Updating workflows/epigenetics/hic-hicup-cooler from 0.3 to 0.4 #971

gxydevbot · 2025-10-06T06:06:15Z

Hello! This is an automated update of the following workflow: workflows/epigenetics/hic-hicup-cooler. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.9+galaxy0

The workflow release number has been updated from 0.3 to 0.4.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

github-actions · 2025-10-06T06:55:40Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	4
Passed	4
Error	0
Failure	0
Skipped	0

Passed Tests

✅ chic-fastq-to-cool-hicup-cooler.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: PE fastq input:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled

Step 11: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: PE fastq input:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled
Step 3: Restriction enzyme:
- step_state: scheduled
Step 4: No fill-in:
- step_state: scheduled
Step 5: minimum MAPQ:
- step_state: scheduled

Step 6: HiCUP:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmphrllkedv/files/3/1/a/dataset_31acbcca-3905-404c-b4c9-85c6adc364da.dat' 'dataset1.fq' &&  ln -f -s '/tmp/tmphrllkedv/files/8/f/6/dataset_8f6511bb-7b28-41d5-b72d-864efc1f9188.dat' 'dataset2.fq' &&    BOWTIE_PATH_BASH="$(which bowtie2)" && hicup_digester --re1 'A^AGCTT,HindIII' --genome 'hg19' '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full'.fa && mv *Digest_* digest_file.txt && hicup --zip --threads ${GALAXY_SLOTS:-1} --digest digest_file.txt --index '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full' --bowtie2 $BOWTIE_PATH_BASH --keep   'dataset1.fq' 'dataset2.fq'

Exit Code:

```
0
```

Standard Error:

Digestion complete
FASTQ quality format not specified, analysing file 'dataset1.fq' to predict file format used
FASTQ quality set to 'Sanger'
Detecting R automatically
Found R at '/usr/local/bin/R'
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Filtering dataset1_2.pair.bam
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories

Standard Output:

HiCUP Digester (version 0.9.2)
Digesting files
Digesting '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full.fa'
Starting HiCUP pipeline (v0.9.2)
PLEASE NOTE: FROM VERSION 8, HICUP REQUIRES THE R PACKAGES TIDYVERSE AND PLOTLY INSTALLED
SEE DOCUMENTATION FOR MORE DETAILS
Reading genome digest file 'digest_file.txt' to determine Hi-C restriction enzyme
Truncating with HiCUP Truncater v0.9.2
Truncating sequences at occurrence of sequences '[AAGCTAGCTT]'
Truncating sequences
Truncating dataset1.fq
Truncating dataset2.fq
Truncating complete
Mapping with HiCUP Mapper v0.9.2
Using aligner 'bowtie2'
Mapping dataset1.trunc.fastq.gz
Mapping dataset2.trunc.fastq.gz
Mapping complete
Pairing files with HiCUP Mapper v0.9.2
Pairing dataset1.map.sam and dataset2.map.sam
Pairing complete
Filtering with HiCUP Filter v0.9.2
Processing digest file digest_file.txt
Sonication protocol followed - Restriction_Enzyme1:HindIII [A^AGCTT]
Filtering complete
Removing duplicates with HiCUP Deduplicator v0.9.2
De-duplicating dataset1_2.filt.bam
De-duplication complete
Creating combined HiCUP summary report
Reading folder '/tmp/tmphrllkedv/job_working_directory/000/14/working'
Writing to: /tmp/tmphrllkedv/job_working_directory/000/14/working/
	1 complete summary results groups identified in folder
Created combined summary reports
Created HTML summary reports
HiCUP processing complete.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger"`
__workflow_invocation_uuid__	`"23e0745fa28011f0a35e6045bd4a93e2"`
advanced_options	`{"longest": "", "nofill": false, "re2": "", "shortest": ""}`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
genome	`"hg19"`
library	`{"__current_case__": 1, "input_1": {"values": [{"id": 38, "src": "dce"}]}, "type": "paired_collection"}`
re1	`"A^AGCTT,HindIII"`
reference_genome	`{"__current_case__": 0, "index": "hg19", "source": "indexed"}`

Step 7: build filtering rule for MAPQ:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23e0745fa28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "(c10>=", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "30", "select_param_type": "integer"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": ") and (c11>=", "select_param_type": "text"}}, {"__index__": 3, "param_type": {"__current_case__": 1, "component_value": "30", "select_param_type": "integer"}}, {"__index__": 4, "param_type": {"__current_case__": 0, "component_value": ")", "select_param_type": "text"}}]
dbkey	`"?"`

Step 8: valid pairs in juicebox format:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmphrllkedv/files/7/0/4/dataset_70425400-9656-4f2e-a824-1794eec0b716.dat' input.bam && hicup2juicer --digest '/tmp/tmphrllkedv/files/2/d/d/dataset_2dd89999-c2cd-4b82-be50-d438366451ae.dat' '--usemid' input.bam

Exit Code:

```
0
```

Standard Output:

Processing digester file
Sonication protocol followed - Restriction_Enzyme1:HindIII [A^AGCTT]
Processing input.bam
The outputfiles generated by this script may be converted to Juicer '.hic' files using the 'pre' command as described at: https://github.com/aidenlab/juicer/wiki/Pre
Processing complete.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"qname_sorted.bam"`
__workflow_invocation_uuid__	`"23e0745fa28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
digester	`{"__current_case__": 0, "digester_file": {"values": [{"id": 45, "src": "dce"}]}, "provide_digester": "yes", "usemid": true}`

Step 9: valid pairs in juicebox format MAPQ filtered:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmphrllkedv/galaxy-dev/tools/stats/filtering.py' '/tmp/tmphrllkedv/files/4/5/2/dataset_452e41b0-4954-4d12-89ba-3ad089eb53c5.dat' '/tmp/tmphrllkedv/job_working_directory/000/19/outputs/dataset_cf00590d-e1e2-4e42-afa9-8664f02a8cdd.dat' '/tmp/tmphrllkedv/job_working_directory/000/19/configs/tmp166ec8ft' 11 "int,int,str,int,int,int,str,int,int,int,int" 0

Exit Code:

```
0
```

Standard Output:

Filtering with (c10>=30) and (c11>=30), 
kept 93.80% of 39962 valid lines (39962 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23e0745fa28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"(c10>=30) and (c11>=30)"`
dbkey	`"?"`
header_lines	`"0"`

Step 12: write filtering for capture region:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23e0745ea28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "(c3=='", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "chr2", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": "' and c4<", "select_param_type": "text"}}, {"__index__": 3, "param_type": {"__current_case__": 1, "component_value": "180000000", "select_param_type": "integer"}}, {"__index__": 4, "param_type": {"__current_case__": 0, "component_value": " and c4>", "select_param_type": "text"}}, {"__index__": 5, "param_type": {"__current_case__": 1, "component_value": "170000000", "select_param_type": "integer"}}, {"__index__": 6, "param_type": {"__current_case__": 0, "component_value": ") and (c7==\"", "select_param_type": "text"}}, {"__index__": 7, "param_type": {"__current_case__": 0, "component_value": "chr2", "select_param_type": "text"}}, {"__index__": 8, "param_type": {"__current_case__": 0, "component_value": "\" and c8<", "select_param_type": "text"}}, {"__index__": 9, "param_type": {"__current_case__": 1, "component_value": "180000000", "select_param_type": "integer"}}, {"__index__": 10, "param_type": {"__current_case__": 0, "component_value": " and c8>", "select_param_type": "text"}}, {"__index__": 11, "param_type": {"__current_case__": 1, "component_value": "170000000", "select_param_type": "integer"}}, {"__index__": 12, "param_type": {"__current_case__": 0, "component_value": ")", "select_param_type": "text"}}]
dbkey	`"?"`

Step 13: write region for pyGenomeTracks:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23e0745ea28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "chr2", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": ":", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 1, "component_value": "170000000", "select_param_type": "integer"}}, {"__index__": 3, "param_type": {"__current_case__": 0, "component_value": "-", "select_param_type": "text"}}, {"__index__": 4, "param_type": {"__current_case__": 1, "component_value": "180000000", "select_param_type": "integer"}}]
dbkey	`"?"`

Step 14: Filter for capture region:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmphrllkedv/galaxy-dev/tools/stats/filtering.py' '/tmp/tmphrllkedv/files/c/f/0/dataset_cf00590d-e1e2-4e42-afa9-8664f02a8cdd.dat' '/tmp/tmphrllkedv/job_working_directory/000/20/outputs/dataset_dd22f176-4fb2-46f9-9292-dc9dc100ebcf.dat' '/tmp/tmphrllkedv/job_working_directory/000/20/configs/tmp6x2nb2uk' 11 "int,int,str,int,int,int,str,int,int,int,int" 0

Exit Code:

```
0
```

Standard Output:

