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Issue with running tf file #272

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shirleytemples opened this issue Mar 6, 2022 · 6 comments
Open

Issue with running tf file #272

shirleytemples opened this issue Mar 6, 2022 · 6 comments

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@shirleytemples
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I have been able to successfully run the chip-seq pipeline for the example json and my own histone bam files. However, while passing in a custom tf .bam file, I am running into errors that I am not too sure how to debug. Any suggestions are much appreciated!

Here are more info about the issue:

I ran caper run chip.wdl -i /mnt/c/users/shirl/Desktop/guttman_lab/CTCF.json --conda

Caper configuration file
Locally run

Input JSON file

{
    
    "chip.title" : "Running all-CTCF.bam through ENCODE",
    "chip.description" : "This is an template input JSON for CTCF.",

    "chip.pipeline_type" : "tf",
    "chip.nodup_bams" : ["/mnt/c/Users/shirl/Desktop/guttman_lab/all-CTCF.bam"],
    "chip.ctl_nodup_bams" : ["/mnt/c/Users/shirl/Desktop/guttman_lab/Control_ChIP-seq_hg38_K562.bam"],
    "chip.genome_tsv" : "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv",
    "chip.enable_gc_bias" : false,
    "chip.paired_end" : false,
    "chip.ctl_paired_ends" : [true]
}

Error message:

