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MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Apache License 2.0
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Error on running prepare: subprocess.CalledProcessError #128

Closed Lozzard closed 10 months ago

Lozzard commented 10 months ago

Hi! I am trying to run maxatac preapre but it fails with finding the file “ATAC_bowtie2_pipeline.sh” I guess. Did I miss some necessary process? Here is the output for reference.

maxatac prepare -i IMR90_rep1_atac.bam -o ./output -prefix IMR90_rep1_atac [2024-02-01 16:40:23,160] Prepare Parameters: Input file: IMR90_rep1_atac.bam Limiting to chromosomes: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22'] Input chromosome sizes file: /root/opt/maxatac/data/hg38/hg38.chrom.sizes Tn5 cut sites will be slopped 20 bps on each side Input blacklist file: /root/opt/maxatac/data/hg38/hg38_maxatac_blacklist.bw Output filename: IMR90_rep1_atac Output directory: ./output Using a millions factor of: 20000000 Using 9 threads to run job. [2024-02-01 16:40:23,162] Generate the normalized signal tracks. [2024-02-01 16:40:23,162] Working on a bulk ATAC-seq BAM file Getting the number of reads in the BAM file There are 60310654 reads in the file [2024-02-01 16:42:34,410] Processing BAM to bigwig. Running eduplication bash: /root/opt/maxatac/data/scripts/ATAC/ATAC_bowtie2_pipeline.sh: No such file or directory Traceback (most recent call last): File "/root/anaconda3/envs/maxatac/bin/maxatac", line 24, in sys.exit(main(sys.argv[1:])) File "/root/anaconda3/envs/maxatac/bin/maxatac", line 20, in main args.func(args) File "/root/anaconda3/envs/maxatac/lib/python3.9/site-packages/maxatac/analyses/prepare.py", line 87, in run_prepare subprocess.run(["bash", File "/root/anaconda3/envs/maxatac/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['bash', '/root/opt/maxatac/data/scripts/ATAC/ATAC_bowtie2_pipeline.sh', 'IMR90_rep1_atac.bam', 'IMR90_rep1_atac', '/mnt/e/CTCF/CTCF feature/output', '9', '/root/opt/maxatac/data/hg38/hg38_maxatac_blacklist.bed', '/root/opt/maxatac/data/hg38/hg38.chrom.sizes', '20', '0.33161636748293266', 'deduplicate', 'chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22']' returned non-zero exit status 127.

Lozzard commented 10 months ago

Sorry, I missed the downloading required reference data step