search

ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
241 stars 123 forks source link

TEST run gave an error. Please help! #265

Closed yingsun-ucsd closed 2 years ago

yingsun-ucsd commented 2 years ago

$ pip install pip --upgrade $ export PATH="/home/ysun/.local/bin:$PATH" $ pip install caper $ pip install caper --upgrade $ caper init local $ git clone https://github.com/ENCODE-DCC/chip-seq-pipeline2 $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh $ bash Miniconda3-latest-Linux-x86_64.sh $ bash Miniconda3-latest-Linux-x86_64.sh -u $ cd chip-seq-pipeline2/ $ conda --version conda 4.11.0 $ caper --version 2.1.3 $ java --version openjdk 11.0.13 2021-10-19 OpenJDK Runtime Environment (build 11.0.13+8-Ubuntu-0ubuntu1.20.04) OpenJDK 64-Bit Server VM (build 11.0.13+8-Ubuntu-0ubuntu1.20.04, mixed mode, sharing) $ python3 --version Python 3.9.7 $ bash scripts/uninstall_conda_env.sh $ bash scripts/install_conda_env.sh $ mkidr /home/ysun/chip-seq-pipeline2-genome/hg38|hg19|mm10|mm9 $ bash scripts/download_genome_data.sh hg38|hg19|mm10|mm9 /home/ysun/chip-seq-pipeline2-genome/hg38|hg19|mm10|mm9

Until this point, everything works fine. Then I tried the example as: THE ERROR HAPPENED AT THIS POINT Debug file attached. Thanks.

$ caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json --conda 2022-02-23 11:57:55,044|caper.cli|INFO| Cromwell stdout: /home/ysun/pipelineTest/cromwell.out 2022-02-23 11:57:55,045|caper.caper_base|INFO| Creating a timestamped temporary directory. /home/ysun/pipelineTest/.caper_tmp/chip/20220223_115755_045003 2022-02-23 11:57:55,045|caper.caper_runner|INFO| Localizing files on work_dir. /home/ysun/pipelineTest/.caper_tmp/chip/20220223_115755_045003 2022-02-23 11:57:55,234|autouri.autouri|INFO| cp: (bb9e1351) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.gz, dest=/home/ysun/pipelineTest/.caper_tmp/dcc664bb3e886aa9127f3bd8522bff3c/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.gz 2022-02-23 11:57:55,350|autouri.autouri|INFO| cp: (bb9e1351) skipped due to md5_match. md5=fbd798407e251364cf52712b461de7bd 2022-02-23 11:57:55,352|autouri.autouri|INFO| cp: (49b1efdb) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.gz, dest=/home/ysun/pipelineTest/.caper_tmp/be275eb60876cf28f4600fb8589afe42/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.gz 2022-02-23 11:57:55,481|autouri.autouri|INFO| cp: (49b1efdb) skipped due to md5_match. md5=05297d96dd1f7cfb45a7b637d6dd7036 2022-02-23 11:57:55,483|autouri.autouri|INFO| cp: (bf4404e0) started. src=https://www.encodeproject.org/files/ENCFF547MET/@@download/ENCFF547MET.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/da42a1c4b0f9d3225600da56b2c9571d/ENCFF547MET.bed.gz 2022-02-23 11:57:55,937|autouri.autouri|INFO| cp: (bf4404e0) skipped due to md5_match. md5=5d19eeb4197ae10540252c61399f3131 2022-02-23 11:57:55,939|autouri.autouri|INFO| cp: (1a966ac4) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes, dest=/home/ysun/pipelineTest/.caper_tmp/f0e538218d74ce7a3850c9605caf2e23/hg38_chr19_chrM.chrom.sizes 2022-02-23 11:57:56,084|autouri.autouri|INFO| cp: (1a966ac4) skipped due to md5_match. md5=a068b95e53225dfb124590e10697d692 2022-02-23 11:57:56,085|autouri.autouri|INFO| cp: (70c34d06) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar, dest=/home/ysun/pipelineTest/.caper_tmp/7b07a4b54cf5f715b174d8e9164d7d9c/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar 2022-02-23 11:57:56,191|autouri.autouri|INFO| cp: (70c34d06) skipped due to md5_match. md5=22f0a7a6c0496b39f329f414fb192f75 2022-02-23 11:57:56,193|autouri.autouri|INFO| cp: (027e571a) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar, dest=/home/ysun/pipelineTest/.caper_tmp/b44489aed009d7741fd44131dcc6b7c8/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar 2022-02-23 11:57:56,295|autouri.autouri|INFO| cp: (027e571a) skipped due to md5_match. md5=c1b0155acebcd0f4d81ca79e8ec8bc79 2022-02-23 11:57:56,296|autouri.autouri|INFO| cp: (5ab45ce5) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar, dest=/home/ysun/pipelineTest/.caper_tmp/542354fad05fedb3cae8c97381031035/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar 2022-02-23 11:57:56,406|autouri.autouri|INFO| cp: (5ab45ce5) skipped due to md5_match. md5=d13bc228457d7b5347383658d1c2c4e8 2022-02-23 11:57:56,408|autouri.autouri|INFO| cp: (c409bf1a) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar, dest=/home/ysun/pipelineTest/.caper_tmp/9b649793fb593506a76c3141180ea657/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar 2022-02-23 11:57:56,520|autouri.autouri|INFO| cp: (c409bf1a) skipped due to md5_match. md5=d7a5706a25bcd14874cac8e24b006e22 2022-02-23 11:57:56,521|autouri.autouri|INFO| cp: (27437b3a) started. src=https://www.encodeproject.org/files/ENCFF493CCB/@@download/ENCFF493CCB.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/0fa7d04b32e66fa02fb2c1ae39e41447/ENCFF493CCB.bed.gz 2022-02-23 11:57:56,912|autouri.autouri|INFO| cp: (27437b3a) skipped due to md5_match. md5=aca8cf959206aa3ad257fc46dc783266 2022-02-23 11:57:56,913|autouri.autouri|INFO| cp: (db11863a) started. src=https://www.encodeproject.org/files/ENCFF304XEX/@@download/ENCFF304XEX.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/805e179275a9c0fb7a37def40c4312d1/ENCFF304XEX.bed.gz 2022-02-23 11:57:57,532|autouri.autouri|INFO| cp: (db11863a) skipped due to name_size_match. size=14377496, mt=1592463730.0 2022-02-23 11:57:57,534|autouri.autouri|INFO| cp: (614823a1) started. src=https://www.encodeproject.org/files/ENCFF140XLU/@@download/ENCFF140XLU.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/0cbd2c602ddad252bc39729fc8a29286/ENCFF140XLU.bed.gz 2022-02-23 11:57:57,941|autouri.autouri|INFO| cp: (614823a1) skipped due to md5_match. md5=91047588129069ff91ec1b0664179f8e 2022-02-23 11:57:57,943|autouri.autouri|INFO| cp: (1902bc93) started. src=https://www.encodeproject.org/files/ENCFF212UAV/@@download/ENCFF212UAV.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/1d3aa436b05f16a509edb94789c061d3/ENCFF212UAV.bed.gz 2022-02-23 11:57:58,646|autouri.autouri|INFO| cp: (1902bc93) skipped due to name_size_match. size=18381891, mt=1592463727.0 2022-02-23 11:57:58,648|autouri.autouri|INFO| cp: (783bb7e1) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz, dest=/home/ysun/pipelineTest/.caper_tmp/3b39284516e676ea52238f0636c0bbbf/hg38_dnase_avg_fseq_signal_formatted.txt.gz 2022-02-23 11:57:58,751|autouri.autouri|INFO| cp: (783bb7e1) skipped due to md5_match. md5=df624401f76fbd4d651e736068c43a1a 2022-02-23 11:57:58,752|autouri.autouri|INFO| cp: (2aaeccad) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/c73f434c3fa4f3f54bc2ecad09c065c2/hg38_celltype_compare_subsample.bed.gz 2022-02-23 11:57:58,937|autouri.autouri|INFO| cp: (2aaeccad) skipped due to md5_match. md5=ced0c653d28628654288f7a8ab052590 2022-02-23 11:57:58,938|autouri.autouri|INFO| cp: (36c97462) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt, dest=/home/ysun/pipelineTest/.caper_tmp/a9745b33b4ffdd83d7d2c5a7d3c8036a/hg38_dnase_avg_fseq_signal_metadata.txt 2022-02-23 11:57:59,048|autouri.autouri|INFO| cp: (36c97462) skipped due to md5_match. md5=3f7fd85ab9a4c6274f28c3e82a79c10d 2022-02-23 11:57:59,050|autouri.autouri|INFO| cp: (c180d00a) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/rep1.subsampled.25.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/41d3a8658bf4f565c08290e386fddccf/rep1.subsampled.25.fastq.gz 2022-02-23 11:57:59,161|autouri.autouri|INFO| cp: (c180d00a) skipped due to md5_match. md5=212ac7a69357df3df077177b44c8cdf0 2022-02-23 11:57:59,162|autouri.autouri|INFO| cp: (fe7084ff) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/rep2.subsampled.20.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/0d5b102d7f21dd009798ae9b2c318b65/rep2.subsampled.20.fastq.gz 2022-02-23 11:57:59,272|autouri.autouri|INFO| cp: (fe7084ff) skipped due to md5_match. md5=4df1a7e6a3a299f6a2355d93b54db48a 2022-02-23 11:57:59,273|autouri.autouri|INFO| cp: (b041e76e) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/ctl1.subsampled.25.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/f4dba75d4430f4702a75554c44265119/ctl1.subsampled.25.fastq.gz 2022-02-23 11:57:59,382|autouri.autouri|INFO| cp: (b041e76e) skipped due to md5_match. md5=3ad89622e0b1269606575d305c5350ef 2022-02-23 11:57:59,383|autouri.autouri|INFO| cp: (78a17723) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/ctl2.subsampled.25.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/7a610dd5397c45a806678efaad824abf/ctl2.subsampled.25.fastq.gz 2022-02-23 11:57:59,487|autouri.autouri|INFO| cp: (78a17723) skipped due to md5_match. md5=b2a184523015df11edf3c670f07e1ed4 2022-02-23 11:58:00,316|caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/home/ysun/pipelineTest/chip.wdl 2022-02-23 11:58:00,320|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool... 2022-02-23 11:58:03,566|caper.cromwell|INFO| Passed Womtool validation. 2022-02-23 11:58:03,567|caper.caper_runner|INFO| launching run: wdl=/home/ysun/pipelineTest/chip.wdl, inputs=/home/ysun/pipelineTest/.caper_tmp/15b4ff439de58d859f4c3ee4482c3bd2/ENCSR000DYI_subsampled_chr19_only.local.json, backend_conf=/home/ysun/pipelineTest/.caper_tmp/chip/20220223_115755_045003/backend.conf 2022-02-23 11:58:12,112|caper.cromwell_workflow_monitor|INFO| Workflow: id=71cc675c-d6a9-493a-b9af-0170726153a3, status=Submitted 2022-02-23 11:58:12,194|caper.cromwell_workflow_monitor|INFO| Workflow: id=71cc675c-d6a9-493a-b9af-0170726153a3, status=Running 2022-02-23 11:58:26,977|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.read_genome_tsv:-1, retry=0, status=Started, job_id=3576061 2022-02-23 11:58:26,983|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode 2022-02-23 11:58:28,966|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.read_genome_tsv:-1, retry=0, status=Done 2022-02-23 11:58:36,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align:1, retry=0, status=Started, job_id=3576208 2022-02-23 11:58:36,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align:0, retry=0, status=Started, job_id=3576162 2022-02-23 11:58:36,961|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:58:36,961|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:58:41,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_R1:1, retry=0, status=Started, job_id=3576315 2022-02-23 11:58:41,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_R1:0, retry=0, status=Started, job_id=3576270 2022-02-23 11:58:41,961|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_R1:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:58:41,961|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_R1:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:58:46,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_ctl:0, retry=0, status=Started, job_id=3576362 2022-02-23 11:58:46,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_ctl:1, retry=0, status=Started, job_id=3576412 2022-02-23 