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