2022-03-06 00:07:20,574|caper.cli|INFO| Cromwell stdout: /home/shirleytemples/chip-seq-pipeline2/cromwell.out.69
2022-03-06 00:07:20,577|caper.caper_base|INFO| Creating a timestamped temporary directory. /home/shirleytemples/chip-seq-pipeline2/.caper_tmp/chip/20220306_000720_576058
2022-03-06 00:07:20,578|caper.caper_runner|INFO| Localizing files on work_dir. /home/shirleytemples/chip-seq-pipeline2/.caper_tmp/chip/20220306_000720_576058
2022-03-06 00:07:20,877|autouri.autouri|INFO| cp: (3596ce88) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/caf534ed3cf684406e731d19be272b4a/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz2022-03-06 00:07:22,661|autouri.autouri|INFO| cp: (3596ce88) skipped due to name_size_match. size=872949833, mt=1549739698.0
2022-03-06 00:07:22,664|autouri.autouri|INFO| cp: (9756f6dd) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only.fasta.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/f43b63a83784d3ec8055f1a22168ed89/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only.fasta.gz
2022-03-06 00:07:23,689|autouri.autouri|INFO| cp: (9756f6dd) skipped due to md5_match. md5=05297d96dd1f7cfb45a7b637d6dd7036
2022-03-06 00:07:23,788|autouri.autouri|INFO| cp: (16a445a9) started. src=https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/f183dcba5d34f959d8b55ed438ee2e22/ENCFF356LFX.bed.gz
2022-03-06 00:07:25,099|autouri.autouri|INFO| cp: (16a445a9) skipped due to md5_match. md5=393688b4f06c9ce26165d47433dd8c37
2022-03-06 00:07:26,624|autouri.autouri|INFO| cp: (32d95d6d) started. src=https://www.encodeproject.org/files/GRCh38_EBV.chrom.sizes/@@download/GRCh38_EBV.chrom.sizes.tsv, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/c52f52c7bfa357f55a39b1de7e4d0b0c/GRCh38_EBV.chrom.sizes.tsv
2022-03-06 00:07:27,861|autouri.autouri|INFO| cp: (32d95d6d) skipped due to md5_match. md5=c95303fb77cc3e11d50e3c3a4b93b3fb
2022-03-06 00:07:27,960|autouri.autouri|INFO| cp: (d2b2384c) started. src=https://www.encodeproject.org/files/ENCFF110MCL/@@download/ENCFF110MCL.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/3ff4ac4c3f59d096b1a3842a182072ae/ENCFF110MCL.tar.gz
2022-03-06 00:07:29,889|autouri.autouri|INFO| cp: (d2b2384c) skipped due to name_size_match. size=3749246230, mt=1571469011.0
2022-03-06 00:07:29,969|autouri.autouri|INFO| cp: (c874ed2c) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/df5193e07055d13c48be59bacd0f56b8/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index.tar.gz
2022-03-06 00:07:31,217|autouri.autouri|INFO| cp: (c874ed2c) skipped due to md5_match. md5=80b263f6ea6ff65d547eef07102535db
2022-03-06 00:07:31,353|autouri.autouri|INFO| cp: (b4264198) started. src=https://www.encodeproject.org/files/ENCFF643CGH/@@download/ENCFF643CGH.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/8c692fba4640609720272154ab0faa30/ENCFF643CGH.tar.gz
2022-03-06 00:07:33,241|autouri.autouri|INFO| cp: (b4264198) skipped due to name_size_match. size=4318261891, mt=1549723866.0
2022-03-06 00:07:33,313|autouri.autouri|INFO| cp: (81deb398) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/d3dff25534e93d893902540d81e4f475/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index.tar.gz
2022-03-06 00:07:34,528|autouri.autouri|INFO| cp: (81deb398) skipped due to md5_match. md5=7e088c24a017a43b1db5e8f50060eec1
2022-03-06 00:07:34,627|autouri.autouri|INFO| cp: (7b90f336) started. src=https://www.encodeproject.org/files/ENCFF766FGL/@@download/ENCFF766FGL.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/f16cc7892540d7a9bc3207cc44eb8288/ENCFF766FGL.bed.gz
2022-03-06 00:07:35,725|autouri.autouri|INFO| cp: (7b90f336) skipped due to md5_match. md5=d108aa2a392ce5dd207fb8769a6e8240
2022-03-06 00:07:35,825|autouri.autouri|INFO| cp: (2f87a11e) started. src=https://www.encodeproject.org/files/ENCFF304XEX/@@download/ENCFF304XEX.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/805e179275a9c0fb7a37def40c4312d1/ENCFF304XEX.bed.gz
