py", line 2779, in
sys.exit(main())
File "/home/amishra/pepatac_tutorial/tools/pepatac/pipelines/pepatac.py", line 602, in main
pm.fail_pipeline(RuntimeError(err_msg))
File "/usr/local/lib/python3.10/dist-packages/pypiper/manager.py", line 1660, in fail_pipeline
raise exc
RuntimeError: Missing required tools. See message above.

[2lore]

I had the same issue in docker when I pulled the most recent pepatac image.
The workaround I used now is going back to an earlier version of the pepatac image in docker (0.10.0) - then the pipeline runs without this error.

[Suncuss]

I am having similar issue with the docker image too