caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/net/waterston/vol2/home/gevirl/chip-seq-pipeline2-2.1.2/chip.wdl #257
Comments
I think you are using an outdated Conda environment and input JSON. This parameter Please get the latest pipeline + caper and reinstall pipeline's Conda environment (DO NOT ACTIVATE PIPELINE's CONDA ENV BEFORE RUNNING A PIPELINE). $ pip install caper --upgrade
# and then git pull (or git clone from scratch) the pipeline git directory to update it
$ scripts/uninstall_conda_env.sh
$ scripts/install_conda_env.shRemove alll |
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I have update Conda and removed alll *_mem_mb from the input JSON |
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Pipeline automatically scales memory according to the size of each task's inputs. |
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The alignment tasks die. I The sge kills them. Here is a typical report of the sge job I don't know what code 100 means (base) [gevirl@grid-head2 execution]$ qacct -j 282137901qname sage-login.q |
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exit_status 152 in the sge report in previous comment may mean a memory limit has been reached |
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Let's separate the job script itself from Caper. Resource parameters: |
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I ran the original job script and got the same error. The script and the qacct results are in the attached file original.txt I increased the memory and the job ran to completion without error. The modified script and the qacct results are in the attached file moreMemory.txt please advise how I should increase memory specification for particular tasks |
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You can increase the memory factor, which is a multiplier for the total memory for each task. |
Describe the bug
When I start a run with this:
caper run /net/waterston/vol2/home/gevirl/chip-seq-pipeline2-2.1.2/chip.wdl -i /net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/6/pipeline.json --conda
I get the following error:
2022-01-11 09:57:17,891|caper.cli|INFO| Cromwell stdout: /net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/cromwell.out.1
2022-01-11 09:57:17,904|caper.caper_base|INFO| Creating a timestamped temporary directory. /net/waterston/vol9/capertmp/chip/20220111_095717_900159
2022-01-11 09:57:17,904|caper.caper_runner|INFO| Localizing files on work_dir. /net/waterston/vol9/capertmp/chip/20220111_095717_900159
2022-01-11 09:57:19,247|caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/net/waterston/vol2/home/gevirl/chip-seq-pipeline2-2.1.2/chip.wdl
2022-01-11 09:57:19,254|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool...
Traceback (most recent call last):
File "/nfs/waterston/miniconda3/envs/py39/bin/caper", line 13, in
main()
File "/nfs/waterston/miniconda3/envs/py39/lib/python3.9/site-packages/caper/cli.py", line 705, in main
return runner(parsed_args, nonblocking_server=nonblocking_server)
File "/nfs/waterston/miniconda3/envs/py39/lib/python3.9/site-packages/caper/cli.py", line 249, in runner
subcmd_run(c, args)