2022-03-06 00:07:37,766|autouri.autouri|INFO| cp: (2f87a11e) skipped due to name_size_match. size=14377496, mt=1592463730.0
2022-03-06 00:07:37,867|autouri.autouri|INFO| cp: (a7a00986) started. src=https://www.encodeproject.org/files/ENCFF140XLU/@@download/ENCFF140XLU.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/0cbd2c602ddad252bc39729fc8a29286/ENCFF140XLU.bed.gz
2022-03-06 00:07:39,122|autouri.autouri|INFO| cp: (a7a00986) skipped due to md5_match. md5=91047588129069ff91ec1b0664179f8e
2022-03-06 00:07:39,215|autouri.autouri|INFO| cp: (db9320cd) started. src=https://www.encodeproject.org/files/ENCFF212UAV/@@download/ENCFF212UAV.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/1d3aa436b05f16a509edb94789c061d3/ENCFF212UAV.bed.gz
2022-03-06 00:07:40,931|autouri.autouri|INFO| cp: (db9320cd) skipped due to name_size_match. size=18381891, mt=1592463727.0
2022-03-06 00:07:41,032|autouri.autouri|INFO| cp: (c192ef15) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/3b39284516e676ea52238f0636c0bbbf/hg38_dnase_avg_fseq_signal_formatted.txt.gz
2022-03-06 00:07:41,485|autouri.autouri|INFO| cp: (c192ef15) skipped due to md5_match. md5=df624401f76fbd4d651e736068c43a1a
2022-03-06 00:07:41,584|autouri.autouri|INFO| cp: (0aa7e5d2) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/c73f434c3fa4f3f54bc2ecad09c065c2/hg38_celltype_compare_subsample.bed.gz
2022-03-06 00:07:42,008|autouri.autouri|INFO| cp: (0aa7e5d2) skipped due to md5_match. md5=ced0c653d28628654288f7a8ab052590
2022-03-06 00:07:42,108|autouri.autouri|INFO| cp: (dfbf40b5) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/a9745b33b4ffdd83d7d2c5a7d3c8036a/hg38_dnase_avg_fseq_signal_metadata.txt
2022-03-06 00:07:42,408|autouri.autouri|INFO| cp: (dfbf40b5) skipped due to md5_match. md5=3f7fd85ab9a4c6274f28c3e82a79c10d
2022-03-06 00:07:44,996|caper.wdl_parser|ERROR| Failed to parse WDL with miniwdl.
2022-03-06 00:07:45,098|caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/home/shirleytemples/chip-seq-pipeline2/chip.wdl
2022-03-06 00:07:45,246|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool...
2022-03-06 00:08:55,449|caper.cromwell|INFO| Passed Womtool validation.
2022-03-06 00:08:55,641|caper.caper_runner|INFO| launching run: wdl=/home/shirleytemples/chip-seq-pipeline2/chip.wdl, inputs=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/mnt/c/users/shirl/Desktop/guttman_lab/CTCF.local.json, backend_conf=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/chip/20220306_000720_576058/backend.conf
2022-03-06 00:10:54,066|caper.cromwell_workflow_monitor|INFO| Workflow: id=f7347247-01cf-446d-8ab2-263fc28712e8, status=Running
2022-03-06 00:10:55,496|caper.cromwell_workflow_monitor|INFO| Workflow: id=f7347247-01cf-446d-8ab2-263fc28712e8, status=Submitted
2022-03-06 00:13:34,964|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.read_genome_tsv:-1, retry=0, status=Started, job_id=4143
2022-03-06 00:13:35,314|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode
2022-03-06 00:13:48,125|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.read_genome_tsv:-1, retry=0, status=Done
2022-03-06 00:14:39,011|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.bam2ta_ctl:0, retry=0, status=Started, job_id=4207
2022-03-06 00:14:39,183|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.bam2ta_ctl:0, retry=0, status=WaitingForReturnCode
2022-03-06 00:15:04,638|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.bam2ta:0, retry=0, status=Started, job_id=4246
2022-03-06 00:15:05,027|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.bam2ta:0, retry=0, status=WaitingForReturnCode
2022-03-06 00:15:54,765|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.jsd:-1, retry=0, status=Started, job_id=4295
2022-03-06 00:15:54,777|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.jsd:-1, retry=0, status=WaitingForReturnCode
2022-03-06 00:36:03,460|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.bam2ta_ctl:0, retry=0, status=Done