Filtering with (c3=='chr2' and c4<180000000 and c4>170000000) and (c7=="chr2" and c8<180000000 and c8>170000000), 
kept 0.11% of 37485 valid lines (37485 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"23e0745ea28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"(c3=='chr2' and c4<180000000 and c4>170000000) and (c7==\"chr2\" and c8<180000000 and c8>170000000)"`
dbkey	`"?"`
header_lines	`"0"`

Step 15: Sort filtered pairs and index:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cooler csort -i tabix -c1 3 -c2 7 -p1 4 -p2 8 -o '/tmp/tmphrllkedv/job_working_directory/000/21/outputs/dataset_4581b8cc-3b79-4bd7-bdde-cd6e5bc47884.dat' '/tmp/tmphrllkedv/files/d/d/2/dataset_dd22f176-4fb2-46f9-9292-dc9dc100ebcf.dat' '/cvmfs/data.galaxyproject.org/byhand/hg19/sam_index/hg19.fa'.fai

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.csort:Enumerating requested chromosomes...
INFO:cooler.cli.csort:chr10	1
INFO:cooler.cli.csort:chr11	2
INFO:cooler.cli.csort:chr11_gl000202_random	3
INFO:cooler.cli.csort:chr12	4
INFO:cooler.cli.csort:chr13	5
INFO:cooler.cli.csort:chr14	6
INFO:cooler.cli.csort:chr15	7
INFO:cooler.cli.csort:chr16	8
INFO:cooler.cli.csort:chr17_ctg5_hap1	9
INFO:cooler.cli.csort:chr17	10
INFO:cooler.cli.csort:chr17_gl000203_random	11
INFO:cooler.cli.csort:chr17_gl000204_random	12
INFO:cooler.cli.csort:chr17_gl000205_random	13
INFO:cooler.cli.csort:chr17_gl000206_random	14
INFO:cooler.cli.csort:chr18	15
INFO:cooler.cli.csort:chr18_gl000207_random	16
INFO:cooler.cli.csort:chr19	17
INFO:cooler.cli.csort:chr19_gl000208_random	18
INFO:cooler.cli.csort:chr19_gl000209_random	19
INFO:cooler.cli.csort:chr1	20
INFO:cooler.cli.csort:chr1_gl000191_random	21
INFO:cooler.cli.csort:chr1_gl000192_random	22
INFO:cooler.cli.csort:chr20	23
INFO:cooler.cli.csort:chr21	24
INFO:cooler.cli.csort:chr21_gl000210_random	25
INFO:cooler.cli.csort:chr22	26
INFO:cooler.cli.csort:chr2	27
INFO:cooler.cli.csort:chr3	28
INFO:cooler.cli.csort:chr4_ctg9_hap1	29
INFO:cooler.cli.csort:chr4	30
INFO:cooler.cli.csort:chr4_gl000193_random	31
INFO:cooler.cli.csort:chr4_gl000194_random	32
INFO:cooler.cli.csort:chr5	33
INFO:cooler.cli.csort:chr6_apd_hap1	34
INFO:cooler.cli.csort:chr6_cox_hap2	35
INFO:cooler.cli.csort:chr6_dbb_hap3	36
INFO:cooler.cli.csort:chr6	37
INFO:cooler.cli.csort:chr6_mann_hap4	38
INFO:cooler.cli.csort:chr6_mcf_hap5	39
INFO:cooler.cli.csort:chr6_qbl_hap6	40
INFO:cooler.cli.csort:chr6_ssto_hap7	41
INFO:cooler.cli.csort:chr7	42
INFO:cooler.cli.csort:chr7_gl000195_random	43
INFO:cooler.cli.csort:chr8	44
INFO:cooler.cli.csort:chr8_gl000196_random	45
INFO:cooler.cli.csort:chr8_gl000197_random	46
INFO:cooler.cli.csort:chr9	47
INFO:cooler.cli.csort:chr9_gl000198_random	48
INFO:cooler.cli.csort:chr9_gl000199_random	49
INFO:cooler.cli.csort:chr9_gl000200_random	50
INFO:cooler.cli.csort:chr9_gl000201_random	51
INFO:cooler.cli.csort:chrM	52
INFO:cooler.cli.csort:chrUn_gl000211	53
INFO:cooler.cli.csort:chrUn_gl000212	54
INFO:cooler.cli.csort:chrUn_gl000213	55
INFO:cooler.cli.csort:chrUn_gl000214	56
INFO:cooler.cli.csort:chrUn_gl000215	57
INFO:cooler.cli.csort:chrUn_gl000216	58
INFO:cooler.cli.csort:chrUn_gl000217	59
INFO:cooler.cli.csort:chrUn_gl000218	60
INFO:cooler.cli.csort:chrUn_gl000219	61
INFO:cooler.cli.csort:chrUn_gl000220	62
INFO:cooler.cli.csort:chrUn_gl000221	63
INFO:cooler.cli.csort:chrUn_gl000222	64
INFO:cooler.cli.csort:chrUn_gl000223	65
INFO:cooler.cli.csort:chrUn_gl000224	66
INFO:cooler.cli.csort:chrUn_gl000225	67
INFO:cooler.cli.csort:chrUn_gl000226	68
INFO:cooler.cli.csort:chrUn_gl000227	69
INFO:cooler.cli.csort:chrUn_gl000228	70
INFO:cooler.cli.csort:chrUn_gl000229	71
INFO:cooler.cli.csort:chrUn_gl000230	72
INFO:cooler.cli.csort:chrUn_gl000231	73
INFO:cooler.cli.csort:chrUn_gl000232	74
INFO:cooler.cli.csort:chrUn_gl000233	75
INFO:cooler.cli.csort:chrUn_gl000234	76
INFO:cooler.cli.csort:chrUn_gl000235	77
INFO:cooler.cli.csort:chrUn_gl000236	78
INFO:cooler.cli.csort:chrUn_gl000237	79
INFO:cooler.cli.csort:chrUn_gl000238	80
INFO:cooler.cli.csort:chrUn_gl000239	81
INFO:cooler.cli.csort:chrUn_gl000240	82
INFO:cooler.cli.csort:chrUn_gl000241	83
INFO:cooler.cli.csort:chrUn_gl000242	84
INFO:cooler.cli.csort:chrUn_gl000243	85
INFO:cooler.cli.csort:chrUn_gl000244	86
INFO:cooler.cli.csort:chrUn_gl000245	87
INFO:cooler.cli.csort:chrUn_gl000246	88
INFO:cooler.cli.csort:chrUn_gl000247	89
INFO:cooler.cli.csort:chrUn_gl000248	90
INFO:cooler.cli.csort:chrUn_gl000249	91
INFO:cooler.cli.csort:chrX	92
INFO:cooler.cli.csort:chrY	93
INFO:cooler.cli.csort:Input: '/tmp/tmphrllkedv/files/d/d/2/dataset_dd22f176-4fb2-46f9-9292-dc9dc100ebcf.dat'
INFO:cooler.cli.csort:Output: '/tmp/tmphrllkedv/job_working_directory/000/21/outputs/dataset_4581b8cc-3b79-4bd7-bdde-cd6e5bc47884.dat'
INFO:cooler.cli.csort:Reordering pair mates and sorting pair records...
INFO:cooler.cli.csort:Sort order: positional (chrom1, pos1, chrom2, pos2)
INFO:cooler.cli.csort:sort -k3,3 -k4,4n -k7,7 -k8,8n
INFO:cooler.cli.csort:Indexing...
INFO:cooler.cli.csort:Indexer: tabix
INFO:cooler.cli.csort:tabix -f -s3 -b4 -e4 /tmp/tmphrllkedv/job_working_directory/000/21/outputs/dataset_4581b8cc-3b79-4bd7-bdde-cd6e5bc47884.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23e0745ea28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format_sel	`{"__current_case__": 0, "format": "juicer_medium"}`
size_source	`{"__current_case__": 0, "fasta_cached": "hg19", "size_source_selector": "cached"}`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Bin size in bp:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled
Step 3: Juicer Medium Tabix with validPairs:
- step_state: scheduled
Step 4: Interactions to consider to calculate weights in normalization step:
- step_state: scheduled

Step 5: make bed with bins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cooler makebins -o '/tmp/tmphrllkedv/job_working_directory/000/22/outputs/dataset_b5c0b04e-84f6-4476-a7ab-1d140bc65d27.dat' '/cvmfs/data.galaxyproject.org/byhand/hg19/sam_index/hg19.fa'.fai 1000000

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23e07460a28011f0a35e6045bd4a93e2"`
binsize	`"1000000"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
size_source	`{"__current_case__": 0, "fasta_cached": "hg19", "size_source_selector": "cached"}`