File "/nfs/waterston/miniconda3/envs/py39/lib/python3.9/site-packages/caper/cli.py", line 379, in subcmd_run
thread = caper_runner.run(
File "/nfs/waterston/miniconda3/envs/py39/lib/python3.9/site-packages/caper/caper_runner.py", line 462, in run
self._cromwell.validate(wdl=wdl, inputs=inputs, imports=imports)
File "/nfs/waterston/miniconda3/envs/py39/lib/python3.9/site-packages/caper/cromwell.py", line 154, in validate
raise WomtoolValidationFailed(
caper.cromwell.WomtoolValidationFailed: RC=1
STDERR=WARNING: Unexpected input provided: chip.align_mem_mb (expected inputs: [chip.fastqs_rep3_R2, chip.align_ctl.trim_bp, chip.filter_disk_factor, chip.gensz, chip.trimmomatic_phred_score_format, chip.peaks_pr1, chip.ctl_nodup_bams, chip.ctl_depth_limit, chip.use_filt_pe_ta_for_xcor, chip.xcor_subsample_reads, chip.call_peak_time_hr, chip.fastqs_rep1_R1, chip.paired_ends, chip.align_R1.multimapping, chip.align.multimapping, chip.gc_bias_picard_java_heap, chip.fdr_thresh, chip.align_trimmomatic_java_heap, chip.align_bwa_mem_factor, chip.fastqs_rep9_R1, chip.ctl_depth_ratio, chip.filter_cpu, chip.xcor_exclusion_range_max, chip.pval_thresh, chip.fastqs_rep6_R2, chip.ctl_fastqs_rep4_R1, chip.fastqs_rep5_R2, chip.peak_pooled, chip.read_genome_tsv.null_s, chip.description, chip.ctl_paired_ends, chip.fastqs_rep4_R1, chip.macs2_signal_track_mem_factor, chip.fastqs_rep5_R1, chip.mapq_thresh, chip.ctl_fastqs_rep6_R1, chip.filter_R1.ref_fa, chip.macs2_signal_track_time_hr, chip.xcor_disk_factor, chip.ctl_fastqs_rep1_R2, chip.fastqs_rep7_R2, chip.filter_chrs, chip.ref_fa, chip.fastqs_rep6_R1, chip.ctl_fastqs_rep5_R2, chip.enable_jsd, chip.dup_marker, chip.call_peak_spp_disk_factor, chip.pool_ta.col, chip.docker, chip.use_bwa_mem_for_pe, chip.ctl_fastqs_rep2_R2, chip.fastqs_rep8_R2, chip.macs2_signal_track_disk_factor, chip.filter_time_hr, chip.peaks, chip.filter_no_dedup.ref_fa, chip.xcor_cpu, chip.call_peak_macs2_mem_factor, chip.peak_ppr1, chip.align_bowtie2_disk_factor, chip.call_peak_cpu, chip.enable_gc_bias, chip.ctl_fastqs_rep3_R1, chip.conda_macs2, chip.nodup_bams, chip.ctl_fastqs_rep6_R2, chip.ctl_fastqs_rep1_R1, chip.use_bowtie2_local_mode, chip.fastqs_rep10_R2, chip.ctl_paired_end, chip.pool_blacklist.prefix, chip.true_rep_only, chip.ctl_subsample_reads, chip.ctl_fastqs_rep8_R2, chip.align_R1.trimmomatic_java_heap, chip.subsample_ctl_mem_factor, chip.ctl_fastqs_rep7_R1, chip.spr_mem_factor, chip.ctl_fastqs_rep5_R1, chip.bam2ta_time_hr, chip.fastqs_rep2_R1, chip.pool_ta_pr1.col, chip.ctl_bams, chip.subsample_reads, chip.align_bowtie2_mem_factor, chip.aligner, chip.blacklist, chip.title, chip.bowtie2_idx_tar, chip.ctl_fastqs_rep2_R1, chip.singularity, chip.align.trim_bp, chip.align_only, chip.align_time_hr, chip.exp_ctl_depth_ratio_limit, chip.bam2ta_cpu, chip.ctl_fastqs_rep9_R1, chip.enable_count_signal_track, chip.call_peak_spp_mem_factor, chip.no_dup_removal, chip.paired_end, chip.chrsz, chip.jsd_mem_factor, chip.ctl_fastqs_rep10_R2, chip.qc_report.qc_json_ref, chip.xcor_trim_bp, chip.bwa_idx_tar, chip.conda, chip.fastqs_rep4_R2, chip.peak_caller, chip.peak_ppr2, chip.fastqs_rep2_R2, chip.ctl_fastqs_rep7_R2, chip.fastqs_rep10_R1, chip.ctl_fastqs_rep3_R2, chip.jsd_disk_factor, chip.fastqs_rep8_R1, chip.align