Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.6 to 0.7 #1013

gxydevbot · 2025-11-03T04:50:21Z

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1

The workflow release number has been updated from 0.6 to 0.7.

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 · 2025-11-03T05:08:19Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ kmer-profiling-hifi-VGP1.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Species Name:
- step_state: scheduled
Step 2: Assembly Name:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

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__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 1, "component_value": "21", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 12: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: PacBio reads:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy3:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpwfmm7c9p/files/b/5/5/dataset_b5534b1d-00f2-4d46-ad1a-08db720f2565.dat'  'm54306U_210519_154448' &&  mash sketch -s '1000' -k '21' -w '0.01' -m '1' -r 'm54306U_210519_154448' -o 'sketch'

Exit Code:

```
0
```

Standard Error:

Estimated genome size: 1.70459e+06
Estimated coverage:    3.782
Writing to sketch.msh...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_size	`"21"`
prob_threshold	`"0.01"`
reads_assembly	`{"__current_case__": 0, "genome_size": null, "minimum_kmer_copies": "1", "reads_assembly_selector": "reads", "reads_input": {"__current_case__": 1, "reads": {"values": [{"id": 1, "src": "dce"}]}, "reads_input_selector": "single"}, "target_coverage": null}`
sketch_size	`"1000"`

Job 2:

Job state is ok

Command Line:

ln -s '/tmp/tmpwfmm7c9p/files/1/f/1/dataset_1f16c813-1393-4d46-bdc4-dd1f181f40e7.dat'  'm54306U_210521_004211' &&  mash sketch -s '1000' -k '21' -w '0.01' -m '1' -r 'm54306U_210521_004211' -o 'sketch'

Exit Code:

```
0
```

Standard Error:

Estimated genome size: 1.62335e+06
Estimated coverage:    4.098
Writing to sketch.msh...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_size	`"21"`
prob_threshold	`"0.01"`
reads_assembly	`{"__current_case__": 0, "genome_size": null, "minimum_kmer_copies": "1", "reads_assembly_selector": "reads", "reads_input": {"__current_case__": 1, "reads": {"values": [{"id": 2, "src": "dce"}]}, "reads_input_selector": "single"}, "target_coverage": null}`
sketch_size	`"1000"`

Job 3:

Job state is ok

Command Line:

ln -s '/tmp/tmpwfmm7c9p/files/4/a/9/dataset_4a97e5b0-0b3e-42e4-9de4-060188af330d.dat'  'm54306Ue_210719_083927' &&  mash sketch -s '1000' -k '21' -w '0.01' -m '1' -r 'm54306Ue_210719_083927' -o 'sketch'

Exit Code:

```
0
```

Standard Error:

Estimated genome size: 1.98968e+06
Estimated coverage:    5.099
Writing to sketch.msh...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_size	`"21"`
prob_threshold	`"0.01"`
reads_assembly	`{"__current_case__": 0, "genome_size": null, "minimum_kmer_copies": "1", "reads_assembly_selector": "reads", "reads_input": {"__current_case__": 1, "reads": {"values": [{"id": 4, "src": "dce"}]}, "reads_input_selector": "single"}, "target_coverage": null}`
sketch_size	`"1000"`

Job 4:

Job state is ok

Command Line:

ln -s '/tmp/tmpwfmm7c9p/files/0/e/7/dataset_0e7d2d5c-2525-4a0a-a3cb-449695af5a19.dat'  'm64055e_210624_223222.' &&  mash sketch -s '1000' -k '21' -w '0.01' -m '1' -r 'm64055e_210624_223222.' -o 'sketch'

Exit Code:

```
0
```

Standard Error:

Estimated genome size: 2.12528e+06
Estimated coverage:    6.205
Writing to sketch.msh...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_size	`"21"`
prob_threshold	`"0.01"`
reads_assembly	`{"__current_case__": 0, "genome_size": null, "minimum_kmer_copies": "1", "reads_assembly_selector": "reads", "reads_input": {"__current_case__": 1, "reads": {"values": [{"id": 5, "src": "dce"}]}, "reads_input_selector": "single"}, "target_coverage": null}`
sketch_size	`"1000"`

Job 5:

Job state is ok

Command Line:

ln -s '/tmp/tmpwfmm7c9p/files/0/3/0/dataset_030807dd-f9cc-4a74-804c-83cf4dcb2bfc.dat'  'm54306Ue_210629_211205' &&  mash sketch -s '1000' -k '21' -w '0.01' -m '1' -r 'm54306Ue_210629_211205' -o 'sketch'

Exit Code:

```
0
```

Standard Error:

Estimated genome size: 2.11161e+06
Estimated coverage:    6.169
Writing to sketch.msh...