Step 6: Load pairs in matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmphrllkedv/files/4/5/8/dataset_4581b8cc-3b79-4bd7-bdde-cd6e5bc47884.dat' pairs.tabix && ln -s '/tmp/tmphrllkedv/files/_metadata_files/b/2/c/metadata_b2c9a24a-c515-435a-89ad-3c1464b185b3.dat' pairs.tabix.tbi && cooler cload tabix --assembly 'hg19' -c2 7 -p2 8 '/tmp/tmphrllkedv/files/b/5/c/dataset_b5c0b04e-84f6-4476-a7ab-1d140bc65d27.dat' pairs.tabix '/tmp/tmphrllkedv/job_working_directory/000/23/outputs/dataset_a53626d7-a8c3-464a-899a-6a57af57ecae.dat'

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.cload:Using 8 cores
INFO:cooler.create:Creating cooler at "/tmp/tmphrllkedv/job_working_directory/000/23/outputs/dataset_a53626d7-a8c3-464a-899a-6a57af57ecae.dat::/"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Binning chr2:0-129000000|*
INFO:cooler.create:Binning chr2:129000000-243199373|*
INFO:cooler.create:Finished chr2:0-129000000|*
INFO:cooler.create:Finished chr2:129000000-243199373|*
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23e07460a28011f0a35e6045bd4a93e2"`
assembly	`"hg19"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format_sel	`{"__current_case__": 0, "format": "juicer_medium", "input_pairs": {"values": [{"id": 73, "src": "dce"}]}}`

Step 7: ICE normalization:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmphrllkedv/files/a/5/3/dataset_a53626d7-a8c3-464a-899a-6a57af57ecae.dat' '/tmp/tmphrllkedv/job_working_directory/000/24/outputs/dataset_11cef4a2-ebaa-40ba-b255-db9ee4e5fdba.dat' && cooler balance -p ${GALAXY_SLOTS:-1} --mad-max 5 --min-nnz 10 --min-count 0 --ignore-diags 2 --ignore-dist 0 --tol 1e-05 --max-iters 200 --cis-only -f --convergence-policy error '/tmp/tmphrllkedv/job_working_directory/000/24/outputs/dataset_11cef4a2-ebaa-40ba-b255-db9ee4e5fdba.dat'

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.balance:Balancing "/tmp/tmphrllkedv/job_working_directory/000/24/outputs/dataset_11cef4a2-ebaa-40ba-b255-db9ee4e5fdba.dat"
INFO:cooler.balance:chr10
INFO:cooler.balance:chr11
INFO:cooler.balance:chr11_gl000202_random
INFO:cooler.balance:chr12
INFO:cooler.balance:chr13
INFO:cooler.balance:chr14
INFO:cooler.balance:chr15
INFO:cooler.balance:chr16
INFO:cooler.balance:chr17_ctg5_hap1
INFO:cooler.balance:chr17
INFO:cooler.balance:chr17_gl000203_random
INFO:cooler.balance:chr17_gl000204_random
INFO:cooler.balance:chr17_gl000205_random
INFO:cooler.balance:chr17_gl000206_random
INFO:cooler.balance:chr18
INFO:cooler.balance:chr18_gl000207_random
INFO:cooler.balance:chr19
INFO:cooler.balance:chr19_gl000208_random
INFO:cooler.balance:chr19_gl000209_random
INFO:cooler.balance:chr1
INFO:cooler.balance:chr1_gl000191_random
INFO:cooler.balance:chr1_gl000192_random
INFO:cooler.balance:chr20
INFO:cooler.balance:chr21
INFO:cooler.balance:chr21_gl000210_random
INFO:cooler.balance:chr22
INFO:cooler.balance:chr2
INFO:cooler.balance:chr3
INFO:cooler.balance:chr4_ctg9_hap1
INFO:cooler.balance:chr4
INFO:cooler.balance:chr4_gl000193_random
INFO:cooler.balance:chr4_gl000194_random
INFO:cooler.balance:chr5
INFO:cooler.balance:chr6_apd_hap1
INFO:cooler.balance:chr6_cox_hap2
INFO:cooler.balance:chr6_dbb_hap3
INFO:cooler.balance:chr6
INFO:cooler.balance:chr6_mann_hap4
INFO:cooler.balance:chr6_mcf_hap5
INFO:cooler.balance:chr6_qbl_hap6
INFO:cooler.balance:chr6_ssto_hap7
INFO:cooler.balance:chr7
INFO:cooler.balance:chr7_gl000195_random
INFO:cooler.balance:chr8
INFO:cooler.balance:chr8_gl000196_random
INFO:cooler.balance:chr8_gl000197_random
INFO:cooler.balance:chr9
INFO:cooler.balance:chr9_gl000198_random
INFO:cooler.balance:chr9_gl000199_random
INFO:cooler.balance:chr9_gl000200_random
INFO:cooler.balance:chr9_gl000201_random
INFO:cooler.balance:chrM
INFO:cooler.balance:chrUn_gl000211
INFO:cooler.balance:chrUn_gl000212
INFO:cooler.balance:chrUn_gl000213
INFO:cooler.balance:chrUn_gl000214
INFO:cooler.balance:chrUn_gl000215
INFO:cooler.balance:chrUn_gl000216
INFO:cooler.balance:chrUn_gl000217
INFO:cooler.balance:chrUn_gl000218
INFO:cooler.balance:chrUn_gl000219
INFO:cooler.balance:chrUn_gl000220
INFO:cooler.balance:chrUn_gl000221
INFO:cooler.balance:chrUn_gl000222
INFO:cooler.balance:chrUn_gl000223
INFO:cooler.balance:chrUn_gl000224
INFO:cooler.balance:chrUn_gl000225
INFO:cooler.balance:chrUn_gl000226
INFO:cooler.balance:chrUn_gl000227
INFO:cooler.balance:chrUn_gl000228
INFO:cooler.balance:chrUn_gl000229
INFO:cooler.balance:chrUn_gl000230
INFO:cooler.balance:chrUn_gl000231
INFO:cooler.balance:chrUn_gl000232
INFO:cooler.balance:chrUn_gl000233
INFO:cooler.balance:chrUn_gl000234
INFO:cooler.balance:chrUn_gl000235
INFO:cooler.balance:chrUn_gl000236
INFO:cooler.balance:chrUn_gl000237
INFO:cooler.balance:chrUn_gl000238
INFO:cooler.balance:chrUn_gl000239
INFO:cooler.balance:chrUn_gl000240
INFO:cooler.balance:chrUn_gl000241
INFO:cooler.balance:chrUn_gl000242
INFO:cooler.balance:chrUn_gl000243
INFO:cooler.balance:chrUn_gl000244
INFO:cooler.balance:chrUn_gl000245
INFO:cooler.balance:chrUn_gl000246
INFO:cooler.balance:chrUn_gl000247
INFO:cooler.balance:chrUn_gl000248
INFO:cooler.balance:chrUn_gl000249
INFO:cooler.balance:chrX
INFO:cooler.balance:chrY

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"23e07460a28011f0a35e6045bd4a93e2"`
blacklist	`None`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cistrans	`"--cis-only"`
convergencepolicy	`"error"`
dbkey	`"?"`
ignorediags	`"2"`
ignoredist	`"0"`
madmax	`"5"`
maxiters	`"200"`
mincount	`"0"`
minnnz	`"10"`
name	`"weight"`
tol	`"1e-05"`

Step 17: final_plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s /tmp/tmphrllkedv/files/1/1/c/dataset_11cef4a2-ebaa-40ba-b255-db9ee4e5fdba.dat 0_0.cool &&   sed '/^$/d' '/tmp/tmphrllkedv/job_working_directory/000/25/configs/tmpmxqhraqh' && pyGenomeTracks --tracks '/tmp/tmphrllkedv/job_working_directory/000/25/configs/tmpmxqhraqh' --region 'chr2:170000000-180000000' --width 40.0 --fontSize 12 --dpi 72 --trackLabelFraction 0.05 --trackLabelHAlign left --outFileName plot.png  && mv plot.png plot

Exit Code:

```
0
```

Standard Error:

WARNING:matplotlib:Matplotlib created a temporary cache directory at /tmp/tmphrllkedv/job_working_directory/000/25/tmp/matplotlib-alk3tpua because the default path (/home/runner/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
WARNING:matplotlib:Matplotlib created a temporary cache directory at /tmp/tmphrllkedv/job_working_directory/000/25/tmp/matplotlib-55chnjfj because the default path (/home/runner/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
INFO:pygenometracks.tracksClass:initialize 1. [hic_section_0_0]
WARNING:hicmatrix.HiCMatrix:Bin size is not homogeneous.                                       Median 1000000.000000