11:58:46,961|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_ctl:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:58:46,961|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_ctl:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:13,415|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align:1, retry=0, status=Done 2022-02-23 11:59:15,695|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_ctl:0, retry=0, status=Done 2022-02-23 11:59:16,645|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align:0, retry=0, status=Done 2022-02-23 11:59:24,544|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_R1:1, retry=0, status=Done 2022-02-23 11:59:26,215|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_ctl:1, retry=0, status=Done 2022-02-23 11:59:26,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_ctl:0, retry=0, status=Started, job_id=3577264 2022-02-23 11:59:26,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter:1, retry=0, status=Started, job_id=3577152 2022-02-23 11:59:26,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter:0, retry=0, status=Started, job_id=3577375 2022-02-23 11:59:26,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:26,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_ctl:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:26,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:28,604|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.align_R1:0, retry=0, status=Done 2022-02-23 11:59:31,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_R1:1, retry=0, status=Started, job_id=3577645 2022-02-23 11:59:31,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_R1:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:33,995|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter:1, retry=0, status=Done 2022-02-23 11:59:34,094|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_ctl:0, retry=0, status=Done 2022-02-23 11:59:36,956|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_ctl:1, retry=0, status=Started, job_id=3577949 2022-02-23 11:59:36,956|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_R1:0, retry=0, status=Started, job_id=3577786 2022-02-23 11:59:36,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_R1:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:36,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_ctl:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:37,534|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter:0, retry=0, status=Done 2022-02-23 11:59:42,864|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_R1:1, retry=0, status=Done 2022-02-23 11:59:43,285|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_R1:0, retry=0, status=Done 2022-02-23 11:59:44,795|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.filter_ctl:1, retry=0, status=Done 2022-02-23 11:59:46,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_ctl:0, retry=0, status=Started, job_id=3578311 2022-02-23 11:59:46,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.gc_bias:1, retry=0, status=Started, job_id=3578365 2022-02-23 11:59:46,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta:1, retry=0, status=Started, job_id=3578563 2022-02-23 11:59:46,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_ctl:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:46,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:46,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.gc_bias:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:48,455|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_ctl:0, retry=0, status=Done 2022-02-23 11:59:51,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta:0, retry=0, status=Started, job_id=3578627 2022-02-23 11:59:51,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.gc_bias:0, retry=0, status=Started, job_id=3578702 2022-02-23 11:59:51,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:51,960|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.gc_bias:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:53,144|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta:1, retry=0, status=Done 2022-02-23 11:59:54,964|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta:0, retry=0, status=Done 2022-02-23 11:59:56,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_no_dedup_R1:1, retry=0, status=Started, job_id=3578949 2022-02-23 11:59:56,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.jsd:-1, retry=0, status=Started, job_id=3579034 2022-02-23 11:59:56,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_no_dedup_R1:0, retry=0, status=Started, job_id=3578887 2022-02-23 11:59:56,963|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_no_dedup_R1:1, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:56,963|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_no_dedup_R1:0, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:56,963|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.jsd:-1, retry=0, status=WaitingForReturnCode 2022-02-23 11:59:57,735|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.gc_bias:1, retry=0, status=Done 2022-02-23 11:59:58,944|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_no_dedup_R1:0, retry=0, status=Done 2022-02-23 12:00:01,194|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_no_dedup_R1:1, retry=0, status=Done 2022-02-23 12:00:01,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.spr:1, retry=0, status=Started, job_id=3579209 2022-02-23 12:00:01,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_ctl:1, retry=0, status=Started, job_id=3579136 2022-02-23 12:00:01,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.spr:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:01,960|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_ctl:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:03,061|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.gc_bias:0, retry=0, status=Done 2022-02-23 12:00:05,085|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.bam2ta_ctl:1, retry=0, status=Done 2022-02-23 12:00:06,674|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.spr:1, retry=0, status=Done 2022-02-23 12:00:06,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta:-1, retry=0, status=Started, job_id=3579381 2022-02-23 12:00:06,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.spr:0, retry=0, status=Started, job_id=3579299 2022-02-23 12:00:06,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:06,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.spr:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:10,935|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.spr:0, retry=0, status=Done 2022-02-23 12:00:11,956|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:0, retry=0, status=Started, job_id=3579442 2022-02-23 12:00:11,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:13,904|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta:-1, retry=0, status=Done 2022-02-23 12:00:16,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:1, retry=0, status=Started, job_id=3579521 2022-02-23 12:00:16,957|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_ctl:-1, retry=0, status=Started, job_id=3579612 2022-02-23 12:00:16,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_ctl:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:16,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:17,754|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:0, retry=0, status=Done 2022-02-23 12:00:20,354|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:1, retry=0, status=Done 2022-02-23 12:00:21,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_pr2:-1, retry=0, status=Started, job_id=3579686 2022-02-23 12:00:21,960|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_pr2:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:22,314|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_ctl:-1, retry=0, status=Done 2022-02-23 12:00:26,504|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_pr2:-1, retry=0, status=Done 2022-02-23 12:00:26,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_pr1:-1, retry=0, status=Started, job_id=3579747 2022-02-23 12:00:26,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:1, retry=1, status=Started, job_id=3579800 2022-02-23 12:00:26,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:0, retry=1, status=Started, job_id=3579874 2022-02-23 12:00:26,959|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:0, retry=1, status=WaitingForReturnCode 2022-02-23 12:00:26,960|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:1, retry=1, status=WaitingForReturnCode 2022-02-23 12:00:26,960|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_pr1:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:28,074|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.pool_ta_pr1:-1, retry=0, status=Done 2022-02-23 12:00:31,524|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:1, retry=1, status=Done 2022-02-23 12:00:31,956|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.choose_ctl:-1, retry=0, status=Started, job_id=3579953 2022-02-23 12:00:31,958|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.choose_ctl:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:00:32,155|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.xcor:0, retry=1, status=Done 2022-02-23 12:00:35,137|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.choose_ctl:-1, retry=0, status=Done 2022-02-23 12:02:44,105|caper.cromwell_workflow_monitor|INFO| Task: id=71cc675c-d6a9-493a-b9af-0170726153a3, task=chip.jsd:-1, retry=0, status=Done 2022-02-23 12:02:45,423|caper.cromwell_workflow_monitor|INFO| Workflow: id=71cc675c-d6a9-493a-b9af-0170726153a3, status=Failed 2022-02-23 12:03:13,157|caper.cromwell_metadata|INFO| Wrote metadata file. /home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/metadata.json 2022-02-23 12:03:13,157|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...