2022-03-06 01:25:58,884|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.bam2ta:0, retry=0, status=Done
2022-03-06 01:26:08,571|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.spr:0, retry=0, status=Started, job_id=5201
2022-03-06 01:26:08,627|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.spr:0, retry=0, status=WaitingForReturnCode
2022-03-06 01:26:13,690|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.choose_ctl:-1, retry=0, status=Started, job_id=5304
2022-03-06 01:26:13,713|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.xcor:0, retry=0, status=Started, job_id=5248
2022-03-06 01:26:13,714|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.choose_ctl:-1, retry=0, status=WaitingForReturnCode
2022-03-06 01:26:13,715|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.xcor:0, retry=0, status=WaitingForReturnCode
2022-03-06 01:26:34,516|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.choose_ctl:-1, retry=0, status=Done
2022-03-06 01:28:30,335|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.jsd:-1, retry=0, status=Done
2022-03-06 01:29:38,842|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.spr:0, retry=0, status=Done
2022-03-06 01:39:08,928|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.xcor:0, retry=0, status=Done
2022-03-06 01:39:18,570|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.fraglen_mean:-1, retry=0, status=Started, job_id=5652
2022-03-06 01:39:18,570|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak:0, retry=0, status=Started, job_id=5605
2022-03-06 01:39:18,571|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.fraglen_mean:-1, retry=0, status=WaitingForReturnCode
2022-03-06 01:39:18,571|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak:0, retry=0, status=WaitingForReturnCode
2022-03-06 01:39:23,563|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.macs2_signal_track:0, retry=0, status=Started, job_id=5745
2022-03-06 01:39:23,566|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr1:0, retry=0, status=Started, job_id=5793
2022-03-06 01:39:23,570|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr2:0, retry=0, status=Started, job_id=5697
2022-03-06 01:39:23,575|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.macs2_signal_track:0, retry=0, status=WaitingForReturnCode
2022-03-06 01:39:23,576|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr1:0, retry=0, status=WaitingForReturnCode
2022-03-06 01:39:23,578|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr2:0, retry=0, status=WaitingForReturnCode
2022-03-06 01:39:25,216|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.fraglen_mean:-1, retry=0, status=Done
2022-03-06 01:41:12,368|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.macs2_signal_track:0, retry=0, status=Done
2022-03-06 02:06:23,162|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr2:0, retry=0, status=Done
2022-03-06 02:06:28,547|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr2:0, retry=1, status=Started, job_id=7669
2022-03-06 02:06:28,549|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr2:0, retry=1, status=WaitingForReturnCode
2022-03-06 02:07:29,211|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr1:0, retry=0, status=Done
2022-03-06 02:07:38,561|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr1:0, retry=1, status=Started, job_id=7775
2022-03-06 02:07:38,562|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr1:0, retry=1, status=WaitingForReturnCode
2022-03-06 02:18:56,769|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak:0, retry=0, status=Done
2022-03-06 02:19:03,559|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak:0, retry=1, status=Started, job_id=8135
2022-03-06 02:19:03,560|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak:0, retry=1, status=WaitingForReturnCode
2022-03-06 02:26:35,273|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr2:0, retry=1, status=Done
2022-03-06 02:30:32,518|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak_pr1:0, retry=1, status=Done
2022-03-06 02:48:37,810|caper.cromwell_workflow_monitor|INFO| Task: id=f7347247-01cf-446d-8ab2-263fc28712e8, task=chip.call_peak:0, retry=1, status=Done
2022-03-06 02:48:38,347|caper.cromwell_workflow_monitor|INFO| Workflow: id=f7347247-01cf-446d-8ab2-263fc28712e8, status=Failed
2022-03-06 02:48:58,507|caper.cromwell_metadata|INFO| Wrote metadata file. /home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/metadata.json
2022-03-06 02:48:58,509|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...
* Started troubleshooting workflow: id=f7347247-01cf-446d-8ab2-263fc28712e8, status=Failed
* Found failures JSON object.
[
    {
        "message": "Workflow failed",
        "causedBy": [
            {
                "causedBy": [],
                "message": "Job chip.call_peak_pr2:0:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
            },
            {
                "causedBy": [],
                "message": "Job chip.call_peak_pr1:0:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
            },
            {
                "causedBy": [],
                "message": "Job chip.call_peak:0:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
            }
        ]
    }
]
* Recursively finding failures in calls (tasks)...