INFO:pygenometracks.tracksClass:initialize 2. [x-axis]
INFO:pygenometracks.tracksClass:time initializing track(s):
INFO:pygenometracks.tracksClass:0.01871180534362793
DEBUG:pygenometracks.tracksClass:Figure size in cm is 40.0 x 15.99027514066047. Dpi is set to 72

INFO:pygenometracks.tracksClass:plotting 1. [hic_section_0_0]
INFO:pygenometracks.tracks.GenomeTrack:setting min, max values for track 1. [hic_section_0_0] to: 0.0, 3.6000000000000005

INFO:pygenometracks.tracksClass:plotting 2. [x-axis]

Standard Output:

[hic_section_0_0]
file = 0_0.cool
file_type = hic_matrix
title = test_dataset
depth = 8000000
colormap = RdYlBu_r
transform = no
scale_factor = 1.0
rasterize = true
[x-axis]
where = bottom

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"cool"`
__workflow_invocation_uuid__	`"23e0745ea28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
global_args	`{"decreasingXAxis": false, "dpi": "72", "fontsize": "12", "height": null, "plotWidth": null, "title": "", "trackLabelFraction": "0.05", "trackLabelHAlign": "left", "width": "40.0"}`
image_file_format	`"png"`
region	`"chr2:170000000-180000000"`
tracks	[{"__index__": 0, "track_file_style_conditional": {"__current_case__": 0, "boundaries_file": null, "colormap": "RdYlBu_r", "depth": "8000000", "height_matrix": null, "invert_orientation": false, "matrix_h5_cooler_multiple": {"values": [{"id": 23, "src": "hdca"}]}, "max_value": null, "min_value": null, "rasterize": true, "scale_factor": "1.0", "show_masked_bins": false, "spacer_height": null, "title": "", "track_file_style_selector": "hic_matrix_option", "transform": "no"}}, {"__index__": 1, "track_file_style_conditional": {"__current_case__": 13, "fontsize": null, "spacer_height": null, "title": "", "track_file_style_selector": "xaxis_option", "xaxis_where": "bottom"}}]

Step 3: Restriction enzyme:
- step_state: scheduled
Step 4: No fill-in:
- step_state: scheduled
Step 5: minimum MAPQ:
- step_state: scheduled
Step 6: Bin size in bp:
- step_state: scheduled
Step 7: Interactions to consider to calculate weights in normalization step:
- step_state: scheduled
Step 8: capture region (chromosome):
- step_state: scheduled
Step 9: capture region (start):
- step_state: scheduled
Step 10: capture region (end):
- step_state: scheduled

Other invocation details
- history_id
  - 06ca28017569fc01
- history_state
  - ok
- invocation_id
  - 260f8995aa0c094e
- invocation_state
  - scheduled
- workflow_id
  - ce825a0c87e5740c

✅ hic-fastq-to-cool-hicup-cooler.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: PE fastq input:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled

Step 11: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Bin size in bp:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled
Step 3: Juicer Medium Tabix with validPairs:
- step_state: scheduled
Step 4: Interactions to consider to calculate weights in normalization step:
- step_state: scheduled

Step 5: make bed with bins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cooler makebins -o '/tmp/tmphrllkedv/job_working_directory/000/8/outputs/dataset_ebf1e9f8-167d-42f0-9238-3ab99e84667c.dat' '/cvmfs/data.galaxyproject.org/byhand/hg19/sam_index/hg19.fa'.fai 1000000

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"65bc1dc2a27f11f0a35e6045bd4a93e2"`
binsize	`"1000000"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
size_source	`{"__current_case__": 0, "fasta_cached": "hg19", "size_source_selector": "cached"}`

Step 6: Load pairs in matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmphrllkedv/files/4/f/8/dataset_4f87824f-cc14-4678-b46f-a7ecc6ca06f7.dat' pairs.tabix && ln -s '/tmp/tmphrllkedv/files/_metadata_files/8/b/2/metadata_8b20309b-0680-42c0-a074-495bafba869a.dat' pairs.tabix.tbi && cooler cload tabix --assembly 'hg19' -c2 7 -p2 8 '/tmp/tmphrllkedv/files/e/b/f/dataset_ebf1e9f8-167d-42f0-9238-3ab99e84667c.dat' pairs.tabix '/tmp/tmphrllkedv/job_working_directory/000/9/outputs/dataset_c639ae43-436f-4cd9-a24d-9230ec97c1f1.dat'

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.cload:Using 8 cores
INFO:cooler.create:Creating cooler at "/tmp/tmphrllkedv/job_working_directory/000/9/outputs/dataset_c639ae43-436f-4cd9-a24d-9230ec97c1f1.dat::/"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Binning chr10:0-135534747|*
INFO:cooler.create:Binning chr11:0-135006516|*
INFO:cooler.create:Binning chr12:0-133851895|*
INFO:cooler.create:Binning chr13:0-115169878|*
INFO:cooler.create:Binning chr14:0-107349540|*
INFO:cooler.create:Binning chr15:0-102531392|*
INFO:cooler.create:Binning chr16:0-90354753|*
INFO:cooler.create:Binning chr17:0-81195210|*
INFO:cooler.create:Finished chr11:0-135006516|*
INFO:cooler.create:Binning chr17_gl000204_random:0-81310|*
INFO:cooler.create:Finished chr17_gl000204_random:0-81310|*
INFO:cooler.create:Binning chr17_gl000205_random:0-174588|*
INFO:cooler.create:Finished chr17_gl000205_random:0-174588|*
INFO:cooler.create:Binning chr18:0-78077248|*
INFO:cooler.create:Finished chr12:0-133851895|*
INFO:cooler.create:Finished chr18:0-78077248|*
INFO:cooler.create:Finished chr15:0-102531392|*
INFO:cooler.create:Finished chr17:0-81195210|*
INFO:cooler.create:Binning chr19:0-59128983|*
INFO:cooler.create:Binning chr1:0-125000000|*
INFO:cooler.create:Binning chr1:125000000-249250621|*
INFO:cooler.create:Finished chr10:0-135534747|*
INFO:cooler.create:Finished chr13:0-115169878|*
INFO:cooler.create:Binning chr1_gl000192_random:0-547496|*
INFO:cooler.create:Binning chr20:0-63025520|*
INFO:cooler.create:Finished chr1_gl000192_random:0-547496|*
INFO:cooler.create:Binning chr21:0-48129895|*
INFO:cooler.create:Finished chr14:0-107349540|*
INFO:cooler.create:Finished chr16:0-90354753|*
INFO:cooler.create:Binning chr22:0-51304566|*
INFO:cooler.create:Binning chr2:0-129000000|*
INFO:cooler.create:Binning chr2:129000000-243199373|*
INFO:cooler.create:Finished chr19:0-59128983|*
INFO:cooler.create:Binning chr3:0-158000000|*
INFO:cooler.create:Finished chr22:0-51304566|*
INFO:cooler.create:Binning chr3:158000000-198022430|*
INFO:cooler.create:Finished chr21:0-48129895|*
INFO:cooler.create:Binning chr4:0-163000000|*
INFO:cooler.create:Finished chr1:125000000-249250621|*
INFO:cooler.create:Binning chr4:163000000-191154276|*
INFO:cooler.create:Finished chr20:0-63025520|*
INFO:cooler.create:Finished chr3:158000000-198022430|*
INFO:cooler.create:Binning chr5:0-173000000|*
INFO:cooler.create:Finished chr1:0-125000000|*
INFO:cooler.create:Binning chr5:173000000-180915260|*
INFO:cooler.create:Finished chr4:163000000-191154276|*
INFO:cooler.create:Binning chr6:0-171115067|*
INFO:cooler.create:Finished chr5:173000000-180915260|*
INFO:cooler.create:Binning chr7:0-159138663|*
INFO:cooler.create:Binning chr7_gl000195_random:0-182896|*
INFO:cooler.create:Finished chr7_gl000195_random:0-182896|*
INFO:cooler.create:Binning chr8:0-146364022|*
INFO:cooler.create:Finished chr2:0-129000000|*
INFO:cooler.create:Binning chr9:0-141213431|*
INFO:cooler.create:Finished chr2:129000000-243199373|*
INFO:cooler.create:Finished chr5:0-173000000|*
INFO:cooler.create:Binning chrM:0-16571|*
INFO:cooler.create:Binning chrUn_gl000211:0-166566|*
INFO:cooler.create:Finished chrM:0-16571|*
INFO:cooler.create:Finished chrUn_gl000211:0-166566|*
INFO:cooler.create:Binning chrUn_gl000220:0-161802|*
INFO:cooler.create:Binning chrX:0-155270560|*
INFO:cooler.create:Finished chr3:0-158000000|*
INFO:cooler.create:Finished chrUn_gl000220:0-161802|*
INFO:cooler.create:Finished chr6:0-171115067|*
INFO:cooler.create:Finished chr4:0-163000000|*
INFO:cooler.create:Finished chr9:0-141213431|*
INFO:cooler.create:Finished chr7:0-159138663|*
INFO:cooler.create:Finished chr8:0-146364022|*
INFO:cooler.create:Finished chrX:0-155270560|*
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"65bc1dc2a27f11f0a35e6045bd4a93e2"`
assembly	`"hg19"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format_sel	`{"__current_case__": 0, "format": "juicer_medium", "input_pairs": {"values": [{"id": 35, "src": "dce"}]}}`