_ctl.multimapping, chip.call_peak_macs2_disk_factor, chip.fraglen, chip.jsd_time_hr, chip.crop_length, chip.conda_spp, chip.genome_name, chip.fastqs_rep7_R1, chip.mito_chr_name, chip.cap_num_peak, chip.always_use_pooled_ctl, chip.ctl_fastqs_rep9_R2, chip.ctl_tas, chip.blacklist2, chip.align_cpu, chip.bwa_mem_read_len_limit, chip.custom_aligner_idx_tar, chip.tas, chip.pseudoreplication_random_seed, chip.fastqs_rep1_R2, chip.fastqs_rep3_R1, chip.filter_picard_java_heap, chip.filter_mem_factor, chip.regex_bfilt_peak_chr_name, chip.spr_disk_factor, chip.crop_length_tol, chip.genome_tsv, chip.pool_ta_pr2.col, chip.bams, chip.xcor_mem_factor, chip.ctl_fastqs_rep10_R1, chip.ctl_fastqs_rep4_R2, chip.fastqs_rep9_R2, chip.pipeline_type, chip.peaks_pr2, chip.align_bwa_disk_factor, chip.jsd_cpu, chip.bam2ta_disk_factor, chip.subsample_ctl_disk_factor, chip.custom_align_py, chip.redact_nodup_bam, chip.xcor_time_hr, chip.bam2ta_mem_factor, chip.ctl_fastqs_rep8_R1, chip.pool_ta_ctl.col, chip.xcor_exclusion_range_min, chip.idr_thresh])
WARNING: Unexpected input provided: chip.cap_num_peak_spp (expected inputs: [chip.fastqs_rep3_R2, chip.align_ctl.trim_bp, chip.filter_disk_factor, chip.gensz, chip.trimmomatic_phred_score_format, chip.peaks_pr1, chip.ctl_nodup_bams, chip.ctl_depth_limit, chip.use_filt_pe_ta_for_xcor, chip.xcor_subsample_reads, chip.call_peak_time_hr, chip.fastqs_rep1_R1, chip.paired_ends, chip.align_R1.multimapping, chip.align.multimapping, chip.gc_bias_picard_java_heap, chip.fdr_thresh, chip.align_trimmomatic_java_heap, chip.align_bwa_mem_factor, chip.fastqs_rep9_R1, chip.ctl_depth_ratio, chip.filter_cpu, chip.xcor_exclusion_range_max, chip.pval_thresh, chip.fastqs_rep6_R2, chip.ctl_fastqs_rep4_R1, chip.fastqs_rep5_R2, chip.peak_pooled, chip.read_genome_tsv.null_s, chip.description, chip.ctl_paired_ends, chip.fastqs_rep4_R1, chip.macs2_signal_track_mem_factor, chip.fastqs_rep5_R1, chip.mapq_thresh, chip.ctl_fastqs_rep6_R1, chip.filter_R1.ref_fa, chip.macs2_signal_track_time_hr, chip.xcor_disk_factor, chip.ctl_fastqs_rep1_R2, chip.fastqs_rep7_R2, chip.filter_chrs, chip.ref_fa, chip.fastqs_rep6_R1, chip.ctl_fastqs_rep5_R2, chip.enable_jsd, chip.dup_marker, chip.call_peak_spp_disk_factor, chip.pool_ta.col, chip.docker, chip.use_bwa_mem_for_pe, chip.ctl_fastqs_rep2_R2, chip.fastqs_rep8_R2, chip.macs2_signal_track_disk_factor, chip.filter_time_hr, chip.peaks, chip.filter_no_dedup.ref_fa, chip.xcor_cpu, chip.call_peak_macs2_mem_factor, chip.peak_ppr1, chip.align_bowtie2_disk_factor, chip.call_peak_cpu, chip.enable_gc_bias, chip.ctl_fastqs_rep3_R1, chip.conda_macs2, chip.nodup_bams, chip.ctl_fastqs_rep6_R2, chip.ctl_fastqs_rep1_R1, chip.use_bowtie2_local_mode, chip.fastqs_rep10_R2, chip.ctl_paired_end, chip.pool_blacklist.prefix, chip.true_rep_only, chip.ctl_subsample_reads, chip.ctl_fastqs_rep8_R2, chip.align_R1.trimmomatic_java_heap, chip.subsample_ctl_mem_factor, chip.ctl_fastqs_rep7_R1, chip.spr_mem_factor, chip.ctl_fastqs_rep5_R1, chip.bam2ta_time_hr, chip.fastqs_rep2_R1, chip.pool_ta_pr1.col, chip.ctl_bams, chip.subsample_reads, chip.align_bowtie2_mem_factor, chip.aligner, chip.blacklist, chip.title, chip.bowtie2_idx_tar, chip.ctl_fastqs_rep2_R1, chip.singularity, chip.align.trim_bp, chip.align_only, chip.align_time_hr, chip.exp_ctl_depth_ratio_limit, chip.bam2ta_cpu, chip.ctl_fastqs_rep9_R1, chip.enable_count_signal_track, chip.call_peak_spp_mem_factor, chip.no_dup_removal, chip.paired_end, chip.chrsz, chip.jsd_mem_factor, chip.ctl_fastqs_rep10_R2, chip.qc_report.qc_json_ref, chip.xcor_trim_bp, chip.bwa_idx_tar, chip.conda, chip.fastqs_rep4_R2, chip.peak_caller, chip.peak_ppr2, chip.fastqs_rep2_R2, chip.ctl_fastqs_rep7_R2, chip.fastqs_rep10_R1, chip.ctl_fastqs_rep3_R2, chip.jsd_disk_factor, chip.fastqs_rep8_R1, chip.align_ctl.multimapping, chip.call_peak_macs2_disk_factor, chip.fraglen, chip.jsd_time_hr, chip.crop_length, chip.conda_spp, chip.genome_name, chip.fastqs_rep7_R1, chip.mito_chr_name, chip.cap_num_peak, chip.always_use_pooled_ctl, chip.ctl_fastqs_rep9_R2, chip.ctl_tas, chip.blacklist2, chip.align_cpu, chip.bwa_mem_read_len_limit, chip.custom_aligner_idx_tar, chip.tas, chip.pseudoreplication_random_seed, chip.fastqs_rep1_R2, chip.fastqs_rep3_R1, chip.filter_picard_java_heap, chip.filter_mem_factor, chip.regex_bfilt_peak_chr_name, chip.spr_disk_factor, chip.crop_length_tol, chip.genome_tsv, chip.pool_ta_pr2.col, chip.bams, chip.xcor_mem_factor, chip.ctl_fastqs_rep10_R1, chip.ctl_fastqs_rep4_R2, chip.fastqs_rep9_R2, chip.pipeline_type, chip.peaks_pr2, chip.align_bwa_disk_factor, chip.jsd_cpu, chip.bam2ta_disk_factor, chip.subsample_ctl_disk_factor, chip.custom_align_py, chip.redact_nodup_bam, chip.xcor_time_hr, chip.bam2ta_mem_factor, chip.ctl_fastqs_rep8_R1, chip.pool_ta_ctl.col, chip.xcor_exclusion_range_min, chip.idr_thresh])
WARNING: Unexpected input provided: chip.call_peak_mem_mb (expected inputs: [chip.fastqs_rep3_R2, chip.align_ctl.trim_bp, chip.filter_disk_factor, chip.gensz, chip.trimmomatic_phred_score_format, chip.peaks_pr1, chip.ctl_nodup_bams, chip.ctl_depth_limit, chip.use_filt_pe_ta_for_xcor, chip.xcor_subsample_reads, chip.call_peak_time_hr, chip.fastqs_rep1_R1, chip.paired_ends, chip.align_R1.multimapping, chip.align.multimapping, chip.gc_bias_picard_java_heap, chip.fdr_thresh, chip.align_trimmomatic_java_heap, chip.align_bwa_mem_factor, chip.fastqs_rep9_R1, chip.ctl_depth_ratio, chip.filter_cpu, chip.xcor_exclusion_range_max, chip.pval_thresh, chip.fastqs_rep6_R2, chip.ctl_fastqs_rep4_R1, chip.fastqs_rep5_R2, chip.peak_pooled, chip.read_genome_tsv.null_s, chip.description, chip.ctl_paired_ends, chip.fastqs_rep4_R1, chip.macs2_signal_track_mem_factor, chip.fastqs_rep5_R1, chip.mapq_thresh, chip.ctl_fastqs_rep6_R1, chip.filter_R1.ref_fa, chip.macs2_signal_track_time_hr, chip.xcor_disk_factor, chip.ctl_fastqs_rep1_R2, chip.fastqs_rep7_R2, chip.filter_chrs, chip.ref_fa, chip.fastqs_rep6_R1, chip.ctl_fastqs_rep5_R2, chip.enable_jsd, chip.dup_marker, chip.call_peak_spp_disk_factor, chip.pool_ta.col, chip.docker, chip.use_bwa_mem_for_pe, chip.ctl_fastqs_rep2_R2, chip.fastqs_rep8_R2, chip.macs2_signal_track_disk_factor, chip.filter_time_hr, chip.peaks, chip.filter_no_dedup.ref_fa, chip.xcor_cpu, chip.call_peak_macs2_mem_factor, chip.peak_ppr1, chip.align_bowtie2_disk_factor, chip.call_peak_cpu, chip.enable_gc_bias, chip.ctl_fastqs_rep3_R1, chip.conda_macs2, chip.nodup_bams, chip.ctl_fastqs_rep6