==== NAME=chip.xcor, STATUS=RetryableFailure, PARENT= SHARD_IDX=0, RC=1, JOB_ID=3579442 START=2022-02-23T20:00:10.027Z, END=2022-02-23T20:00:21.965Z STDOUT=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/execution/stdout STDERR=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579494, PGID=3579494, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579494, PGID=3579494, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/execution/.cc.qc': No such file or directory

==== NAME=chip.xcor, STATUS=Failed, PARENT= SHARD_IDX=0, RC=1, JOB_ID=3579874 START=2022-02-23T20:00:26.013Z, END=2022-02-23T20:00:32.159Z STDOUT=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/attempt-2/execution/stdout STDERR=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/attempt-2/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579930, PGID=3579930, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579930, PGID=3579930, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/attempt-2/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/attempt-2/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/attempt-2/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-0/attempt-2/execution/.cc.qc': No such file or directory

==== NAME=chip.xcor, STATUS=RetryableFailure, PARENT= SHARD_IDX=1, RC=1, JOB_ID=3579521 START=2022-02-23T20:00:14.019Z, END=2022-02-23T20:00:21.965Z STDOUT=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/execution/stdout STDERR=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579574, PGID=3579574, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579574, PGID=3579574, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/execution/.cc.qc': No such file or directory

==== NAME=chip.xcor, STATUS=Failed, PARENT= SHARD_IDX=1, RC=1, JOB_ID=3579800 START=2022-02-23T20:00:24.012Z, END=2022-02-23T20:00:31.528Z STDOUT=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/attempt-2/execution/stdout STDERR=/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/attempt-2/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579852, PGID=3579852, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3579852, PGID=3579852, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/attempt-2/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/attempt-2/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/attempt-2/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/71cc675c-d6a9-493a-b9af-0170726153a3/call-xcor/shard-1/attempt-2/execution/.cc.qc': No such file or directory

cromwell.txt

leepc12 commented 2 years ago

This looks like pipeline's Conda env installer issue. I will fix it in the next release. Until then please run the following to manually install ncurses version 5.

$ conda install -n encode-chip-seq-pipeline-spp --no-deps --no-update-deps -y ncurses==5.9 -c conda-forge

Please ignore all warnings and let me know if it works.

yingsun-ucsd commented 2 years ago

Here was what I did. It looked like before. Should I do anything else before the test run? New debug file attached too. Thank you!

$ conda install -n encode-chip-seq-pipeline-spp --no-deps --no-update-deps -y ncurses==5.9 -c conda-forge LOGOUT LOGIN $ cd chip-seq-pipeline2/ $ bash scripts/uninstall_conda_env.sh $ bash scripts/install_conda_env.sh LOGOUT LOGIN $ caper run chip.wdl -i https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json --conda