Step 7: ICE normalization:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmphrllkedv/files/c/6/3/dataset_c639ae43-436f-4cd9-a24d-9230ec97c1f1.dat' '/tmp/tmphrllkedv/job_working_directory/000/10/outputs/dataset_05be6ebe-654a-4f70-a384-2625d601ffda.dat' && cooler balance -p ${GALAXY_SLOTS:-1} --mad-max 5 --min-nnz 10 --min-count 0 --ignore-diags 2 --ignore-dist 0 --tol 1e-05 --max-iters 200  -f --convergence-policy error '/tmp/tmphrllkedv/job_working_directory/000/10/outputs/dataset_05be6ebe-654a-4f70-a384-2625d601ffda.dat'

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.balance:Balancing "/tmp/tmphrllkedv/job_working_directory/000/10/outputs/dataset_05be6ebe-654a-4f70-a384-2625d601ffda.dat"
INFO:cooler.balance:variance is 32.14115008705733
INFO:cooler.balance:variance is 1.9639478587655248
INFO:cooler.balance:variance is 0.24716400930194715
INFO:cooler.balance:variance is 0.04094621381897245
INFO:cooler.balance:variance is 0.0074257541155607724
INFO:cooler.balance:variance is 0.0014584217826405
INFO:cooler.balance:variance is 0.00029808774941172587
INFO:cooler.balance:variance is 6.323059230174223e-05
INFO:cooler.balance:variance is 1.3743638412433148e-05
INFO:cooler.balance:variance is 3.0518688388225226e-06

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"65bc1dc2a27f11f0a35e6045bd4a93e2"`
blacklist	`None`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cistrans	`""`
convergencepolicy	`"error"`
dbkey	`"?"`
ignorediags	`"2"`
ignoredist	`"0"`
madmax	`"5"`
maxiters	`"200"`
mincount	`"0"`
minnnz	`"10"`
name	`"weight"`
tol	`"1e-05"`

Step 12: final plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s /tmp/tmphrllkedv/files/0/5/b/dataset_05be6ebe-654a-4f70-a384-2625d601ffda.dat 0_0.cool &&   sed '/^$/d' '/tmp/tmphrllkedv/job_working_directory/000/11/configs/tmpqa06_cyr' && pyGenomeTracks --tracks '/tmp/tmphrllkedv/job_working_directory/000/11/configs/tmpqa06_cyr' --region 'chr2:175,689,620-178,604,461' --width 40.0 --fontSize 12 --dpi 72 --trackLabelFraction 0.05 --trackLabelHAlign left --outFileName plot.png  && mv plot.png plot

Exit Code:

```
0
```

Standard Error:

WARNING:matplotlib:Matplotlib created a temporary cache directory at /tmp/tmphrllkedv/job_working_directory/000/11/tmp/matplotlib-sxl9w9ws because the default path (/home/runner/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
WARNING:matplotlib:Matplotlib created a temporary cache directory at /tmp/tmphrllkedv/job_working_directory/000/11/tmp/matplotlib-hpqou1nr because the default path (/home/runner/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
INFO:pygenometracks.tracksClass:initialize 1. [hic_section_0_0]
WARNING:hicmatrix.HiCMatrix:Bin size is not homogeneous.                                       Median 1000000.000000

INFO:pygenometracks.tracksClass:initialize 2. [x-axis]
INFO:pygenometracks.tracksClass:time initializing track(s):
INFO:pygenometracks.tracksClass:0.021510839462280273
DEBUG:pygenometracks.tracksClass:Figure size in cm is 40.0 x 23.862795428091413. Dpi is set to 72

INFO:pygenometracks.tracksClass:plotting 1. [hic_section_0_0]
WARNING:pygenometracks.tracks.HiCMatrixTrack:The depth was set to 8000000 which is more than 125% of the region plotted. The depth will be set to 3643551.

INFO:pygenometracks.tracks.GenomeTrack:setting min, max values for track 1. [hic_section_0_0] to: 0.0517567934545867, 0.12924814515458122

INFO:pygenometracks.tracksClass:plotting 2. [x-axis]

Standard Output:

[hic_section_0_0]
file = 0_0.cool
file_type = hic_matrix
title = test_dataset
depth = 8000000
colormap = RdYlBu_r
transform = no
scale_factor = 1.0
rasterize = true
[x-axis]
where = bottom

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"cool"`
__workflow_invocation_uuid__	`"65bc1dc0a27f11f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
global_args	`{"decreasingXAxis": false, "dpi": "72", "fontsize": "12", "height": null, "plotWidth": null, "title": "", "trackLabelFraction": "0.05", "trackLabelHAlign": "left", "width": "40.0"}`
image_file_format	`"png"`
region	`"chr2:175,689,620-178,604,461"`
tracks	[{"__index__": 0, "track_file_style_conditional": {"__current_case__": 0, "boundaries_file": null, "colormap": "RdYlBu_r", "depth": "8000000", "height_matrix": null, "invert_orientation": false, "matrix_h5_cooler_multiple": {"values": [{"id": 11, "src": "hdca"}]}, "max_value": null, "min_value": null, "rasterize": true, "scale_factor": "1.0", "show_masked_bins": false, "spacer_height": null, "title": "", "track_file_style_selector": "hic_matrix_option", "transform": "no"}}, {"__index__": 1, "track_file_style_conditional": {"__current_case__": 13, "fontsize": null, "spacer_height": null, "title": "", "track_file_style_selector": "xaxis_option", "xaxis_where": "bottom"}}]

Step 3: Restriction enzyme:
- step_state: scheduled
Step 4: No fill-in:
- step_state: scheduled
Step 5: minimum MAPQ:
- step_state: scheduled
Step 6: Bin size in bp:
- step_state: scheduled
Step 7: Interactions to consider to calculate weights in normalization step:
- step_state: scheduled
Step 8: region for matrix plotting:
- step_state: scheduled

Step 9: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: PE fastq input:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled
Step 3: Restriction enzyme:
- step_state: scheduled
Step 4: No fill-in:
- step_state: scheduled
Step 5: minimum MAPQ:
- step_state: scheduled

Step 6: HiCUP:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmphrllkedv/files/4/1/9/dataset_419bd96f-b037-49d7-8713-b85ef3392534.dat' 'dataset1.fq' &&  ln -f -s '/tmp/tmphrllkedv/files/d/5/0/dataset_d50d0a95-6d86-4c1b-a37a-1a62985f04d0.dat' 'dataset2.fq' &&    BOWTIE_PATH_BASH="$(which bowtie2)" && hicup_digester --re1 'A^AGCTT,HindIII' --genome 'hg19' '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full'.fa && mv *Digest_* digest_file.txt && hicup --zip --threads ${GALAXY_SLOTS:-1} --digest digest_file.txt --index '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full' --bowtie2 $BOWTIE_PATH_BASH --keep   'dataset1.fq' 'dataset2.fq'

Exit Code:

```
0
```

Standard Error:

Digestion complete
FASTQ quality format not specified, analysing file 'dataset1.fq' to predict file format used
FASTQ quality set to 'Sanger'
Detecting R automatically
Found R at '/usr/local/bin/R'
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Filtering dataset1_2.pair.bam
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories

Standard Output:

HiCUP Digester (version 0.9.2)
Digesting files
Digesting '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full.fa'
Starting HiCUP pipeline (v0.9.2)
PLEASE NOTE: FROM VERSION 8, HICUP REQUIRES THE R PACKAGES TIDYVERSE AND PLOTLY INSTALLED
SEE DOCUMENTATION FOR MORE DETAILS
Reading genome digest file 'digest_file.txt' to determine Hi-C restriction enzyme
Truncating with HiCUP Truncater v0.9.2
Truncating sequences at occurrence of sequences '[AAGCTAGCTT]'
Truncating sequences
Truncating dataset1.fq
Truncating dataset2.fq
Truncating complete
Mapping with HiCUP Mapper v0.9.2
Using aligner 'bowtie2'
Mapping dataset1.trunc.fastq.gz
Mapping dataset2.trunc.fastq.gz
Mapping complete
Pairing files with HiCUP Mapper v0.9.2
Pairing dataset1.map.sam and dataset2.map.sam
Pairing complete
Filtering with HiCUP Filter v0.9.2
Processing digest file digest_file.txt
Sonication protocol followed - Restriction_Enzyme1:HindIII [A^AGCTT]
Filtering complete
Removing duplicates with HiCUP Deduplicator v0.9.2
De-duplicating dataset1_2.filt.bam
De-duplication complete
Creating combined HiCUP summary report
Reading folder '/tmp/tmphrllkedv/job_working_directory/000/3/working'
Writing to: /tmp/tmphrllkedv/job_working_directory/000/3/working/
	1 complete summary results groups identified in folder
Created combined summary reports
Created HTML summary reports
HiCUP processing complete.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger"`
__workflow_invocation_uuid__	`"65bc1dc1a27f11f0a35e6045bd4a93e2"`
advanced_options	`{"longest": "", "nofill": false, "re2": "", "shortest": ""}`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
genome	`"hg19"`
library	`{"__current_case__": 1, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "type": "paired_collection"}`
re1	`"A^AGCTT,HindIII"`
reference_genome	`{"__current_case__": 0, "index": "hg19", "source": "indexed"}`