==== NAME=chip.call_peak, STATUS=RetryableFailure, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=5605
START=2022-03-06T09:39:15.370Z, END=2022-03-06T10:18:58.555Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.bfilt.regionPeak.bb': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.bfilt.regionPeak.starch': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory



==== NAME=chip.call_peak, STATUS=Failed, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=8135
START=2022-03-06T10:18:59.364Z, END=2022-03-06T10:48:37.827Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.bfilt.regionPeak.bb': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.bfilt.regionPeak.starch': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory



==== NAME=chip.call_peak_pr1, STATUS=RetryableFailure, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=5793
START=2022-03-06T09:39:23.366Z, END=2022-03-06T10:07:33.559Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr1_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr1_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.bfilt.regionPeak.bb': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.bfilt.regionPeak.starch': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory



==== NAME=chip.call_peak_pr1, STATUS=Failed, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=7775
START=2022-03-06T10:07:35.892Z, END=2022-03-06T10:30:32.521Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr1_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr1_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.bfilt.regionPeak.bb': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.bfilt.regionPeak.starch': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr1/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory



==== NAME=chip.call_peak_pr2, STATUS=RetryableFailure, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=5697
START=2022-03-06T09:39:19.347Z, END=2022-03-06T10:06:23.592Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.bb': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.starch': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory



==== NAME=chip.call_peak_pr2, STATUS=Failed, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=7669
START=2022-03-06T10:06:25.414Z, END=2022-03-06T10:26:35.301Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-CTCF.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.bb': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.starch': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/f7347247-01cf-446d-8ab2-263fc28712e8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory


2022-03-06 02:48:58,707|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
2022-03-06 02:48:58,709|caper.cli|ERROR| Check stdout in /home/shirleytemples/chip-seq-pipeline2/cromwell.out.69
@shirleytemples
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The issue is solved and pipeline ran successfully after I changed the json file "chip.ctl_paired_ends" from true to false.

"chip.ctl_paired_ends" : [false]

@shirleytemples shirleytemples reopened this Mar 7, 2022
@shirleytemples
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shirleytemples commented Mar 7, 2022 •
edited
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Even though I was able to run the all-CTCF.bam file (tf) from above, however, I am having a similar issue with the tf file all-POLR2A.bam

I ran caper run chip.wdl -i /mnt/c/users/shirl/Desktop/guttman_lab/POLR2A.json --conda

I made the same change in the JSON file for all-POLR2A.bam that helped me to get the tf file all-CTCF.bam to run:

{
    "chip.title" : "Running all-POLR2A.bam through ENCODE",
    "chip.description" : "This is an template input JSON for POLR2A.",