2022-02-23 12:48:24,378|caper.cli|INFO| Cromwell stdout: /home/ysun/pipelineTest/cromwell.out 2022-02-23 12:48:24,379|caper.caper_base|INFO| Creating a timestamped temporary directory. /home/ysun/pipelineTest/.caper_tmp/chip/20220223_124824_379319 2022-02-23 12:48:24,379|caper.caper_runner|INFO| Localizing files on work_dir. /home/ysun/pipelineTest/.caper_tmp/chip/20220223_124824_379319 2022-02-23 12:48:24,577|autouri.autouri|INFO| cp: (69593d5a) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.gz, dest=/home/ysun/pipelineTest/.caper_tmp/dcc664bb3e886aa9127f3bd8522bff3c/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.gz 2022-02-23 12:48:24,872|autouri.autouri|INFO| cp: (69593d5a) skipped due to md5_match. md5=fbd798407e251364cf52712b461de7bd 2022-02-23 12:48:24,873|autouri.autouri|INFO| cp: (313e9ea1) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.gz, dest=/home/ysun/pipelineTest/.caper_tmp/be275eb60876cf28f4600fb8589afe42/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.gz 2022-02-23 12:48:24,903|autouri.autouri|INFO| cp: (313e9ea1) skipped due to md5_match. md5=05297d96dd1f7cfb45a7b637d6dd7036 2022-02-23 12:48:24,903|autouri.autouri|INFO| cp: (6093c5dd) started. src=https://www.encodeproject.org/files/ENCFF547MET/@@download/ENCFF547MET.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/da42a1c4b0f9d3225600da56b2c9571d/ENCFF547MET.bed.gz 2022-02-23 12:48:25,315|autouri.autouri|INFO| cp: (6093c5dd) skipped due to md5_match. md5=5d19eeb4197ae10540252c61399f3131 2022-02-23 12:48:25,316|autouri.autouri|INFO| cp: (36769306) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes, dest=/home/ysun/pipelineTest/.caper_tmp/f0e538218d74ce7a3850c9605caf2e23/hg38_chr19_chrM.chrom.sizes 2022-02-23 12:48:25,346|autouri.autouri|INFO| cp: (36769306) skipped due to md5_match. md5=a068b95e53225dfb124590e10697d692 2022-02-23 12:48:25,347|autouri.autouri|INFO| cp: (c722e214) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar, dest=/home/ysun/pipelineTest/.caper_tmp/7b07a4b54cf5f715b174d8e9164d7d9c/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar 2022-02-23 12:48:25,471|autouri.autouri|INFO| cp: (c722e214) skipped due to md5_match. md5=22f0a7a6c0496b39f329f414fb192f75 2022-02-23 12:48:25,472|autouri.autouri|INFO| cp: (b5bc7ef9) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar, dest=/home/ysun/pipelineTest/.caper_tmp/b44489aed009d7741fd44131dcc6b7c8/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar 2022-02-23 12:48:25,640|autouri.autouri|INFO| cp: (b5bc7ef9) skipped due to md5_match. md5=c1b0155acebcd0f4d81ca79e8ec8bc79 2022-02-23 12:48:25,641|autouri.autouri|INFO| cp: (deb867ca) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar, dest=/home/ysun/pipelineTest/.caper_tmp/542354fad05fedb3cae8c97381031035/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar 2022-02-23 12:48:25,762|autouri.autouri|INFO| cp: (deb867ca) skipped due to md5_match. md5=d13bc228457d7b5347383658d1c2c4e8 2022-02-23 12:48:25,763|autouri.autouri|INFO| cp: (ce0020cf) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar, dest=/home/ysun/pipelineTest/.caper_tmp/9b649793fb593506a76c3141180ea657/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.chrM.fa.tar 2022-02-23 12:48:25,791|autouri.autouri|INFO| cp: (ce0020cf) skipped due to md5_match. md5=d7a5706a25bcd14874cac8e24b006e22 2022-02-23 12:48:25,792|autouri.autouri|INFO| cp: (eecb52f7) started. src=https://www.encodeproject.org/files/ENCFF493CCB/@@download/ENCFF493CCB.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/0fa7d04b32e66fa02fb2c1ae39e41447/ENCFF493CCB.bed.gz 2022-02-23 12:48:26,245|autouri.autouri|INFO| cp: (eecb52f7) skipped due to md5_match. md5=aca8cf959206aa3ad257fc46dc783266 2022-02-23 12:48:26,247|autouri.autouri|INFO| cp: (2b6c0b08) started. src=https://www.encodeproject.org/files/ENCFF304XEX/@@download/ENCFF304XEX.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/805e179275a9c0fb7a37def40c4312d1/ENCFF304XEX.bed.gz 2022-02-23 12:48:26,865|autouri.autouri|INFO| cp: (2b6c0b08) skipped due to name_size_match. size=14377496, mt=1592463730.0 2022-02-23 12:48:26,867|autouri.autouri|INFO| cp: (695689bc) started. src=https://www.encodeproject.org/files/ENCFF140XLU/@@download/ENCFF140XLU.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/0cbd2c602ddad252bc39729fc8a29286/ENCFF140XLU.bed.gz 2022-02-23 12:48:27,232|autouri.autouri|INFO| cp: (695689bc) skipped due to md5_match. md5=91047588129069ff91ec1b0664179f8e 2022-02-23 12:48:27,234|autouri.autouri|INFO| cp: (5ee69075) started. src=https://www.encodeproject.org/files/ENCFF212UAV/@@download/ENCFF212UAV.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/1d3aa436b05f16a509edb94789c061d3/ENCFF212UAV.bed.gz 2022-02-23 12:48:27,820|autouri.autouri|INFO| cp: (5ee69075) skipped due to name_size_match. size=18381891, mt=1592463727.0 2022-02-23 12:48:27,822|autouri.autouri|INFO| cp: (4e56099f) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz, dest=/home/ysun/pipelineTest/.caper_tmp/3b39284516e676ea52238f0636c0bbbf/hg38_dnase_avg_fseq_signal_formatted.txt.gz 2022-02-23 12:48:28,009|autouri.autouri|INFO| cp: (4e56099f) skipped due to md5_match. md5=df624401f76fbd4d651e736068c43a1a 2022-02-23 12:48:28,011|autouri.autouri|INFO| cp: (f11b6128) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz, dest=/home/ysun/pipelineTest/.caper_tmp/c73f434c3fa4f3f54bc2ecad09c065c2/hg38_celltype_compare_subsample.bed.gz 2022-02-23 12:48:28,188|autouri.autouri|INFO| cp: (f11b6128) skipped due to md5_match. md5=ced0c653d28628654288f7a8ab052590 2022-02-23 12:48:28,189|autouri.autouri|INFO| cp: (99db00d0) started. src=https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt, dest=/home/ysun/pipelineTest/.caper_tmp/a9745b33b4ffdd83d7d2c5a7d3c8036a/hg38_dnase_avg_fseq_signal_metadata.txt 2022-02-23 12:48:28,222|autouri.autouri|INFO| cp: (99db00d0) skipped due to md5_match. md5=3f7fd85ab9a4c6274f28c3e82a79c10d 2022-02-23 12:48:28,223|autouri.autouri|INFO| cp: (6905f1d4) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/rep1.subsampled.25.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/41d3a8658bf4f565c08290e386fddccf/rep1.subsampled.25.fastq.gz 2022-02-23 12:48:28,494|autouri.autouri|INFO| cp: (6905f1d4) skipped due to md5_match. md5=212ac7a69357df3df077177b44c8cdf0 2022-02-23 12:48:28,495|autouri.autouri|INFO| cp: (bab26e92) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/rep2.subsampled.20.