Step 7: build filtering rule for MAPQ:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"65bc1dc1a27f11f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "(c10>=", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "30", "select_param_type": "integer"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": ") and (c11>=", "select_param_type": "text"}}, {"__index__": 3, "param_type": {"__current_case__": 1, "component_value": "30", "select_param_type": "integer"}}, {"__index__": 4, "param_type": {"__current_case__": 0, "component_value": ")", "select_param_type": "text"}}]
dbkey	`"?"`

Step 8: valid pairs in juicebox format:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmphrllkedv/files/3/d/6/dataset_3d61e463-f4b5-429d-b50d-b6e5554e32f1.dat' input.bam && hicup2juicer --digest '/tmp/tmphrllkedv/files/3/d/b/dataset_3dbd1873-3f4f-4eab-b111-2e4056be4e1f.dat' '--usemid' input.bam

Exit Code:

```
0
```

Standard Output:

Processing digester file
Sonication protocol followed - Restriction_Enzyme1:HindIII [A^AGCTT]
Processing input.bam
The outputfiles generated by this script may be converted to Juicer '.hic' files using the 'pre' command as described at: https://github.com/aidenlab/juicer/wiki/Pre
Processing complete.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"qname_sorted.bam"`
__workflow_invocation_uuid__	`"65bc1dc1a27f11f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
digester	`{"__current_case__": 0, "digester_file": {"values": [{"id": 8, "src": "dce"}]}, "provide_digester": "yes", "usemid": true}`

Step 9: valid pairs in juicebox format MAPQ filtered:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmphrllkedv/galaxy-dev/tools/stats/filtering.py' '/tmp/tmphrllkedv/files/e/3/9/dataset_e39c04e8-a4ad-4695-92f9-d87455a3a1c1.dat' '/tmp/tmphrllkedv/job_working_directory/000/6/outputs/dataset_d9fb8f53-d9fa-4f6c-9fca-a7a416d11748.dat' '/tmp/tmphrllkedv/job_working_directory/000/6/configs/tmp78nve639' 11 "int,int,str,int,int,int,str,int,int,int,int" 0

Exit Code:

```
0
```

Standard Output:

Filtering with (c10>=30) and (c11>=30), 
kept 93.80% of 39962 valid lines (39962 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"65bc1dc1a27f11f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"(c10>=30) and (c11>=30)"`
dbkey	`"?"`
header_lines	`"0"`

Step 10: Sort pairs and index:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cooler csort -i tabix -c1 3 -c2 7 -p1 4 -p2 8 -o '/tmp/tmphrllkedv/job_working_directory/000/7/outputs/dataset_4f87824f-cc14-4678-b46f-a7ecc6ca06f7.dat' '/tmp/tmphrllkedv/files/e/3/9/dataset_e39c04e8-a4ad-4695-92f9-d87455a3a1c1.dat' '/cvmfs/data.galaxyproject.org/byhand/hg19/sam_index/hg19.fa'.fai

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.csort:Enumerating requested chromosomes...
INFO:cooler.cli.csort:chr10	1
INFO:cooler.cli.csort:chr11	2
INFO:cooler.cli.csort:chr11_gl000202_random	3
INFO:cooler.cli.csort:chr12	4
INFO:cooler.cli.csort:chr13	5
INFO:cooler.cli.csort:chr14	6
INFO:cooler.cli.csort:chr15	7
INFO:cooler.cli.csort:chr16	8
INFO:cooler.cli.csort:chr17_ctg5_hap1	9
INFO:cooler.cli.csort:chr17	10
INFO:cooler.cli.csort:chr17_gl000203_random	11
INFO:cooler.cli.csort:chr17_gl000204_random	12
INFO:cooler.cli.csort:chr17_gl000205_random	13
INFO:cooler.cli.csort:chr17_gl000206_random	14
INFO:cooler.cli.csort:chr18	15
INFO:cooler.cli.csort:chr18_gl000207_random	16
INFO:cooler.cli.csort:chr19	17
INFO:cooler.cli.csort:chr19_gl000208_random	18
INFO:cooler.cli.csort:chr19_gl000209_random	19
INFO:cooler.cli.csort:chr1	20
INFO:cooler.cli.csort:chr1_gl000191_random	21
INFO:cooler.cli.csort:chr1_gl000192_random	22
INFO:cooler.cli.csort:chr20	23
INFO:cooler.cli.csort:chr21	24
INFO:cooler.cli.csort:chr21_gl000210_random	25
INFO:cooler.cli.csort:chr22	26
INFO:cooler.cli.csort:chr2	27
INFO:cooler.cli.csort:chr3	28
INFO:cooler.cli.csort:chr4_ctg9_hap1	29
INFO:cooler.cli.csort:chr4	30
INFO:cooler.cli.csort:chr4_gl000193_random	31
INFO:cooler.cli.csort:chr4_gl000194_random	32
INFO:cooler.cli.csort:chr5	33
INFO:cooler.cli.csort:chr6_apd_hap1	34
INFO:cooler.cli.csort:chr6_cox_hap2	35
INFO:cooler.cli.csort:chr6_dbb_hap3	36
INFO:cooler.cli.csort:chr6	37
INFO:cooler.cli.csort:chr6_mann_hap4	38
INFO:cooler.cli.csort:chr6_mcf_hap5	39
INFO:cooler.cli.csort:chr6_qbl_hap6	40
INFO:cooler.cli.csort:chr6_ssto_hap7	41
INFO:cooler.cli.csort:chr7	42
INFO:cooler.cli.csort:chr7_gl000195_random	43
INFO:cooler.cli.csort:chr8	44
INFO:cooler.cli.csort:chr8_gl000196_random	45
INFO:cooler.cli.csort:chr8_gl000197_random	46
INFO:cooler.cli.csort:chr9	47
INFO:cooler.cli.csort:chr9_gl000198_random	48
INFO:cooler.cli.csort:chr9_gl000199_random	49
INFO:cooler.cli.csort:chr9_gl000200_random	50
INFO:cooler.cli.csort:chr9_gl000201_random	51
INFO:cooler.cli.csort:chrM	52
INFO:cooler.cli.csort:chrUn_gl000211	53
INFO:cooler.cli.csort:chrUn_gl000212	54
INFO:cooler.cli.csort:chrUn_gl000213	55
INFO:cooler.cli.csort:chrUn_gl000214	56
INFO:cooler.cli.csort:chrUn_gl000215	57
INFO:cooler.cli.csort:chrUn_gl000216	58
INFO:cooler.cli.csort:chrUn_gl000217	59
INFO:cooler.cli.csort:chrUn_gl000218	60
INFO:cooler.cli.csort:chrUn_gl000219	61
INFO:cooler.cli.csort:chrUn_gl000220	62
INFO:cooler.cli.csort:chrUn_gl000221	63
INFO:cooler.cli.csort:chrUn_gl000222	64
INFO:cooler.cli.csort:chrUn_gl000223	65
INFO:cooler.cli.csort:chrUn_gl000224	66
INFO:cooler.cli.csort:chrUn_gl000225	67
INFO:cooler.cli.csort:chrUn_gl000226	68
INFO:cooler.cli.csort:chrUn_gl000227	69
INFO:cooler.cli.csort:chrUn_gl000228	70
INFO:cooler.cli.csort:chrUn_gl000229	71
INFO:cooler.cli.csort:chrUn_gl000230	72
INFO:cooler.cli.csort:chrUn_gl000231	73
INFO:cooler.cli.csort:chrUn_gl000232	74
INFO:cooler.cli.csort:chrUn_gl000233	75
INFO:cooler.cli.csort:chrUn_gl000234	76
INFO:cooler.cli.csort:chrUn_gl000235	77
INFO:cooler.cli.csort:chrUn_gl000236	78
INFO:cooler.cli.csort:chrUn_gl000237	79
INFO:cooler.cli.csort:chrUn_gl000238	80
INFO:cooler.cli.csort:chrUn_gl000239	81
INFO:cooler.cli.csort:chrUn_gl000240	82
INFO:cooler.cli.csort:chrUn_gl000241	83
INFO:cooler.cli.csort:chrUn_gl000242	84
INFO:cooler.cli.csort:chrUn_gl000243	85
INFO:cooler.cli.csort:chrUn_gl000244	86
INFO:cooler.cli.csort:chrUn_gl000245	87
INFO:cooler.cli.csort:chrUn_gl000246	88
INFO:cooler.cli.csort:chrUn_gl000247	89
INFO:cooler.cli.csort:chrUn_gl000248	90
INFO:cooler.cli.csort:chrUn_gl000249	91
INFO:cooler.cli.csort:chrX	92
INFO:cooler.cli.csort:chrY	93
INFO:cooler.cli.csort:Input: '/tmp/tmphrllkedv/files/e/3/9/dataset_e39c04e8-a4ad-4695-92f9-d87455a3a1c1.dat'
INFO:cooler.cli.csort:Output: '/tmp/tmphrllkedv/job_working_directory/000/7/outputs/dataset_4f87824f-cc14-4678-b46f-a7ecc6ca06f7.dat'
INFO:cooler.cli.csort:Reordering pair mates and sorting pair records...
INFO:cooler.cli.csort:Sort order: positional (chrom1, pos1, chrom2, pos2)
INFO:cooler.cli.csort:sort -k3,3 -k4,4n -k7,7 -k8,8n
INFO:cooler.cli.csort:Indexing...
INFO:cooler.cli.csort:Indexer: tabix
INFO:cooler.cli.csort:tabix -f -s3 -b4 -e4 /tmp/tmphrllkedv/job_working_directory/000/7/outputs/dataset_4f87824f-cc14-4678-b46f-a7ecc6ca06f7.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"65bc1dc0a27f11f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format_sel	`{"__current_case__": 0, "format": "juicer_medium"}`
size_source	`{"__current_case__": 0, "fasta_cached": "hg19", "size_source_selector": "cached"}`