    "chip.pipeline_type" : "tf",
    "chip.nodup_bams" : ["/mnt/c/Users/shirl/Desktop/guttman_lab/all-POLR2A.bam"],
    "chip.ctl_nodup_bams" : ["/mnt/c/Users/shirl/Desktop/guttman_lab/Control_ChIP-seq_hg38_K562.bam"],
    "chip.genome_tsv" : "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv",
    "chip.enable_gc_bias" : false,
    "chip.paired_end" : false,
    "chip.ctl_paired_ends" : [false]
}

However, I still got the error message:

2022-03-07 04:08:01,451|caper.cli|INFO| Cromwell stdout: /home/shirleytemples/chip-seq-pipeline2/cromwell.out.3
2022-03-07 04:08:01,454|caper.caper_base|INFO| Creating a timestamped temporary directory. /home/shirleytemples/chip-seq-pipeline2/.caper_tmp/chip/20220307_040801_453090
2022-03-07 04:08:01,454|caper.caper_runner|INFO| Localizing files on work_dir. /home/shirleytemples/chip-seq-pipeline2/.caper_tmp/chip/20220307_040801_453090
2022-03-07 04:08:01,700|autouri.autouri|INFO| cp: (1e4ed2c7) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/caf534ed3cf684406e731d19be272b4a/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz
2022-03-07 04:08:03,362|autouri.autouri|INFO| cp: (1e4ed2c7) skipped due to name_size_match. size=872949833, mt=1549739698.0
2022-03-07 04:08:03,363|autouri.autouri|INFO| cp: (dbdf3dbd) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only.fasta.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/f43b63a83784d3ec8055f1a22168ed89/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only.fasta.gz
2022-03-07 04:08:03,987|autouri.autouri|INFO| cp: (dbdf3dbd) skipped due to md5_match. md5=05297d96dd1f7cfb45a7b637d6dd7036
2022-03-07 04:08:03,988|autouri.autouri|INFO| cp: (771e91e5) started. src=https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/f183dcba5d34f959d8b55ed438ee2e22/ENCFF356LFX.bed.gz
2022-03-07 04:08:04,723|autouri.autouri|INFO| cp: (771e91e5) skipped due to md5_match. md5=393688b4f06c9ce26165d47433dd8c37
2022-03-07 04:08:05,326|autouri.autouri|INFO| cp: (5798a8ee) started. src=https://www.encodeproject.org/files/GRCh38_EBV.chrom.sizes/@@download/GRCh38_EBV.chrom.sizes.tsv, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/c52f52c7bfa357f55a39b1de7e4d0b0c/GRCh38_EBV.chrom.sizes.tsv
2022-03-07 04:08:05,809|autouri.autouri|INFO| cp: (5798a8ee) skipped due to md5_match. md5=c95303fb77cc3e11d50e3c3a4b93b3fb
2022-03-07 04:08:05,811|autouri.autouri|INFO| cp: (81a35cb0) started. src=https://www.encodeproject.org/files/ENCFF110MCL/@@download/ENCFF110MCL.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/3ff4ac4c3f59d096b1a3842a182072ae/ENCFF110MCL.tar.gz
2022-03-07 04:08:07,433|autouri.autouri|INFO| cp: (81a35cb0) skipped due to name_size_match. size=3749246230, mt=1571469011.0
2022-03-07 04:08:07,435|autouri.autouri|INFO| cp: (808b9fa1) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/df5193e07055d13c48be59bacd0f56b8/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index.tar.gz
2022-03-07 04:08:08,282|autouri.autouri|INFO| cp: (808b9fa1) skipped due to md5_match. md5=80b263f6ea6ff65d547eef07102535db
2022-03-07 04:08:08,283|autouri.autouri|INFO| cp: (1d3e41ad) started. src=https://www.encodeproject.org/files/ENCFF643CGH/@@download/ENCFF643CGH.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/8c692fba4640609720272154ab0faa30/ENCFF643CGH.tar.gz
2022-03-07 04:08:09,778|autouri.autouri|INFO| cp: (1d3e41ad) skipped due to name_size_match. size=4318261891, mt=1549723866.0
2022-03-07 04:08:09,780|autouri.autouri|INFO| cp: (a4d03689) started. src=https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index.tar.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/d3dff25534e93d893902540d81e4f475/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index.tar.gz
2022-03-07 04:08:10,452|autouri.autouri|INFO| cp: (a4d03689) skipped due to md5_match. md5=7e088c24a017a43b1db5e8f50060eec1
2022-03-07 04:08:10,454|autouri.autouri|INFO| cp: (94e2b8f6) started. src=https://www.encodeproject.org/files/ENCFF766FGL/@@download/ENCFF766FGL.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/f16cc7892540d7a9bc3207cc44eb8288/ENCFF766FGL.bed.gz
2022-03-07 04:08:11,212|autouri.autouri|INFO| cp: (94e2b8f6) skipped due to md5_match. md5=d108aa2a392ce5dd207fb8769a6e8240
2022-03-07 04:08:11,214|autouri.autouri|INFO| cp: (616b519e) started. src=https://www.encodeproject.org/files/ENCFF304XEX/@@download/ENCFF304XEX.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/805e179275a9c0fb7a37def40c4312d1/ENCFF304XEX.bed.gz
2022-03-07 04:08:12,578|autouri.autouri|INFO| cp: (616b519e) skipped due to name_size_match. size=14377496, mt=1592463730.0
2022-03-07 04:08:12,579|autouri.autouri|INFO| cp: (afefbc93) started. src=https://www.encodeproject.org/files/ENCFF140XLU/@@download/ENCFF140XLU.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/0cbd2c602ddad252bc39729fc8a29286/ENCFF140XLU.bed.gz
2022-03-07 04:08:13,316|autouri.autouri|INFO| cp: (afefbc93) skipped due to md5_match. md5=91047588129069ff91ec1b0664179f8e
2022-03-07 04:08:13,318|autouri.autouri|INFO| cp: (c81021fa) started. src=https://www.encodeproject.org/files/ENCFF212UAV/@@download/ENCFF212UAV.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/1d3aa436b05f16a509edb94789c061d3/ENCFF212UAV.bed.gz
2022-03-07 04:08:14,933|autouri.autouri|INFO| cp: (c81021fa) skipped due to name_size_match. size=18381891, mt=1592463727.0
2022-03-07 04:08:14,935|autouri.autouri|INFO| cp: (a00d24dc) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/3b39284516e676ea52238f0636c0bbbf/hg38_dnase_avg_fseq_signal_formatted.txt.gz
2022-03-07 04:08:15,341|autouri.autouri|INFO| cp: (a00d24dc) skipped due to md5_match. md5=df624401f76fbd4d651e736068c43a1a
2022-03-07 04:08:15,343|autouri.autouri|INFO| cp: (18128f68) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/c73f434c3fa4f3f54bc2ecad09c065c2/hg38_celltype_compare_subsample.bed.gz
2022-03-07 04:08:15,617|autouri.autouri|INFO| cp: (18128f68) skipped due to md5_match. md5=ced0c653d28628654288f7a8ab052590
2022-03-07 04:08:15,618|autouri.autouri|INFO| cp: (e061ae42) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt, dest=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/a9745b33b4ffdd83d7d2c5a7d3c8036a/hg38_dnase_avg_fseq_signal_metadata.txt
2022-03-07 04:08:15,872|autouri.autouri|INFO| cp: (e061ae42) skipped due to md5_match. md5=3f7fd85ab9a4c6274f28c3e82a79c10d
2022-03-07 04:08:16,515|caper.wdl_parser|ERROR| Failed to parse WDL with miniwdl.
2022-03-07 04:08:16,516|caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/home/shirleytemples/chip-seq-pipeline2/chip.wdl
2022-03-07 04:08:16,526|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool...
2022-03-07 04:08:20,148|caper.cromwell|INFO| Passed Womtool validation.