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_size	`"21"`
prob_threshold	`"0.01"`
reads_assembly	`{"__current_case__": 0, "genome_size": null, "minimum_kmer_copies": "1", "reads_assembly_selector": "reads", "reads_input": {"__current_case__": 1, "reads": {"values": [{"id": 3, "src": "dce"}]}, "reads_input_selector": "single"}, "target_coverage": null}`
sketch_size	`"1000"`

Step 3: toolshed.g2.bx.psu.edu/repos/iuc/mash_paste/mash_paste/2.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s /tmp/tmpwfmm7c9p/files/f/a/d/dataset_fadfb362-ba15-400d-9347-3b309c3d156d.dat "m54306U_210519_154448.msh" &&  ln -s /tmp/tmpwfmm7c9p/files/1/2/1/dataset_121bc4a8-9ec8-4b1d-9201-8581103c867f.dat "m54306U_210521_004211.msh" &&  ln -s /tmp/tmpwfmm7c9p/files/e/5/4/dataset_e5403939-74cf-4a2d-9bfc-c33e5317d649.dat "m54306Ue_210629_211205.msh" &&  ln -s /tmp/tmpwfmm7c9p/files/6/3/8/dataset_638988c8-a8d3-4e51-889a-df5fb871e695.dat "m54306Ue_210719_083927.msh" &&  ln -s /tmp/tmpwfmm7c9p/files/e/0/5/dataset_e059a3d6-a026-4a40-970b-2e6e90b8dd82.dat "m64055e_210624_223222..msh" &&   mash paste result.msh 'm54306U_210519_154448.msh' 'm54306U_210521_004211.msh' 'm54306Ue_210629_211205.msh' 'm54306Ue_210719_083927.msh' 'm64055e_210624_223222..msh' && mv result.msh /tmp/tmpwfmm7c9p/job_working_directory/000/40/outputs/dataset_0b5044c8-a9cb-4027-8c14-23737b8ee45d.dat

Exit Code:

```
0
```

Standard Error:

```
Writing result.msh...
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/mash_dist/mash_dist/2.3+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpwfmm7c9p/files/0/b/5/dataset_0b5044c8-a9cb-4027-8c14-23737b8ee45d.dat' reference.msh && ln -s '/tmp/tmpwfmm7c9p/files/0/b/5/dataset_0b5044c8-a9cb-4027-8c14-23737b8ee45d.dat' query.msh && mash dist -t -p ${GALAXY_SLOTS:-1} -v 1.0 -d 1.0 reference.msh query.msh > '/tmp/tmpwfmm7c9p/job_working_directory/000/41/outputs/dataset_40b125a0-6f26-4783-84f6-227de85f4476.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
distance	`"1.0"`
pvalue	`"1.0"`
table_output	`true`

Step 5: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/find_and_replace' -o '/tmp/tmpwfmm7c9p/job_working_directory/000/42/outputs/dataset_9090350a-afbb-49be-b17b-9a016baefd95.dat' -g     '.fastq.gz' '' '/tmp/tmpwfmm7c9p/files/4/0/b/dataset_40b125a0-6f26-4783-84f6-227de85f4476.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": ".fastq.gz", "global": true, "is_regex": false, "replace_pattern": null, "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpwfmm7c9p/job_working_directory/000/43/configs/tmpruk0oiv7' && Rscript '/tmp/tmpwfmm7c9p/job_working_directory/000/43/configs/tmpruk0oiv7'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Using X.query as id variables

Standard Output:

options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("reshape2")

input <- read.csv('/tmp/tmpwfmm7c9p/files/9/0/9/dataset_9090350a-afbb-49be-b17b-9a016baefd95.dat', sep='\t', header=TRUE)
minput <- melt(input)
write.table(minput, "output.tabular", sep="\t", quote=FALSE, row.names=FALSE)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpwfmm7c9p/job_working_directory/000/44/configs/tmpfftzfezz' && Rscript '/tmp/tmpwfmm7c9p/job_working_directory/000/44/configs/tmpfftzfezz'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Warning message:
In brewer.pal(ncolors, "BrBG") :
  n too large, allowed maximum for palette BrBG is 11
Returning the palette you asked for with that many colors

Standard Output:

options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("RColorBrewer")
library("gplots")

input <- read.delim('/tmp/tmpwfmm7c9p/files/9/0/9/dataset_9090350a-afbb-49be-b17b-9a016baefd95.dat', sep='\t', header=TRUE)

mat_input <- data.matrix(input[,2:ncol(input)])
rownames(mat_input) <- input[,1]

    linput <- mat_input

    scale <- "none"

srtCol <- 30
    rlabs <- NULL
    clabs <- NULL
    label_margins <- c(8,8)

    dendrogramtoplot <- "both"
        reorder_cols <- TRUE
        reorder_rows <- TRUE
        # Layout is:
        # 4 = color key           | 3 = dendrogram for columns
        # 2 = dendrogram for rows | 1 = heatmap
        layout_matrix <- rbind(c(4,3), c(2,1))
        key_margins <- list(mar=c(4,0.5,2,1))
        lheight <- c(1, 5)
        lwidth <- c(1,3)
    hclust_fun <- function(x) hclust(x, method='complete')
        dist_fun <- function(x) dist(x, method='euclidean')

ncolors <- 50
    colused <- brewer.pal(ncolors, "BrBG")

    png(file='/tmp/tmpwfmm7c9p/job_working_directory/000/44/outputs/dataset_6adf6994-7e08-478e-bb5a-2830e19e6b6d.dat', res=240, height=2000, width=2000)

heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
    distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
    col=colused, trace="none", density.info = "none", margins=label_margins,
    main = 'Mash Dist', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
    keysize=3, key.xlab='', key.title='', key.par=key_margins,
    lmat=layout_matrix, lhei=lheight, lwid=lwidth)

dev.off()
        null device 
          1

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_cond	`{"__current_case__": 0, "cluster": "yes", "cluster_cols_rows": "both", "clustering": "complete", "distance": "euclidean"}`
colorchoice	`{"__current_case__": 0, "name": "BrBG", "type": "palettes"}`
dbkey	`"?"`
image_file_format	`"png"`
key	`None`
labels	`"both"`
title	`"Mash Dist"`
transform	`"none"`
zscore_cond	`{"__current_case__": 0, "scale": "none", "zscore": "none"}`

Step 8: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

tail --lines +2 '/tmp/tmpwfmm7c9p/files/2/d/9/dataset_2d9d693b-b7e5-486d-9ef6-0369b23b48db.dat' > '/tmp/tmpwfmm7c9p/job_working_directory/000/45/outputs/dataset_09ed9b03-69e0-4508-af1d-a851a3ca5c5c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e8b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"+"`
dbkey	`"?"`
num_lines	`"2"`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.3+galaxy7:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && mkdir -p ./tmp_folder_0/ && tar -xmf /tmp/tmpwfmm7c9p/files/6/5/e/dataset_65e13598-4faa-4c8c-8a56-a0fa0541013c.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_0 && mv ./tmp_folder_0/* db_'0'.meryl && mkdir -p ./tmp_folder_1/ && tar -xmf /tmp/tmpwfmm7c9p/files/0/2/2/dataset_022720c0-9ae6-4371-b99d-fad1118ebbcc.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_1 && mv ./tmp_folder_1/* db_'1'.meryl && mkdir -p ./tmp_folder_2/ && tar -xmf /tmp/tmpwfmm7c9p/files/1/2/1/dataset_121521ed-dc65-4cf3-b3d4-22d3630e0650.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_2 && mv ./tmp_folder_2/* db_'2'.meryl && mkdir -p ./tmp_folder_3/ && tar -xmf /tmp/tmpwfmm7c9p/files/1/1/c/dataset_11c34224-9ccb-4d80-9c42-aa302528a508.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_3 && mv ./tmp_folder_3/* db_'3'.meryl && mkdir -p ./tmp_folder_4/ && tar -xmf /tmp/tmpwfmm7c9p/files/7/1/2/dataset_71262507-54b5-4ad3-81ab-40d44fadc7de.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_4 && mv ./tmp_folder_4/* db_'4'.meryl && meryl union-sum output read-db.meryl db_*  && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
0
```