Other invocation details
- history_id
  - c37a1862d8a437d3
- history_state
  - ok
- invocation_id
  - c37a1862d8a437d3
- invocation_state
  - scheduled
- workflow_id
  - 0e87a3ab9cda1742

✅ hic-fastq-to-pairs-hicup.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: PE fastq input:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled
Step 3: Restriction enzyme:
- step_state: scheduled
Step 4: No fill-in:
- step_state: scheduled
Step 5: minimum MAPQ:
- step_state: scheduled

Step 6: HiCUP:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmphrllkedv/files/f/c/e/dataset_fce62a6d-c071-42ce-9f94-f6e40ac2a464.dat' 'dataset1.fq' &&  ln -f -s '/tmp/tmphrllkedv/files/1/b/f/dataset_1bf5ae7a-bb46-4a28-879f-46847a398554.dat' 'dataset2.fq' &&    BOWTIE_PATH_BASH="$(which bowtie2)" && hicup_digester --re1 'A^AGCTT,HindIII' --genome 'hg19' '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full'.fa && mv *Digest_* digest_file.txt && hicup --zip --threads ${GALAXY_SLOTS:-1} --digest digest_file.txt --index '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full' --bowtie2 $BOWTIE_PATH_BASH --keep   'dataset1.fq' 'dataset2.fq'

Exit Code:

```
0
```

Standard Error:

Digestion complete
FASTQ quality format not specified, analysing file 'dataset1.fq' to predict file format used
FASTQ quality set to 'Sanger'
Detecting R automatically
Found R at '/usr/local/bin/R'
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Filtering dataset1_2.pair.bam
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories

Standard Output:

HiCUP Digester (version 0.9.2)
Digesting files
Digesting '/cvmfs/data.galaxyproject.org/byhand/hg19/hg19full/bowtie2_index/hg19full.fa'
Starting HiCUP pipeline (v0.9.2)
PLEASE NOTE: FROM VERSION 8, HICUP REQUIRES THE R PACKAGES TIDYVERSE AND PLOTLY INSTALLED
SEE DOCUMENTATION FOR MORE DETAILS
Reading genome digest file 'digest_file.txt' to determine Hi-C restriction enzyme
Truncating with HiCUP Truncater v0.9.2
Truncating sequences at occurrence of sequences '[AAGCTAGCTT]'
Truncating sequences
Truncating dataset1.fq
Truncating dataset2.fq
Truncating complete
Mapping with HiCUP Mapper v0.9.2
Using aligner 'bowtie2'
Mapping dataset1.trunc.fastq.gz
Mapping dataset2.trunc.fastq.gz
Mapping complete
Pairing files with HiCUP Mapper v0.9.2
Pairing dataset1.map.sam and dataset2.map.sam
Pairing complete
Filtering with HiCUP Filter v0.9.2
Processing digest file digest_file.txt
Sonication protocol followed - Restriction_Enzyme1:HindIII [A^AGCTT]
Filtering complete
Removing duplicates with HiCUP Deduplicator v0.9.2
De-duplicating dataset1_2.filt.bam
De-duplication complete
Creating combined HiCUP summary report
Reading folder '/tmp/tmphrllkedv/job_working_directory/000/32/working'
Writing to: /tmp/tmphrllkedv/job_working_directory/000/32/working/
	1 complete summary results groups identified in folder
Created combined summary reports
Created HTML summary reports
HiCUP processing complete.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastqsanger"`
__workflow_invocation_uuid__	`"c516391ca28011f0a35e6045bd4a93e2"`
advanced_options	`{"longest": "", "nofill": false, "re2": "", "shortest": ""}`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
genome	`"hg19"`
library	`{"__current_case__": 1, "input_1": {"values": [{"id": 79, "src": "dce"}]}, "type": "paired_collection"}`
re1	`"A^AGCTT,HindIII"`
reference_genome	`{"__current_case__": 0, "index": "hg19", "source": "indexed"}`

Step 7: build filtering rule for MAPQ:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c516391ca28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "(c10>=", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "30", "select_param_type": "integer"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": ") and (c11>=", "select_param_type": "text"}}, {"__index__": 3, "param_type": {"__current_case__": 1, "component_value": "30", "select_param_type": "integer"}}, {"__index__": 4, "param_type": {"__current_case__": 0, "component_value": ")", "select_param_type": "text"}}]
dbkey	`"?"`

Step 8: valid pairs in juicebox format:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmphrllkedv/files/b/9/7/dataset_b97a7db9-5551-492b-a6a7-0d06eb85521e.dat' input.bam && hicup2juicer --digest '/tmp/tmphrllkedv/files/e/9/8/dataset_e9834721-cb8f-46a7-8a71-5d2953d05303.dat' '--usemid' input.bam

Exit Code:

```
0
```

Standard Output:

Processing digester file
Sonication protocol followed - Restriction_Enzyme1:HindIII [A^AGCTT]
Processing input.bam
The outputfiles generated by this script may be converted to Juicer '.hic' files using the 'pre' command as described at: https://github.com/aidenlab/juicer/wiki/Pre
Processing complete.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"qname_sorted.bam"`
__workflow_invocation_uuid__	`"c516391ca28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
digester	`{"__current_case__": 0, "digester_file": {"values": [{"id": 86, "src": "dce"}]}, "provide_digester": "yes", "usemid": true}`

Step 9: valid pairs in juicebox format MAPQ filtered:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmphrllkedv/galaxy-dev/tools/stats/filtering.py' '/tmp/tmphrllkedv/files/f/c/f/dataset_fcfdb2a7-ad5d-4dc8-a3ae-3cc85d50e2ad.dat' '/tmp/tmphrllkedv/job_working_directory/000/35/outputs/dataset_8b26e957-29c2-4368-9233-c82ddc758a2c.dat' '/tmp/tmphrllkedv/job_working_directory/000/35/configs/tmp902nxuru' 11 "int,int,str,int,int,int,str,int,int,int,int" 0

Exit Code:

```
0
```

Standard Output:

Filtering with (c10>=30) and (c11>=30), 
kept 93.80% of 39962 valid lines (39962 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c516391ca28011f0a35e6045bd4a93e2"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"(c10>=30) and (c11>=30)"`
dbkey	`"?"`
header_lines	`"0"`

Other invocation details
- history_id
  - 260f8995aa0c094e
- history_state
  - ok
- invocation_id
  - 018fea460231f69d
- invocation_state
  - scheduled
- workflow_id
  - 018fea460231f69d

✅ hic-juicermediumtabix-to-cool-cooler.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Bin size in bp:
- step_state: scheduled
Step 2: genome name:
- step_state: scheduled
Step 3: Juicer Medium Tabix with validPairs:
- step_state: scheduled
Step 4: Interactions to consider to calculate weights in normalization step:
- step_state: scheduled

