Error with Chip-Seq Singularity Pipeline at Macs2 Peak Calling

During MACS2 processing with Singularity Chip-Seq pipeline, the pipeline throws up an error. I Tried but couldn’t identify the origin of the error.

Can you help me? What am I missing?

I appreciate a lot thanks!

singularity --version
2.6.1-dist

Input.json:

{
    "chip.genome_tsv" : "mm10.tsv",
    "chip.paired_end" : false,

    "chip.fastqs_rep1_R1" : [ "ChIP_R1.fastq.gz"],
    "chip.ctl_fastqs_rep1_R1" : [ "ChIP_Input_R1.fastq.gz" ],

    "chip.title" : "ChIP",
    "chip.description" : "ChIP Project",

    "chip.pipeline_type" : "tf",
    "chip.peak_caller" : "spp",

    "chip.align_only" : false,
    "chip.true_rep_only" : false,

    "chip.disable_fingerprint" : false,
    "chip.enable_count_signal_track" : false,

    "chip.xcor_pe_trim_bp" : 50,

    "chip.dup_marker" : "picard",
    "chip.mapq_thresh" : 30,
    "chip.no_dup_removal" : false,

    "chip.mito_chr_name" : "chrM",
    "chip.regex_filter_reads" : "chrM",
    "chip.subsample_reads" : 0,
    "chip.ctl_subsample_reads" : 0,
    "chip.xcor_subsample_reads" : 15000000,

    "chip.keep_irregular_chr_in_bfilt_peak" : false,
    
    "chip.always_use_pooled_ctl" : true,
    "chip.ctl_depth_ratio" : 1.2,

    "chip.macs2_cap_num_peak" : 500000,
    "chip.pval_thresh" : 0.01,
    "chip.idr_thresh" : 0.05,
    "chip.spp_cap_num_peak" : 300000,

    "chip.bwa_cpu" : 12,
    "chip.bwa_mem_mb" : 200000,
    "chip.bwa_time_hr" : 480,
    "chip.bwa_disks" : "local-disk 100 HDD",

    "chip.filter_cpu" : 12,
    "chip.filter_mem_mb" : 20000,
    "chip.filter_time_hr" : 24,
    "chip.filter_disks" : "local-disk 100 HDD",

    "chip.bam2ta_cpu" : 12,
    "chip.bam2ta_mem_mb" : 100000,
    "chip.bam2ta_time_hr" : 6,
    "chip.bam2ta_disks" : "local-disk 100 HDD",

    "chip.spr_mem_mb" : 16000,

    "chip.fingerprint_cpu" : 12,
    "chip.fingerprint_mem_mb" : 12000,
    "chip.fingerprint_time_hr" : 6,
    "chip.fingerprint_disks" : "local-disk 100 HDD",

    "chip.xcor_cpu" : 12,
    "chip.xcor_mem_mb" : 16000,
    "chip.xcor_time_hr" : 24,
    "chip.xcor_disks" : "local-disk 100 HDD",

    "chip.macs2_mem_mb" : 16000,
    "chip.macs2_time_hr" : 24,
    "chip.macs2_disks" : "local-disk 100 HDD",

    "chip.spp_cpu" : 12,
    "chip.spp_mem_mb" : 16000,
    "chip.spp_time_hr" : 72,
    "chip.spp_disks" : "local-disk 100 HDD"
}

find -name stderr -not -empty | xargs tail -n +1
Traceback (most recent call last):
  File "/software/chip-seq-pipeline/src/encode_macs2_chip.py", line 225, in <module>
    main()
  File "/software/chip-seq-pipeline/src/encode_macs2_chip.py", line 200, in main
    args.out_dir)
  File "/software/chip-seq-pipeline/src/encode_macs2_chip.py", line 88, in macs2
    run_shell_cmd(cmd0)
  File "/software/chip-seq-pipeline/src/encode_common.py", line 252, in run_shell_cmd
    raise Exception(err_str)
Exception: PID=28849, PGID=28849, RC=1
STDERR=ERROR:root:--extsize must >= 1!
STDOUT=

[leepc12]

@tiagobrc : TF ChIP-seq cannot run without inputs but histone ChIP-seq can do .

[leepc12]

Use : instead of =

“chip.fraglen”: [200, 150],