Standard Error:

Found 1 command tree.

PROCESSING TREE #1 using 4 threads.
  opUnionSum
    db_0.meryl
    db_1.meryl
    db_2.meryl
    db_3.meryl
    db_4.meryl
    output to read-db.meryl

Cleaning up.

Bye.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
groups_operations	`"union-sum"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.3+galaxy7:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && mkdir  -p ./temp_db/ && tar -xmf /tmp/tmpwfmm7c9p/files/1/d/8/dataset_1d8c9ce7-2ba2-4ba0-875a-fdf41918bd58.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./temp_db/ && mv ./temp_db/* tmp.meryl && meryl histogram tmp.meryl > read-db.hist

Exit Code:

```
0
```

Standard Error:

```
Found 1 command tree.
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

genomescope2 --input '/tmp/tmpwfmm7c9p/files/4/c/3/dataset_4c3ade33-fc63-411f-8cc0-32989b494bf6.dat' --output . --kmer_length 21  --testing  --ploidy 2

Exit Code:

```
0
```

Standard Output:

GenomeScope analyzing /tmp/tmpwfmm7c9p/files/4/c/3/dataset_4c3ade33-fc63-411f-8cc0-32989b494bf6.dat p=2 k=21 outdir=.
aa:97.8% ab:2.18%
Model converged het:0.0218 kcov:20 err:0.00875 model fit:1.01 len:1262028

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
advanced_options	`{"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": true, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""}`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_length	`"21"`
lambda	`None`
max_kmercov	`None`
output_options	`{"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]}`
ploidy	`"2"`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Genomescope model:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -G -A 0 -B 0 --no-group-separator  -i -- 'kmercov [0-9]' '/tmp/tmpwfmm7c9p/files/d/9/a/dataset_d9a3f3cb-d51b-454f-b9fc-57e7ba0a5e84.dat' > '/tmp/tmpwfmm7c9p/job_working_directory/000/22/outputs/dataset_8375da2c-17e0-4032-83a0-65e28e739750.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e9b87211f08270000d3a55ec24"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-G"`
url_paste	`"kmercov [0-9]"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/c41d78ae5fee/text_processing/find_and_replace' -o '/tmp/tmpwfmm7c9p/job_working_directory/000/23/outputs/dataset_4ad287d8-a1b3-4051-9315-8fb8f6eb98bf.dat' -g -i   -r '\s+' ',' '/tmp/tmpwfmm7c9p/files/8/3/7/dataset_8375da2c-17e0-4032-83a0-65e28e739750.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e9b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": true, "find_pattern": "\\s+", "global": true, "is_regex": true, "replace_pattern": ",", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpwfmm7c9p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwfmm7c9p/files/4/a/d/dataset_4ad287d8-a1b3-4051-9315-8fb8f6eb98bf.dat' 'c2' C '/tmp/tmpwfmm7c9p/job_working_directory/000/24/outputs/dataset_86da9dfc-f700-4bbf-bb09-b673d5762459.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4b2400e9b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"C"`

Step 17: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: GenomeScope summary:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -G -A 0 -B 0 --no-group-separator  -i -- 'Haploid' '/tmp/tmpwfmm7c9p/files/1/d/3/dataset_1d3355dc-2550-40f0-9df0-5d2a778cff62.dat' > '/tmp/tmpwfmm7c9p/job_working_directory/000/25/outputs/dataset_4d8f06f2-f44e-44af-8a46-5fe6cfb5837b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400eab87211f08270000d3a55ec24"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-G"`
url_paste	`"Haploid"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed -r --sandbox -e '' -e 's/bp//g' -e '' -e 's/,//g' -e '' -e 's/([a-z])\s+([A-Z])/\1_\2/g' '/tmp/tmpwfmm7c9p/files/4/d/8/dataset_4d8f06f2-f44e-44af-8a46-5fe6cfb5837b.dat' > '/tmp/tmpwfmm7c9p/job_working_directory/000/26/outputs/dataset_e0b6116c-99aa-4f05-ba8e-88679d44aa9e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400eab87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": "bp", "replace_pattern": null, "sed_options": null}, {"__index__": 1, "find_pattern": ",", "replace_pattern": null, "sed_options": null}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2", "sed_options": null}]`

Step 4: Convert characters1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpwfmm7c9p/galaxy-dev/tools/filters/convert_characters.py' --strip --condense '/tmp/tmpwfmm7c9p/files/e/0/b/dataset_e0b6116c-99aa-4f05-ba8e-88679d44aa9e.dat' 's' '/tmp/tmpwfmm7c9p/job_working_directory/000/27/outputs/dataset_fafd359d-50e6-492a-a1f6-e23a630de9f6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400eab87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
condense	`true`
convert_from	`"s"`
dbkey	`"?"`
strip	`true`

Step 5: Estimated Genome Size File:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpwfmm7c9p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwfmm7c9p/files/f/a/f/dataset_fafd359d-50e6-492a-a1f6-e23a630de9f6.dat' 'c3' T '/tmp/tmpwfmm7c9p/job_working_directory/000/28/outputs/dataset_4322962b-df92-4ac6-95c7-8d1090fc50ad.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"4b2400eab87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: Homozygous Read Coverage:

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__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"float"`
remove_newlines	`true`

Step 19: Estimated Genome Size:

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__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 20: param_value_from_file:

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__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 3: Collection of Pacbio Data:
- step_state: scheduled

Step 21: Rdeval Stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpwfmm7c9p/files/b/5/5/dataset_b5534b1d-00f2-4d46-ad1a-08db720f2565.dat' 'm54306U_210519_154448.fastq.gz' && ln -s '/tmp/tmpwfmm7c9p/files/1/f/1/dataset_1f16c813-1393-4d46-bdc4-dd1f181f40e7.dat' 'm54306U_210521_004211.fastq.gz' && ln -s '/tmp/tmpwfmm7c9p/files/0/3/0/dataset_030807dd-f9cc-4a74-804c-83cf4dcb2bfc.dat' 'm54306Ue_210629_211205.fastq.gz' && ln -s '/tmp/tmpwfmm7c9p/files/4/a/9/dataset_4a97e5b0-0b3e-42e4-9de4-060188af330d.dat' 'm54306Ue_210719_083927.fastq.gz' && ln -s '/tmp/tmpwfmm7c9p/files/0/e/7/dataset_0e7d2d5c-2525-4a0a-a3cb-449695af5a19.dat' 'm64055e_210624_223222_.fastq.gz' && rdeval --input-reads 'm54306U_210519_154448.fastq.gz' 'm54306U_210521_004211.fastq.gz' 'm54306Ue_210629_211205.fastq.gz' 'm54306Ue_210719_083927.fastq.gz' 'm64055e_210624_223222_.fastq.gz' '1287751' -o output.rd --verbose --tabular --threads ${GALAXY_SLOTS:-2} > '/tmp/tmpwfmm7c9p/job_working_directory/000/46/outputs/dataset_62bfe8af-a730-4fea-a72d-970825cc1803.dat'

Exit Code:

```
0
```

Standard Error:

Loaded user input (done in 0.000084 s).
Read object generated (done in 0.000007 s).
Generating threadpool with 1 threads (done in 0.000007 s).
Processing 5 files (done in 0.000070 s).
Created stream object from input.
Stream type (file/gzip).
Streaming started. (done in 0.004034 s).
Processing batch N: 0 (done in 0.011502 s).
Processing batch N: 1 (done in 0.000027 s).
Processing batch N: 2 (done in 0.000182 s).
Processing batch N: 3 (done in 0.000090 s).
Processing batch N: 4 (done in 0.000127 s).
Processing batch N: 5 (done in 0.000098 s).
Processing batch N: 6 (done in 0.000539 s).
Processing batch N: 7 (done in 0.000131 s).
Processing batch N: 8 (done in 0.000176 s).
File stream closed (done in 0.000006 s).
Created stream object from input.
Stream type (file/gzip).
Streaming started. (done in 0.000161 s).
Processing batch N: 9 (done in 0.000101 s).
Processing batch N: 10 (done in 0.000101 s).
Processing batch N: 11 (done in 0.004725 s).
Processing batch N: 12 (done in 0.000330 s).
Processing batch N: 13 (done in 0.000033 s).
Processing batch N: 14 (done in 0.000145 s).
Processing batch N: 15 (done in 0.000271 s).
Processing batch N: 16 (done in 0.000003 s).
Processing batch N: 17 (done in 0.000108 s).
File stream closed (done in 0.000009 s).
Created stream object from input.
Stream type (file/gzip).
Streaming started. (done in 0.000072 s).
Processing batch N: 18 (done in 0.000170 s).
Processing batch N: 19 (done in 0.000341 s).
Processing batch N: 20 (done in 0.000337 s).
Processing batch N: 21 (done in 0.000521 s).
Processing batch N: 22 (done in 0.002151 s).
Processing batch N: 23 (done in 0.000152 s).
Processing batch N: 24 (done in 0.001023 s).
Processing batch N: 25 (done in 0.000149 s).
Processing batch N: 26 (done in 0.000121 s).
Processing batch N: 27 (done in 0.000245 s).
Processing batch N: 28 (done in 0.000256 s).
Processing batch N: 29 (done in 0.000206 s).
Processing batch N: 30 (done in 0.000077 s).
Processing batch N: 31 (done in 0.000051 s).
Processing batch N: 32 (done in 0.000363 s).
Processing batch N: 33 (done in 0.000211 s).
Processing batch N: 34 (done in 0.000458 s).
File stream closed (done in 0.000009 s).
Created stream object from input.
Stream type (file/gzip).
Streaming started. (done in 0.000144 s).
Processing batch N: 35 (done in 0.000160 s).
Processing batch N: 36 (done in 0.000219 s).
Processing batch N: 37 (done in 0.000193 s).
Processing batch N: 38 (done in 0.000262 s).
Processing batch N: 39 (done in 0.000140 s).
Processing batch N: 40 (done in 0.000080 s).
Processing batch N: 41 (done in 0.000178 s).
Processing batch N: 42 (done in 0.000225 s).
Processing batch N: 43 (done in 0.000009 s).
Processing batch N: 44 (done in 0.069871 s).
Processing batch N: 45 (done in 0.011883 s).
Processing batch N: 46 (done in 0.000135 s).
Processing batch N: 47 (done in 0.000232 s).
File stream closed (done in 0.000006 s).
Created stream object from input.
Stream type (file/gzip).
Streaming started. (done in 0.000090 s).
Processing batch N: 48 (done in 0.000281 s).
Processing batch N: 49 (done in 0.000140 s).
Processing batch N: 50 (done in 0.000178 s).
Processing batch N: 51 (done in 0.000102 s).
Processing batch N: 52 (done in 0.000088 s).
Processing batch N: 53 (done in 0.000034 s).
Processing batch N: 54 (done in 0.000124 s).
Processing batch N: 55 (done in 0.000021 s).
Processing batch N: 56 (done in 0.000092 s).
Processing batch N: 57 (done in 0.001813 s).
Processing batch N: 58 (done in 0.000041 s).
Processing batch N: 59 (done in 0.000543 s).
Processing batch N: 60 (done in 0.000016 s).
Processing batch N: 61 (done in 0.000012 s).
Processing batch N: 62 (done in 0.000135 s).
Processing batch N: 63 (done in 0.000058 s).
Processing batch N: 64 (done in 0.000124 s).
File stream closed (done in 0.000015 s).

Jobs waiting/running: 41/1 memory in use/allocated/total: 0.000000/0.104496/15.620682 GB      
Jobs waiting/running: 0/1 memory in use/allocated/total: 0.000000/0.105595/15.620682 GB      
      Data loaded (done in 0.000075 s).
Generating output (done in 0.000002 s).
Writing rd file: output.rd (done in 0.000531 s).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
expected_gsize	`"1287751"`
input_compress	`{"__current_case__": 0, "compress_selector": "no"}`
input_filter	`{"exclude_list": null, "filter_expression": {"__current_case__": 0, "filter_selector": "no_exp"}, "include_list": null}`
input_subsample	`{"random_seed": {"__current_case__": 0, "seed_selector": "no"}, "sample": "1.0"}`
output_options	`{"output_type": {"__current_case__": 1, "md5": false, "type_selector": "rd_file"}, "stats_flavor": {"__current_case__": 0, "flavor_selector": "stats", "sequence_report": false}}`

Step 22: toolshed.g2.bx.psu.edu/repos/richard-burhans/rdeval/rdeval_report/0.0.7+galaxy5:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir render && cd render && export RDEVAL_SHARE_DIR="$(dirname $(dirname $(type -P rdeval)))/share/rdeval" && ln -s "$RDEVAL_SHARE_DIR/figures.Rmd" && ln -s "$RDEVAL_SHARE_DIR/rdeval_interface.R" && ln -s '/tmp/tmpwfmm7c9p/files/b/4/9/dataset_b49d9780-a773-4657-844b-c61cd993caca.dat' '0.rd' && R -e "rmarkdown::render('figures.Rmd', output_file='/tmp/tmpwfmm7c9p/job_working_directory/000/47/outputs/dataset_4412b3cb-e9ad-49f1-b6db-52462512089d.dat', output_format='html_document', params=list(input_files=c('0.rd'), interactive='FALSE'))"

Exit Code:

```
0
```

Standard Error:

processing file: figures.Rmd
output file: figures.knit.md


Output created: /tmp/tmpwfmm7c9p/job_working_directory/000/47/outputs/dataset_4412b3cb-e9ad-49f1-b6db-52462512089d.dat

Standard Output:

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> rmarkdown::render('figures.Rmd', output_file='/tmp/tmpwfmm7c9p/job_working_directory/000/47/outputs/dataset_4412b3cb-e9ad-49f1-b6db-52462512089d.dat', output_format='html_document', params=list(input_files=c('0.rd'), interactive='FALSE'))
1/15                  
2/15 [setup]          
3/15                  
4/15 [unnamed-chunk-1]
5/15                  
6/15 [unnamed-chunk-2]
7/15                  
8/15 [unnamed-chunk-3]
9/15                  
10/15 [unnamed-chunk-4]
11/15                  
12/15 [unnamed-chunk-5]
13/15                  
14/15 [unnamed-chunk-6]
15/15                  
/usr/local/bin/pandoc +RTS -K512m -RTS figures.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/tmpwfmm7c9p/job_working_directory/000/47/outputs/dataset_4412b3cb-e9ad-49f1-b6db-52462512089d.dat --lua-filter /usr/local/lib/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /usr/local/lib/R/library/rmarkdown/rmarkdown/lua/table-classes.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/tmpwfmm7c9p/job_working_directory/000/47/tmp/RtmpGGHB9I/rmarkdown-str2b35af515a.html 
> 
>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
interactive	`false`

Step 4: K-mer length:
- step_state: scheduled
Step 5: Ploidy:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
images	`[{"__index__": 0, "input": {"__class__": "ConnectedValue"}}, {"__index__": 1, "input": {"__class__": "ConnectedValue"}}]`
input	`None`
label_options	`{"__current_case__": 0, "label": "true", "label_indexes": false}`
pointsize	`"14"`
resize	`"60"`
title	`None`
width	`"2"`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

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__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Test Species", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

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__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "toLidId", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 9: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Unlabelled step:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpwfmm7c9p/job_working_directory/000/9/configs/tmpy3ig5j9y' '/tmp/tmpwfmm7c9p/job_working_directory/000/9/outputs/dataset_b800974c-cbea-48b2-a84e-8db691d838f7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastq.gz"`
__workflow_invocation_uuid__	`"4b2400e7b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: wc_gnu:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo "#lines	words	characters" > /tmp/tmpwfmm7c9p/job_working_directory/000/10/outputs/dataset_7922350b-9a52-46b4-8e93-69a35cac076f.dat &&  cat '/tmp/tmpwfmm7c9p/files/b/8/0/dataset_b800974c-cbea-48b2-a84e-8db691d838f7.dat' | wc -l -w -m | awk '{ print $1"\t"$2"\t"$3 }' >> /tmp/tmpwfmm7c9p/job_working_directory/000/10/outputs/dataset_7922350b-9a52-46b4-8e93-69a35cac076f.dat

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"4b2400e7b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`true`
options	`["lines", "words", "characters"]`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpwfmm7c9p/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpwfmm7c9p/files/7/9/2/dataset_7922350b-9a52-46b4-8e93-69a35cac076f.dat' 'c1' T '/tmp/tmpwfmm7c9p/job_working_directory/000/11/outputs/dataset_a4e4607e-9a19-4ff2-b25c-0ac183af7cf0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"4b2400e7b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1"`
dbkey	`"?"`
delimiter	`"T"`

Step 5: param_value_from_file:

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__	`"4b2400e7b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0:

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__	`"4b2400e7b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "5", "mappings": [{"__index__": 0, "from": "0", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0:

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__	`"4b2400e7b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "5", "mappings": [{"__index__": 0, "from": "1", "to": "True"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0:

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__	`"4b2400e7b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 0, "input_param": "5", "mappings": [{"__index__": 0, "from": "0", "to": "False"}, {"__index__": 1, "from": "1", "to": "False"}], "type": "text"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 2, "default_value": "True", "on_unmapped": "default"}`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.3+galaxy7:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpwfmm7c9p/files/4/a/9/dataset_4a97e5b0-0b3e-42e4-9de4-060188af330d.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
0
```

Standard Error:

Found 1 command tree.

Counting 25 (estimated) million canonical 21-mers from 1 input file:
    sequence-file: ./input.fastq.gz


SIMPLE MODE
-----------

  21-mers
    -> 4398046511104 entries for counts up to 65535.
    -> 64 Tbits memory used

  26400909 input bases
    -> expected max count of 105603, needing 2 extra bits.
    -> 8192 Gbits memory used

  9216 GB memory needed


COMPLEX MODE
------------

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P   135 kB  6445 kM  8261  S  8192  B    64 MB    64 MB
     2     4  P   138 kB  3222 kM  4030  S    16 kB    62 MB    63 MB
     3     8  P   148 kB  1611 kM  1965  S    32 kB    61 MB    61 MB
     4    16  P   170 kB   805 kM   958  S    64 kB    59 MB    60 MB
     5    32  P   217 kB   402 kM   467  S   128 kB    58 MB    58 MB
     6    64  P   315 kB   201 kM   227  S   256 kB    56 MB    57 MB
     7   128  P   515 kB   100 kM   111  S   512 kB    55 MB    56 MB
     8   256  P   916 kB    50 kM    54  S  1024 kB    54 MB    54 MB
     9   512  P  1720 kB    25 kM    26  S  2048 kB    52 MB    53 MB
    10  1024  P  3336 kB    12 kM    13  S  4096 kB    52 MB    55 MB  Best Value!
    11  2048  P  6576 kB  6446  M     7  S  8192 kB    56 MB    62 MB
    12  4096  P    12 MB  3223  M     3  S    16 MB    48 MB    60 MB
    13  8192  P    25 MB  1612  M     2  S    32 MB    64 MB    89 MB
    14    16 kP    50 MB   806  M     1  S    64 MB    64 MB   114 MB
    15    32 kP   101 MB   403  M     1  S   128 MB   128 MB   229 MB
    16    64 kP   202 MB   202  M     1  S   256 MB   256 MB   458 MB
    17   128 kP   405 MB   101  M     1  S   512 MB   512 MB   917 MB
    18   256 kP   810 MB    51  M     1  S  1024 MB  1024 MB  1834 MB


FINAL CONFIGURATION
-------------------

Estimated to require 107 MB memory out of 8192 MB allowed.
Estimated to require 2 batches.