Step 5: make bed with bins:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cooler makebins -o '/tmp/tmphrllkedv/job_working_directory/000/27/outputs/dataset_e1d9987c-8d44-4b88-8da4-44a69ace6c7c.dat' '/cvmfs/data.galaxyproject.org/byhand/hg19/sam_index/hg19.fa'.fai 1000000

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b1ec1d5ca28011f0a35e6045bd4a93e2"`
binsize	`"1000000"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
size_source	`{"__current_case__": 0, "fasta_cached": "hg19", "size_source_selector": "cached"}`

Step 6: Load pairs in matrix:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmphrllkedv/files/e/b/d/dataset_ebd3d469-b042-47b6-a777-712fdf38ad53.dat' pairs.tabix && ln -s '/tmp/tmphrllkedv/files/_metadata_files/d/e/0/metadata_de0d9b94-c295-4f8d-9a30-675dcd17a508.dat' pairs.tabix.tbi && cooler cload tabix --assembly 'hg19' -c2 7 -p2 8 '/tmp/tmphrllkedv/files/e/1/d/dataset_e1d9987c-8d44-4b88-8da4-44a69ace6c7c.dat' pairs.tabix '/tmp/tmphrllkedv/job_working_directory/000/28/outputs/dataset_9789789a-0f76-4176-a341-57f428a38ff3.dat'

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.cload:Using 8 cores
INFO:cooler.create:Creating cooler at "/tmp/tmphrllkedv/job_working_directory/000/28/outputs/dataset_9789789a-0f76-4176-a341-57f428a38ff3.dat::/"
INFO:cooler.create:Writing chroms
INFO:cooler.create:Writing bins
INFO:cooler.create:Writing pixels
INFO:cooler.create:Binning chr2:0-129000000|*
INFO:cooler.create:Binning chr2:129000000-243199373|*
INFO:cooler.create:Finished chr2:0-129000000|*
INFO:cooler.create:Finished chr2:129000000-243199373|*
INFO:cooler.create:Writing indexes
INFO:cooler.create:Writing info

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b1ec1d5ca28011f0a35e6045bd4a93e2"`
assembly	`"hg19"`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format_sel	`{"__current_case__": 0, "format": "juicer_medium", "input_pairs": {"values": [{"id": 76, "src": "dce"}]}}`

Step 7: ICE normalization:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmphrllkedv/files/9/7/8/dataset_9789789a-0f76-4176-a341-57f428a38ff3.dat' '/tmp/tmphrllkedv/job_working_directory/000/29/outputs/dataset_7400cd1f-8581-4c8e-8bfe-2c636f6d0c71.dat' && cooler balance -p ${GALAXY_SLOTS:-1} --mad-max 5 --min-nnz 10 --min-count 0 --ignore-diags 2 --ignore-dist 0 --tol 1e-05 --max-iters 200 --cis-only -f --convergence-policy error '/tmp/tmphrllkedv/job_working_directory/000/29/outputs/dataset_7400cd1f-8581-4c8e-8bfe-2c636f6d0c71.dat'

Exit Code:

```
0
```

Standard Error:

INFO:cooler.cli.balance:Balancing "/tmp/tmphrllkedv/job_working_directory/000/29/outputs/dataset_7400cd1f-8581-4c8e-8bfe-2c636f6d0c71.dat"
INFO:cooler.balance:chr10
INFO:cooler.balance:chr11
INFO:cooler.balance:chr11_gl000202_random
INFO:cooler.balance:chr12
INFO:cooler.balance:chr13
INFO:cooler.balance:chr14
INFO:cooler.balance:chr15
INFO:cooler.balance:chr16
INFO:cooler.balance:chr17_ctg5_hap1
INFO:cooler.balance:chr17
INFO:cooler.balance:chr17_gl000203_random
INFO:cooler.balance:chr17_gl000204_random
INFO:cooler.balance:chr17_gl000205_random
INFO:cooler.balance:chr17_gl000206_random
INFO:cooler.balance:chr18
INFO:cooler.balance:chr18_gl000207_random
INFO:cooler.balance:chr19
INFO:cooler.balance:chr19_gl000208_random
INFO:cooler.balance:chr19_gl000209_random
INFO:cooler.balance:chr1
INFO:cooler.balance:chr1_gl000191_random
INFO:cooler.balance:chr1_gl000192_random
INFO:cooler.balance:chr20
INFO:cooler.balance:chr21
INFO:cooler.balance:chr21_gl000210_random
INFO:cooler.balance:chr22
INFO:cooler.balance:chr2
INFO:cooler.balance:chr3
INFO:cooler.balance:chr4_ctg9_hap1
INFO:cooler.balance:chr4
INFO:cooler.balance:chr4_gl000193_random
INFO:cooler.balance:chr4_gl000194_random
INFO:cooler.balance:chr5
INFO:cooler.balance:chr6_apd_hap1
INFO:cooler.balance:chr6_cox_hap2
INFO:cooler.balance:chr6_dbb_hap3
INFO:cooler.balance:chr6
INFO:cooler.balance:chr6_mann_hap4
INFO:cooler.balance:chr6_mcf_hap5
INFO:cooler.balance:chr6_qbl_hap6
INFO:cooler.balance:chr6_ssto_hap7
INFO:cooler.balance:chr7
INFO:cooler.balance:chr7_gl000195_random
INFO:cooler.balance:chr8
INFO:cooler.balance:chr8_gl000196_random
INFO:cooler.balance:chr8_gl000197_random
INFO:cooler.balance:chr9
INFO:cooler.balance:chr9_gl000198_random
INFO:cooler.balance:chr9_gl000199_random
INFO:cooler.balance:chr9_gl000200_random
INFO:cooler.balance:chr9_gl000201_random
INFO:cooler.balance:chrM
INFO:cooler.balance:chrUn_gl000211
INFO:cooler.balance:chrUn_gl000212
INFO:cooler.balance:chrUn_gl000213
INFO:cooler.balance:chrUn_gl000214
INFO:cooler.balance:chrUn_gl000215
INFO:cooler.balance:chrUn_gl000216
INFO:cooler.balance:chrUn_gl000217
INFO:cooler.balance:chrUn_gl000218
INFO:cooler.balance:chrUn_gl000219
INFO:cooler.balance:chrUn_gl000220
INFO:cooler.balance:chrUn_gl000221
INFO:cooler.balance:chrUn_gl000222
INFO:cooler.balance:chrUn_gl000223
INFO:cooler.balance:chrUn_gl000224
INFO:cooler.balance:chrUn_gl000225
INFO:cooler.balance:chrUn_gl000226
INFO:cooler.balance:chrUn_gl000227
INFO:cooler.balance:chrUn_gl000228
INFO:cooler.balance:chrUn_gl000229
INFO:cooler.balance:chrUn_gl000230
INFO:cooler.balance:chrUn_gl000231
INFO:cooler.balance:chrUn_gl000232
INFO:cooler.balance:chrUn_gl000233
INFO:cooler.balance:chrUn_gl000234
INFO:cooler.balance:chrUn_gl000235
INFO:cooler.balance:chrUn_gl000236
INFO:cooler.balance:chrUn_gl000237
INFO:cooler.balance:chrUn_gl000238
INFO:cooler.balance:chrUn_gl000239
INFO:cooler.balance:chrUn_gl000240
INFO:cooler.balance:chrUn_gl000241
INFO:cooler.balance:chrUn_gl000242
INFO:cooler.balance:chrUn_gl000243
INFO:cooler.balance:chrUn_gl000244
INFO:cooler.balance:chrUn_gl000245
INFO:cooler.balance:chrUn_gl000246
INFO:cooler.balance:chrUn_gl000247
INFO:cooler.balance:chrUn_gl000248
INFO:cooler.balance:chrUn_gl000249
INFO:cooler.balance:chrX
INFO:cooler.balance:chrY

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b1ec1d5ca28011f0a35e6045bd4a93e2"`
blacklist	`None`
chromInfo	`"/tmp/tmphrllkedv/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cistrans	`"--cis-only"`
convergencepolicy	`"error"`
dbkey	`"?"`
ignorediags	`"2"`
ignoredist	`"0"`
madmax	`"5"`
maxiters	`"200"`
mincount	`"0"`
minnnz	`"10"`
name	`"weight"`
tol	`"1e-05"`

Other invocation details
- history_id
  - 0e87a3ab9cda1742
- history_state
  - ok
- invocation_id
  - ce29a6a513f7d228
- invocation_state
  - scheduled
- workflow_id
  - ce29a6a513f7d228

Updating workflows/epigenetics/hic-hicup-cooler from 0.3 to 0.4

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