_R2, chip.ctl_fastqs_rep1_R1, chip.use_bowtie2_local_mode, chip.fastqs_rep10_R2, chip.ctl_paired_end, chip.pool_blacklist.prefix, chip.true_rep_only, chip.ctl_subsample_reads, chip.ctl_fastqs_rep8_R2, chip.align_R1.trimmomatic_java_heap, chip.subsample_ctl_mem_factor, chip.ctl_fastqs_rep7_R1, chip.spr_mem_factor, chip.ctl_fastqs_rep5_R1, chip.bam2ta_time_hr, chip.fastqs_rep2_R1, chip.pool_ta_pr1.col, chip.ctl_bams, chip.subsample_reads, chip.align_bowtie2_mem_factor, chip.aligner, chip.blacklist, chip.title, chip.bowtie2_idx_tar, chip.ctl_fastqs_rep2_R1, chip.singularity, chip.align.trim_bp, chip.align_only, chip.align_time_hr, chip.exp_ctl_depth_ratio_limit, chip.bam2ta_cpu, chip.ctl_fastqs_rep9_R1, chip.enable_count_signal_track, chip.call_peak_spp_mem_factor, chip.no_dup_removal, chip.paired_end, chip.chrsz, chip.jsd_mem_factor, chip.ctl_fastqs_rep10_R2, chip.qc_report.qc_json_ref, chip.xcor_trim_bp, chip.bwa_idx_tar, chip.conda, chip.fastqs_rep4_R2, chip.peak_caller, chip.peak_ppr2, chip.fastqs_rep2_R2, chip.ctl_fastqs_rep7_R2, chip.fastqs_rep10_R1, chip.ctl_fastqs_rep3_R2, chip.jsd_disk_factor, chip.fastqs_rep8_R1, chip.align_ctl.multimapping, chip.call_peak_macs2_disk_factor, chip.fraglen, chip.jsd_time_hr, chip.crop_length, chip.conda_spp, chip.genome_name, chip.fastqs_rep7_R1, chip.mito_chr_name, chip.cap_num_peak, chip.always_use_pooled_ctl, chip.ctl_fastqs_rep9_R2, chip.ctl_tas, chip.blacklist2, chip.align_cpu, chip.bwa_mem_read_len_limit, chip.custom_aligner_idx_tar, chip.tas, chip.pseudoreplication_random_seed, chip.fastqs_rep1_R2, chip.fastqs_rep3_R1, chip.filter_picard_java_heap, chip.filter_mem_factor, chip.regex_bfilt_peak_chr_name, chip.spr_disk_factor, chip.crop_length_tol, chip.genome_tsv, chip.pool_ta_pr2.col, chip.bams, chip.xcor_mem_factor, chip.ctl_fastqs_rep10_R1, chip.ctl_fastqs_rep4_R2, chip.fastqs_rep9_R2, chip.pipeline_type, chip.peaks_pr2, chip.align_bwa_disk_factor, chip.jsd_cpu, chip.bam2ta_disk_factor, chip.subsample_ctl_disk_factor, chip.custom_align_py, chip.redact_nodup_bam, chip.xcor_time_hr, chip.bam2ta_mem_factor, chip.ctl_fastqs_rep8_R1, chip.pool_ta_ctl.col, chip.xcor_exclusion_range_min, chip.idr_thresh])
OS/Platform
Caper configuration file
backend=sge
Parallel environement is required, ask your administrator to create one
If your cluster doesn't support PE then edit 'sge-resource-param'
to fit your cluster's configuration.
sge-pe=serial
This parameter is NOT for 'caper submit' BUT for 'caper run' and 'caper server' only.
This resource parameter string will be passed to sbatch, qsub, bsub, ...
You can customize it according to your cluster's configuration.
Note that Cromwell's implicit type conversion (String to Integer)
seems to be buggy for WomLong type memory variables (memory_mb and memory_gb).
So be careful about using the + operator between WomLong and other types (String, even Int).
For example, ${"--mem=" + memory_mb} will not work since memory_mb is WomLong.
Use ${"if defined(memory_mb) then "--mem=" else ""}{memory_mb}${"if defined(memory_mb) then "mb " else " "}
See broadinstitute/cromwell#4659 for details
Cromwell's built-in variables (attributes defined in WDL task's runtime)
Use them within ${} notation.