2022-03-07 04:08:20,151|caper.caper_runner|INFO| launching run: wdl=/home/shirleytemples/chip-seq-pipeline2/chip.wdl, inputs=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/mnt/c/users/shirl/Desktop/guttman_lab/POLR2A.local.json, backend_conf=/home/shirleytemples/chip-seq-pipeline2/.caper_tmp/chip/20220307_040801_453090/backend.conf
2022-03-07 04:08:30,793|caper.cromwell_workflow_monitor|INFO| Workflow: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, status=Submitted
2022-03-07 04:08:30,838|caper.cromwell_workflow_monitor|INFO| Workflow: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, status=Running
2022-03-07 04:08:45,581|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.read_genome_tsv:-1, retry=0, status=Started, job_id=16849
2022-03-07 04:08:45,585|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode
2022-03-07 04:08:47,507|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.read_genome_tsv:-1, retry=0, status=Done
2022-03-07 04:09:00,575|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.bam2ta_ctl:0, retry=0, status=Started, job_id=16915
2022-03-07 04:09:00,577|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.bam2ta:0, retry=0, status=Started, job_id=16913
2022-03-07 04:09:00,578|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.bam2ta:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:09:00,578|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.bam2ta_ctl:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:09:05,570|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.jsd:-1, retry=0, status=Started, job_id=17009
2022-03-07 04:09:05,571|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.jsd:-1, retry=0, status=WaitingForReturnCode
2022-03-07 04:09:10,300|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.bam2ta:0, retry=0, status=Done
2022-03-07 04:09:20,579|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.spr:0, retry=0, status=Started, job_id=17075
2022-03-07 04:09:20,581|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.spr:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:09:25,567|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.xcor:0, retry=0, status=Started, job_id=17125
2022-03-07 04:09:25,568|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.xcor:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:09:31,938|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.spr:0, retry=0, status=Done
2022-03-07 04:10:01,799|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.bam2ta_ctl:0, retry=0, status=Done
2022-03-07 04:10:15,568|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.choose_ctl:-1, retry=0, status=Started, job_id=17268
2022-03-07 04:10:15,569|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.choose_ctl:-1, retry=0, status=WaitingForReturnCode
2022-03-07 04:10:26,088|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.choose_ctl:-1, retry=0, status=Done
2022-03-07 04:10:54,423|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.xcor:0, retry=0, status=Done
2022-03-07 04:11:05,585|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr1:0, retry=0, status=Started, job_id=17419
2022-03-07 04:11:05,586|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.fraglen_mean:-1, retry=0, status=Started, job_id=17376
2022-03-07 04:11:05,587|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr2:0, retry=0, status=Started, job_id=17467
2022-03-07 04:11:05,593|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr2:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:11:05,597|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.fraglen_mean:-1, retry=0, status=WaitingForReturnCode
2022-03-07 04:11:05,607|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr1:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:11:07,806|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.fraglen_mean:-1, retry=0, status=Done
2022-03-07 04:11:10,613|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak:0, retry=0, status=Started, job_id=17520
2022-03-07 04:11:10,615|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.macs2_signal_track:0, retry=0, status=Started, job_id=17567
2022-03-07 04:11:10,616|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.macs2_signal_track:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:11:10,617|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak:0, retry=0, status=WaitingForReturnCode
2022-03-07 04:18:50,862|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.jsd:-1, retry=0, status=Done
2022-03-07 07:12:41,978|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.macs2_signal_track:0, retry=0, status=Done
Exception in thread Thread-5:
2022-03-07 11:08:12,864|caper.cromwell_workflow_monitor|INFO| Workflow: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, status=Failed
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/lib/python3.8/threading.py", line 932, in _bootstrap_inner
2022-03-07 11:55:28,395|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr2:0, retry=0, status=Done
2022-03-07 11:55:28,398|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr2:0, retry=1, status=Started, job_id=18629
2022-03-07 11:55:28,401|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr2:0, retry=1, status=WaitingForReturnCode
2022-03-07 11:55:28,401|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr1:0, retry=0, status=Done
2022-03-07 11:55:28,401|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak:0, retry=0, status=Done
2022-03-07 11:55:28,401|caper.cromwell_workflow_monitor|INFO| Task: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, task=chip.call_peak_pr2:0, retry=1, status=Done
    self.run()
  File "/home/shirleytemples/miniconda3/lib/python3.8/threading.py", line 870, in run
    self._target(*self._args, **self._kwargs)
  File "/home/shirleytemples/miniconda3/lib/python3.8/site-packages/caper/nb_subproc_thread.py", line 186, in read_from_stdout_obj
    for line in iter(stdout.readline, b''):
ValueError: readline of closed file
2022-03-07 11:55:28,438|caper.cromwell_metadata|INFO| Wrote metadata file. /home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/metadata.json
2022-03-07 11:55:28,438|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...
* Started troubleshooting workflow: id=c2323035-49ad-4622-8ba9-c1e5687bb0d8, status=Failed
* Found failures JSON object.
[
    {
        "causedBy": [
            {
                "causedBy": [],
                "message": "Job chip.call_peak_pr2:0:2 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."
            }
        ],
        "message": "Workflow failed"
    }
]
* Recursively finding failures in calls (tasks)...