Configured complex mode for 0.105 GB memory per batch, and up to 2 batches.

Start counting with THREADED method.
Used 0.270 GB / 7.992 GB to store      2092594 kmers; need 0.000 GB to sort        14627 kmers

Input complete.  Writing results to 'read-db.meryl', using 1 thread.
finishIteration()--

Finished counting.

Cleaning up.

Bye.

Standard Output:

```
K-mer size: 21
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 2:

Job state is ok

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpwfmm7c9p/files/1/f/1/dataset_1f16c813-1393-4d46-bdc4-dd1f181f40e7.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
0
```

Standard Error:

Found 1 command tree.

Counting 17 (estimated) million canonical 21-mers from 1 input file:
    sequence-file: ./input.fastq.gz


SIMPLE MODE
-----------

  21-mers
    -> 4398046511104 entries for counts up to 65535.
    -> 64 Tbits memory used

  18832617 input bases
    -> expected max count of 75330, needing 2 extra bits.
    -> 8192 Gbits memory used

  9216 GB memory needed


COMPLEX MODE
------------

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P    98 kB  4597 kM  5893  S  8192  B    46 MB    46 MB
     2     4  P   102 kB  2298 kM  2875  S    16 kB    44 MB    45 MB
     3     8  P   112 kB  1149 kM  1402  S    32 kB    43 MB    43 MB
     4    16  P   135 kB   574 kM   683  S    64 kB    42 MB    42 MB
     5    32  P   184 kB   287 kM   333  S   128 kB    41 MB    41 MB
     6    64  P   283 kB   143 kM   162  S   256 kB    40 MB    40 MB
     7   128  P   483 kB    71 kM    79  S   512 kB    39 MB    39 MB
     8   256  P   886 kB    35 kM    39  S  1024 kB    39 MB    39 MB
     9   512  P  1692 kB    17 kM    19  S  2048 kB    38 MB    39 MB
    10  1024  P  3304 kB  9196  M     9  S  4096 kB    36 MB    39 MB  Best Value!
    11  2048  P  6544 kB  4598  M     5  S  8192 kB    40 MB    46 MB
    12  4096  P    12 MB  2299  M     3  S    16 MB    48 MB    60 MB
    13  8192  P    25 MB  1150  M     2  S    32 MB    64 MB    89 MB
    14    16 kP    50 MB   575  M     1  S    64 MB    64 MB   114 MB
    15    32 kP   101 MB   288  M     1  S   128 MB   128 MB   229 MB
    16    64 kP   202 MB   144  M     1  S   256 MB   256 MB   458 MB
    17   128 kP   405 MB    72  M     1  S   512 MB   512 MB   917 MB
    18   256 kP   810 MB    36  M     1  S  1024 MB  1024 MB  1834 MB


FINAL CONFIGURATION
-------------------

Estimated to require 75 MB memory out of 8192 MB allowed.
Estimated to require 2 batches.

Configured complex mode for 0.074 GB memory per batch, and up to 2 batches.

Start counting with THREADED method.
Used 0.270 GB / 7.992 GB to store      2093917 kmers; need 0.000 GB to sort        16304 kmers

Input complete.  Writing results to 'read-db.meryl', using 1 thread.
finishIteration()--

Finished counting.

Cleaning up.

Bye.

Standard Output:

```
K-mer size: 21
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 3:

Job state is ok

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpwfmm7c9p/files/b/5/5/dataset_b5534b1d-00f2-4d46-ad1a-08db720f2565.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
0
```

Standard Error:

Found 1 command tree.

Counting 16 (estimated) million canonical 21-mers from 1 input file:
    sequence-file: ./input.fastq.gz


SIMPLE MODE
-----------

  21-mers
    -> 4398046511104 entries for counts up to 65535.
    -> 64 Tbits memory used

  16978584 input bases
    -> expected max count of 67914, needing 2 extra bits.
    -> 8192 Gbits memory used

  9216 GB memory needed


COMPLEX MODE
------------

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P    89 kB  4145 kM  5313  S  8192  B    41 MB    41 MB
     2     4  P    93 kB  2072 kM  2592  S    16 kB    40 MB    40 MB
     3     8  P   104 kB  1036 kM  1264  S    32 kB    39 MB    39 MB
     4    16  P   127 kB   518 kM   616  S    64 kB    38 MB    38 MB
     5    32  P   176 kB   259 kM   300  S   128 kB    37 MB    37 MB
     6    64  P   275 kB   129 kM   146  S   256 kB    36 MB    36 MB
     7   128  P   475 kB    64 kM    71  S   512 kB    35 MB    35 MB
     8   256  P   878 kB    32 kM    35  S  1024 kB    35 MB    35 MB
     9   512  P  1684 kB    16 kM    17  S  2048 kB    34 MB    35 MB
    10  1024  P  3304 kB  8291  M     9  S  4096 kB    36 MB    39 MB  Best Value!
    11  2048  P  6528 kB  4146  M     4  S  8192 kB    32 MB    38 MB
    12  4096  P    12 MB  2073  M     2  S    16 MB    32 MB    44 MB
    13  8192  P    25 MB  1037  M     1  S    32 MB    32 MB    57 MB
    14    16 kP    50 MB   519  M     1  S    64 MB    64 MB   114 MB
    15    32 kP   101 MB   260  M     1  S   128 MB   128 MB   229 MB
    16    64 kP   202 MB   130  M     1  S   256 MB   256 MB   458 MB
    17   128 kP   405 MB    65  M     1  S   512 MB   512 MB   917 MB
    18   256 kP   810 MB    33  M     1  S  1024 MB  1024 MB  1834 MB


FINAL CONFIGURATION
-------------------

Estimated to require 71 MB memory out of 8192 MB allowed.
Estimated to require 2 batches.