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/0d5b102d7f21dd009798ae9b2c318b65/rep2.subsampled.20.fastq.gz 2022-02-23 12:48:28,628|autouri.autouri|INFO| cp: (bab26e92) skipped due to md5_match. md5=4df1a7e6a3a299f6a2355d93b54db48a 2022-02-23 12:48:28,629|autouri.autouri|INFO| cp: (71e1e0dd) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/ctl1.subsampled.25.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/f4dba75d4430f4702a75554c44265119/ctl1.subsampled.25.fastq.gz 2022-02-23 12:48:28,927|autouri.autouri|INFO| cp: (71e1e0dd) skipped due to md5_match. md5=3ad89622e0b1269606575d305c5350ef 2022-02-23 12:48:28,928|autouri.autouri|INFO| cp: (13bc80c6) started. src=https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI/fastq_subsampled/ctl2.subsampled.25.fastq.gz, dest=/home/ysun/pipelineTest/.caper_tmp/7a610dd5397c45a806678efaad824abf/ctl2.subsampled.25.fastq.gz 2022-02-23 12:48:29,056|autouri.autouri|INFO| cp: (13bc80c6) skipped due to md5_match. md5=b2a184523015df11edf3c670f07e1ed4 2022-02-23 12:48:29,781|caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/home/ysun/pipelineTest/chip.wdl 2022-02-23 12:48:29,784|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool... 2022-02-23 12:48:32,815|caper.cromwell|INFO| Passed Womtool validation. 2022-02-23 12:48:32,816|caper.caper_runner|INFO| launching run: wdl=/home/ysun/pipelineTest/chip.wdl, inputs=/home/ysun/pipelineTest/.caper_tmp/15b4ff439de58d859f4c3ee4482c3bd2/ENCSR000DYI_subsampled_chr19_only.local.json, backend_conf=/home/ysun/pipelineTest/.caper_tmp/chip/20220223_124824_379319/backend.conf 2022-02-23 12:48:40,974|caper.cromwell_workflow_monitor|INFO| Workflow: id=9e218900-f98a-41ef-9222-685795cafbc4, status=Submitted 2022-02-23 12:48:41,085|caper.cromwell_workflow_monitor|INFO| Workflow: id=9e218900-f98a-41ef-9222-685795cafbc4, status=Running 2022-02-23 12:48:55,881|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.read_genome_tsv:-1, retry=0, status=Started, job_id=3591500 2022-02-23 12:48:55,887|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.read_genome_tsv:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:48:57,502|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.read_genome_tsv:-1, retry=0, status=Done 2022-02-23 12:49:05,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_ctl:1, retry=0, status=Started, job_id=3591574 2022-02-23 12:49:05,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align:0, retry=0, status=Started, job_id=3591621 2022-02-23 12:49:05,868|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:05,868|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_ctl:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:10,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_ctl:0, retry=0, status=Started, job_id=3591671 2022-02-23 12:49:10,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align:1, retry=0, status=Started, job_id=3591717 2022-02-23 12:49:10,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_ctl:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:10,867|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:15,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_R1:1, retry=0, status=Started, job_id=3591829 2022-02-23 12:49:15,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_R1:0, retry=0, status=Started, job_id=3591767 2022-02-23 12:49:15,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_R1:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:15,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_R1:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:40,141|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_ctl:1, retry=0, status=Done 2022-02-23 12:49:41,281|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_ctl:0, retry=0, status=Done 2022-02-23 12:49:46,891|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align:0, retry=0, status=Done 2022-02-23 12:49:48,681|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align:1, retry=0, status=Done 2022-02-23 12:49:50,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_ctl:1, retry=0, status=Started, job_id=3592485 2022-02-23 12:49:50,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_ctl:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:55,341|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_R1:1, retry=0, status=Done 2022-02-23 12:49:55,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter:0, retry=0, status=Started, job_id=3592771 2022-02-23 12:49:55,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_ctl:0, retry=0, status=Started, job_id=3592655 2022-02-23 12:49:55,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:55,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_ctl:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:49:57,181|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.align_R1:0, retry=0, status=Done 2022-02-23 12:49:58,450|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_ctl:1, retry=0, status=Done 2022-02-23 12:50:00,580|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_ctl:0, retry=0, status=Done 2022-02-23 12:50:00,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter:1, retry=0, status=Started, job_id=3593026 2022-02-23 12:50:00,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_R1:1, retry=0, status=Started, job_id=3593183 2022-02-23 12:50:00,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:00,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_R1:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:05,240|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter:0, retry=0, status=Done 2022-02-23 12:50:05,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_R1:0, retry=0, status=Started, job_id=3593318 2022-02-23 12:50:05,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_ctl:1, retry=0, status=Started, job_id=3593603 2022-02-23 12:50:05,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_R1:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:05,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_ctl:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:07,941|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter:1, retry=0, status=Done 2022-02-23 12:50:10,862|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_ctl:0, retry=0, status=Started, job_id=3593710 2022-02-23 12:50:10,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_ctl:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:11,791|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_R1:0, retry=0, status=Done 2022-02-23 12:50:12,061|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.filter_R1:1, retry=0, status=Done 2022-02-23 12:50:12,571|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_ctl:1, retry=0, status=Done 