==== NAME=chip.call_peak_pr2, STATUS=RetryableFailure, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=17467
START=2022-03-07T12:11:04.711Z, END=2022-03-07T17:03:05.623Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-POLR2A.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-POLR2A.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.bb': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/execution/*.bfilt.regionPeak.starch': No such file or directory



==== NAME=chip.call_peak_pr2, STATUS=Failed, PARENT=
SHARD_IDX=0, RC=1, JOB_ID=18629
START=2022-03-07T17:03:06.760Z, END=2022-03-07T19:07:40.511Z
STDOUT=/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/stdout
STDERR=/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/stderr
STDERR_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-POLR2A.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?

STDERR_BACKGROUND_CONTENTS=
Traceback (most recent call last):
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 133, in <module>
    main()
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_spp.py", line 123, in main
    'No peaks found. FDR threshold (fdr_thresh in your input JSON) '
  File "/home/shirleytemples/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 218, in assert_file_not_empty
    raise Exception('File is empty ({}). Help: {}'.format(f, help))
Exception: File is empty (all-POLR2A.pr2_x_Control_ChIP-seq_hg38_K562.300K.regionPeak.gz). Help: No peaks found. FDR threshold (fdr_thresh in your input JSON) might be too stringent or poor quality sample?
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.num_peak.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.peak_region_size.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.peak_region_size.png': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.frip.qc': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.bb': No such file or directory
mkdir: cannot create directory ‘/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/glob-c71d4cca8627aab27dc3503b7db7a39d’: File exists
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.hammock.gz*': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.gz': No such file or directory
ln: failed to access '/home/shirleytemples/chip-seq-pipeline2/chip/c2323035-49ad-4622-8ba9-c1e5687bb0d8/call-call_peak_pr2/shard-0/attempt-2/execution/*.bfilt.regionPeak.starch': No such file or directory


2022-03-07 11:55:28,515|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
2022-03-07 11:55:28,519|caper.cli|ERROR| Check stdout in /home/shirleytemples/chip-seq-pipeline2/cromwell.out.3

I am not sure how to further debug this, any suggestions would be helpful!

@leepc12
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leepc12 commented Mar 14, 2022 •
edited
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How did you align your FASTQs into BAM files (all-CTCF.bam and the control BAM)?

@shirleytemples
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For all-CTCF.bam, the FASTQs were aligned using bowtie2 and I got the control BAM from [ENCFF178EJY] (https://www.encodeproject.org/files/ENCFF178EJY/). The same for all-POLR2A.bam and its control bam.

@leepc12
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leepc12 commented Mar 14, 2022

What reference genome files did you use when you align FASTQs? They should match with files (e.g. FASTA, chromsizes, ...) in the TSV file https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv defined in your input JSON.

$ curl https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv
genome_name     hg38
ref_fa  https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz
ref_mito_fa     https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only.fasta.gz
mito_chr_name   chrM
blacklist       https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz
chrsz   https://www.encodeproject.org/files/GRCh38_EBV.chrom.sizes/@@download/GRCh38_EBV.chrom.sizes.tsv
gensz   hs
bowtie2_idx_tar https://www.encodeproject.org/files/ENCFF110MCL/@@download/ENCFF110MCL.tar.gz
bowtie2_mito_idx_tar    https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bowtie2_index.tar.gz
bwa_idx_tar     https://www.encodeproject.org/files/ENCFF643CGH/@@download/ENCFF643CGH.tar.gz
bwa_mito_idx_tar        https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15_mito_only_bwa_index.tar.gz
tss     https://www.encodeproject.org/files/ENCFF766FGL/@@download/ENCFF766FGL.bed.gz
dnase   https://www.encodeproject.org/files/ENCFF304XEX/@@download/ENCFF304XEX.bed.gz
prom    https://www.encodeproject.org/files/ENCFF140XLU/@@download/ENCFF140XLU.bed.gz
enh     https://www.encodeproject.org/files/ENCFF212UAV/@@download/ENCFF212UAV.bed.gz
reg2map https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz
reg2map_bed     https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz
roadmap_meta    https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt

@leepc12
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leepc12 commented Mar 14, 2022

Also the control https://www.encodeproject.org/files/ENCFF178EJY/ is a single-ended one but chip.ctl_paired_ends : [false] defined in your input JSON. Please change it to chip.ctl_paired_end : false and try again.

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