- cpu: number of cores for a job (default = 1)
- memory_mb, memory_gb: total memory for a job in MB, GB
* these are converted from 'memory' string attribute (including size unit)
defined in WDL task's runtime
- time: time limit for a job in hour
- gpu: specified gpu name or number of gpus (it's declared as String)
Parallel environment of SGE:
Find one with
$ qconf -splor ask you admin to add one if not exists.If your cluster works without PE then edit the below sge-resource-param
#sge-pe=serial${true="-l s_vmem=$ (expr " false="" defined(memory_mb)}${memory_mb}$#{true=" / " false="" defined(memory_mb)}${if defined(memory_mb) then cpu else ""}${true=")m" false="" defined(memory_mb)} ${"-l h_rt=" + time + ":00:00"} ${"-l s_rt=" + time + ":00:00"} ${"-l gpu=" + gpu}
sge-resource-param=${if cpu > 1 then "-pe " + sge_pe + " " else ""} ${if cpu > 1 then cpu else ""} ${true="-l h_vmem=$(expr " false="" defined(memory_mb)}${memory_mb}${true=" / " false=""
defined(memory_mb)}${if defined(memory_mb) then cpu else ""}${true=")m" false="" defined(memory_mb)}
If needed uncomment and define any extra SGE qsub parameters here
YOU CANNOT USE WDL SYNTAX AND CROMWELL BUILT-IN VARIABLES HERE
#sge-extra-param=
Hashing strategy for call-caching (3 choices)
This parameter is for local (local/slurm/sge/pbs/lsf) backend only.
This is important for call-caching,
which means re-using outputs from previous/failed workflows.
Cache will miss if different strategy is used.
"file" method has been default for all old versions of Caper<1.0.
"path+modtime" is a new default for Caper>=1.0,
file: use md5sum hash (slow).
path: use path.
path+modtime: use path and modification time.
local-hash-strat=path+modtime
Metadata DB for call-caching (reusing previous outputs):
Cromwell supports restarting workflows based on a metadata DB
DB is in-memory by default
#db=in-memory
If you use 'caper server' then you can use one unified '--file-db'
for all submitted workflows. In such case, uncomment the following two lines
and defined file-db as an absolute path to store metadata of all workflows
#db=file
#file-db=
If you use 'caper run' and want to use call-caching:
Make sure to define different 'caper run ... --db file --file-db DB_PATH'
for each pipeline run.
But if you want to restart then define the same '--db file --file-db DB_PATH'
then Caper will collect/re-use previous outputs without running the same task again
Previous outputs will be simply hard/soft-linked.
Local directory for localized files and Cromwell's intermediate files
If not defined, Caper will make .caper_tmp/ on local-out-dir or CWD.
/tmp is not recommended here since Caper store all localized data files
on this directory (e.g. input FASTQs defined as URLs in input JSON).
local-loc-dir=/net/waterston/vol9/capertmp
cromwell=/net/waterston/vol2/home/gevirl/.caper/cromwell_jar/cromwell-65.jar
womtool=/net/waterston/vol2/home/gevirl/.caper/womtool_jar/womtool-65.jar
Input JSON file
{"chip.title":"arid-1_RW12194_L4larva_1_6","chip.description":"gevirl","chip.always_use_pooled_ctl":false,"chip.true_rep_only":false,"chip.enable_count_signal_track":true,"chip.aligner":"bwa","chip.use_bwa_mem_for_pe":true,"chip.align_only":false,"chip.genome_tsv":"/net/waterston/vol9/WS245chr/WS245chr.tsv","chip.peak_caller":"spp","chip.pipeline_type":"tf","chip.cap_num_peak_spp":300000,"chip.idr_thresh":0.01,"chip.call_peak_mem_mb":16000,"chip.align_mem_mb":20000,"chip.filter_picard_java_heap":"4G","chip.fastqs_rep1_R1":["/net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/ARDIP3_240_337_S33_L001_R1_001.fastq.gz"],"chip.fastqs_rep1_R2":["/net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/ARDIP3_240_337_S33_L001_R2_001.fastq.gz"],"chip.fastqs_rep2_R1":["/net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/ARDIP4_228_349_S34_L001_R1_001.fastq.gz"],"chip.fastqs_rep2_R2":["/net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/ARDIP4_228_349_S34_L001_R2_001.fastq.gz"],"chip.paired_ends":[true,true],"chip.ctl_fastqs_rep1_R1":["/net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/ARDinp3_263_314_S39_L001_R1_001.fastq.gz"],"chip.ctl_fastqs_rep1_R2":["/net/waterston/vol9/ChipSeqPipeline/arid-1_RW12194_L4larva_1/ARDinp3_263_314_S39_L001_R2_001.fastq.gz"],"chip.ctl_paired_ends":[true]}
Troubleshooting result
If you ran
caper runwithout Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.If you ran
caper submitwith a running Caper server then first find your workflow ID (1st column) withcaper listand runcaper debug [WORKFLOW_ID].Paste troubleshooting result.
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