2022-02-23 12:50:15,821|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_ctl:0, retry=0, status=Done 2022-02-23 12:50:15,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta:0, retry=0, status=Started, job_id=3593830 2022-02-23 12:50:15,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:20,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_no_dedup_R1:1, retry=0, status=Started, job_id=3594057 2022-02-23 12:50:20,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.gc_bias:0, retry=0, status=Started, job_id=3593884 2022-02-23 12:50:20,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.gc_bias:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:20,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_no_dedup_R1:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:21,221|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta:0, retry=0, status=Done 2022-02-23 12:50:25,690|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_no_dedup_R1:1, retry=0, status=Done 2022-02-23 12:50:25,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_no_dedup_R1:0, retry=0, status=Started, job_id=3594119 2022-02-23 12:50:25,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.gc_bias:1, retry=0, status=Started, job_id=3594253 2022-02-23 12:50:25,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta:1, retry=0, status=Started, job_id=3594192 2022-02-23 12:50:25,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.gc_bias:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:25,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_no_dedup_R1:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:25,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:27,151|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta_no_dedup_R1:0, retry=0, status=Done 2022-02-23 12:50:28,530|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.gc_bias:0, retry=0, status=Done 2022-02-23 12:50:28,851|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.bam2ta:1, retry=0, status=Done 2022-02-23 12:50:30,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.jsd:-1, retry=0, status=Started, job_id=3594435 2022-02-23 12:50:30,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_ctl:-1, retry=0, status=Started, job_id=3594546 2022-02-23 12:50:30,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_ctl:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:30,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.jsd:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:35,301|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_ctl:-1, retry=0, status=Done 2022-02-23 12:50:35,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.spr:0, retry=0, status=Started, job_id=3594623 2022-02-23 12:50:35,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.spr:1, retry=0, status=Started, job_id=3594701 2022-02-23 12:50:35,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.spr:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:35,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.spr:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:37,290|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.spr:0, retry=0, status=Done 2022-02-23 12:50:38,300|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.gc_bias:1, retry=0, status=Done 2022-02-23 12:50:40,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta:-1, retry=0, status=Started, job_id=3594862 2022-02-23 12:50:40,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:1, retry=0, status=Started, job_id=3594795 2022-02-23 12:50:40,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:40,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:41,551|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.spr:1, retry=0, status=Done 2022-02-23 12:50:43,200|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:1, retry=0, status=Done 2022-02-23 12:50:45,111|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta:-1, retry=0, status=Done 2022-02-23 12:50:45,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:0, retry=0, status=Started, job_id=3594922 2022-02-23 12:50:45,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:0, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:47,080|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:0, retry=0, status=Done 2022-02-23 12:50:50,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:1, retry=1, status=Started, job_id=3595045 2022-02-23 12:50:50,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:1, retry=1, status=WaitingForReturnCode 2022-02-23 12:50:53,780|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:1, retry=1, status=Done 2022-02-23 12:50:55,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_pr2:-1, retry=0, status=Started, job_id=3595197 2022-02-23 12:50:55,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_pr1:-1, retry=0, status=Started, job_id=3595246 2022-02-23 12:50:55,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.choose_ctl:-1, retry=0, status=Started, job_id=3595113 2022-02-23 12:50:55,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_pr2:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:55,865|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_pr1:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:55,866|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.choose_ctl:-1, retry=0, status=WaitingForReturnCode 2022-02-23 12:50:56,890|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.choose_ctl:-1, retry=0, status=Done 2022-02-23 12:50:59,411|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_pr2:-1, retry=0, status=Done 2022-02-23 12:51:00,863|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:0, retry=1, status=Started, job_id=3595311 2022-02-23 12:51:00,864|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:0, retry=1, status=WaitingForReturnCode 2022-02-23 12:51:01,750|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.pool_ta_pr1:-1, retry=0, status=Done 2022-02-23 12:51:03,360|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.xcor:0, retry=1, status=Done 2022-02-23 12:53:13,411|caper.cromwell_workflow_monitor|INFO| Task: id=9e218900-f98a-41ef-9222-685795cafbc4, task=chip.jsd:-1, retry=0, status=Done 2022-02-23 12:53:14,381|caper.cromwell_workflow_monitor|INFO| Workflow: id=9e218900-f98a-41ef-9222-685795cafbc4, status=Failed 2022-02-23 12:54:11,968|caper.cromwell_metadata|INFO| Wrote metadata file. /home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/metadata.json 2022-02-23 12:54:11,968|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...

==== NAME=chip.xcor, STATUS=RetryableFailure, PARENT= SHARD_IDX=0, RC=1, JOB_ID=3594922 START=2022-02-23T20:50:40.932Z, END=2022-02-23T20:50:50.864Z STDOUT=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/execution/stdout STDERR=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3594974, PGID=3594974, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3594974, PGID=3594974, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/execution/.cc.qc': No such file or directory

==== NAME=chip.xcor, STATUS=Failed, PARENT= SHARD_IDX=0, RC=1, JOB_ID=3595311 START=2022-02-23T20:50:56.927Z, END=2022-02-23T20:51:03.362Z STDOUT=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/attempt-2/execution/stdout STDERR=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/attempt-2/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3595363, PGID=3595363, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3595363, PGID=3595363, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/attempt-2/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/attempt-2/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/attempt-2/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-0/attempt-2/execution/.cc.qc': No such file or directory

==== NAME=chip.xcor, STATUS=RetryableFailure, PARENT= SHARD_IDX=1, RC=1, JOB_ID=3594795 START=2022-02-23T20:50:36.933Z, END=2022-02-23T20:50:45.869Z STDOUT=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/execution/stdout STDERR=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3594847, PGID=3594847, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3594847, PGID=3594847, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/execution/.cc.qc': No such file or directory

==== NAME=chip.xcor, STATUS=Failed, PARENT= SHARD_IDX=1, RC=1, JOB_ID=3595045 START=2022-02-23T20:50:46.928Z, END=2022-02-23T20:50:53.784Z STDOUT=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/attempt-2/execution/stdout STDERR=/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/attempt-2/execution/stderr STDERR_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3595097, PGID=3595097, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT=

STDERR_BACKGROUND_CONTENTS= Traceback (most recent call last): File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 156, in main() File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 144, in main args.chip_seq_type, args.exclusion_range_min, args.exclusion_range_max) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_task_xcor.py", line 105, in xcor run_shell_cmd(cmd1) File "/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/bin/encode_lib_common.py", line 359, in run_shell_cmd raise Exception(err_str) Exception: PID=3595097, PGID=3595097, RC=127, DURATION_SEC=0.0 STDERR=/home/ysun/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/R/bin/exec/R: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory STDOUT= ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/attempt-2/execution/.cc.plot.png': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/attempt-2/execution/.cc.fraglen.txt': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/attempt-2/execution/.cc.plot.pdf': No such file or directory ln: failed to access '/home/ysun/pipelineTest/chip/9e218900-f98a-41ef-9222-685795cafbc4/call-xcor/shard-1/attempt-2/execution/.cc.qc': No such file or directory

cromwell.out.txt

leepc12 commented 2 years ago

Please check if libncurses.so.5 exists under your env's lib/ directory.

Get your conda root first.

$ which conda
/users/leepc12/miniconda3/condabin/conda

Remove the /condabin/conda part and make a lib path for the env. e.g. /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/.

$ ls -l /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncurses*
-rw-rw-r-- 2 leepc12 users 329020 Nov 30  2016 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncurses.a
-rw-rw-r-- 2 leepc12 users 239130 Nov 30  2016 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncurses++.a
lrwxrwxrwx 1 leepc12 users     17 Feb 23 12:36 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncurses.so -> libncurses.so.5.9
lrwxrwxrwx 1 leepc12 users     17 Feb 23 12:36 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncurses.so.5 -> libncurses.so.5.9
-rwxrwxr-x 2 leepc12 users 176142 Nov 30  2016 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncurses.so.5.9
-rw-rw-r-- 2 leepc12 users 239130 Nov 30  2016 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncurses++w.a
-rw-rw-r-- 2 leepc12 users 422234 Nov 30  2016 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncursesw.a
lrwxrwxrwx 1 leepc12 users     18 Feb 23 12:36 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncursesw.so -> libncursesw.so.5.9
lrwxrwxrwx 1 leepc12 users     18 Feb 23 12:36 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncursesw.so.5 -> libncursesw.so.5.9
-rwxrwxr-x 2 leepc12 users 232030 Nov 30  2016 /users/leepc12/miniconda3/envs/encode-chip-seq-pipeline-spp/lib/libncursesw.so.5.9
yingsun-ucsd commented 2 years ago

Thank you! I can successfully run the test as well as croo.

  1. I am planning to use ENCODE pipeline for ATAC-seq and RNA-seq too. Do you have any suggestions on what I should pay attention to since I already have this one set up?

  2. If I have several jobs I want to run, is there a possible way to name the output folder?

Thank you again for all your help.

leepc12 commented 2 years ago
  1. RNA-seq pipeline does not support Conda. You may need to install docker (use --docker) or singularity (use --singularity).
  2. No, Caper is a wrapper for Cromwell and Cromwell does not allow it. But you can do something like caper run chip.wdl -i input.json --conda --local-out-dir YOUR_OUTPUT_DIR. This will store all outputs under YOUR_OUTPUT_DIR/chip/WORKFLOW_UUID/.
yingsun-ucsd commented 2 years ago

Thank you so much for all your help.