Configured complex mode for 0.070 GB memory per batch, and up to 2 batches.

Start counting with THREADED method.
Used 0.270 GB / 7.992 GB to store      2093770 kmers; need 0.000 GB to sort        14313 kmers

Input complete.  Writing results to 'read-db.meryl', using 1 thread.
finishIteration()--

Finished counting.

Cleaning up.

Bye.

Standard Output:

```
K-mer size: 21
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 4:

Job state is ok

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpwfmm7c9p/files/0/e/7/dataset_0e7d2d5c-2525-4a0a-a3cb-449695af5a19.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
0
```

Standard Error:

Found 1 command tree.

Counting 32 (estimated) million canonical 21-mers from 1 input file:
    sequence-file: ./input.fastq.gz


SIMPLE MODE
-----------

  21-mers
    -> 4398046511104 entries for counts up to 65535.
    -> 64 Tbits memory used

  33758286 input bases
    -> expected max count of 135033, needing 3 extra bits.
    -> 12 Tbits memory used

  9728 GB memory needed


COMPLEX MODE
------------

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P   171 kB  8241 kM    10 kS  8192  B    82 MB    82 MB
     2     4  P   173 kB  4120 kM  5153  S    16 kB    80 MB    80 MB
     3     8  P   182 kB  2060 kM  2512  S    32 kB    78 MB    78 MB
     4    16  P   203 kB  1030 kM  1224  S    64 kB    76 MB    76 MB
     5    32  P   250 kB   515 kM   597  S   128 kB    74 MB    74 MB
     6    64  P   347 kB   257 kM   290  S   256 kB    72 MB    72 MB
     7   128  P   545 kB   128 kM   141  S   512 kB    70 MB    71 MB
     8   256  P   946 kB    64 kM    69  S  1024 kB    69 MB    69 MB
     9   512  P  1752 kB    32 kM    34  S  2048 kB    68 MB    69 MB
    10  1024  P  3368 kB    16 kM    17  S  4096 kB    68 MB    71 MB  Best Value!
    11  2048  P  6592 kB  8242  M     8  S  8192 kB    64 MB    70 MB
    12  4096  P    12 MB  4121  M     4  S    16 MB    64 MB    76 MB
    13  8192  P    25 MB  2061  M     2  S    32 MB    64 MB    89 MB
    14    16 kP    50 MB  1031  M     1  S    64 MB    64 MB   114 MB
    15    32 kP   101 MB   516  M     1  S   128 MB   128 MB   229 MB
    16    64 kP   202 MB   258  M     1  S   256 MB   256 MB   458 MB
    17   128 kP   405 MB   129  M     1  S   512 MB   512 MB   917 MB
    18   256 kP   810 MB    65  M     1  S  1024 MB  1024 MB  1834 MB
    19   512 kP  1620 MB    33  M     1  S  2048 MB  2048 MB  3668 MB


FINAL CONFIGURATION
-------------------

Estimated to require 135 MB memory out of 8192 MB allowed.
Estimated to require 2 batches.

Configured complex mode for 0.132 GB memory per batch, and up to 2 batches.

Start counting with THREADED method.
Used 0.270 GB / 7.992 GB to store      2092552 kmers; need 0.000 GB to sort        15733 kmers

Input complete.  Writing results to 'read-db.meryl', using 1 thread.
finishIteration()--

Finished counting.

Cleaning up.

Bye.

Standard Output:

```
K-mer size: 21
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 5:

Job state is ok

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpwfmm7c9p/files/0/3/0/dataset_030807dd-f9cc-4a74-804c-83cf4dcb2bfc.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
0
```

Standard Error:

Found 1 command tree.

Counting 33 (estimated) million canonical 21-mers from 1 input file:
    sequence-file: ./input.fastq.gz


SIMPLE MODE
-----------

  21-mers
    -> 4398046511104 entries for counts up to 65535.
    -> 64 Tbits memory used

  35473530 input bases
    -> expected max count of 141894, needing 3 extra bits.
    -> 12 Tbits memory used

  9728 GB memory needed


COMPLEX MODE
------------

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P   179 kB  8660 kM    10 kS  8192  B    86 MB    86 MB
     2     4  P   181 kB  4330 kM  5415  S    16 kB    84 MB    84 MB
     3     8  P   190 kB  2165 kM  2640  S    32 kB    82 MB    82 MB
     4    16  P   211 kB  1082 kM  1287  S    64 kB    80 MB    80 MB
     5    32  P   257 kB   541 kM   627  S   128 kB    78 MB    78 MB
     6    64  P   354 kB   270 kM   305  S   256 kB    76 MB    76 MB
     7   128  P   553 kB   135 kM   149  S   512 kB    74 MB    75 MB
     8   256  P   952 kB    67 kM    72  S  1024 kB    72 MB    72 MB
     9   512  P  1756 kB    33 kM    35  S  2048 kB    70 MB    71 MB
    10  1024  P  3368 kB    16 kM    17  S  4096 kB    68 MB    71 MB  Best Value!
    11  2048  P  6608 kB  8661  M     9  S  8192 kB    72 MB    78 MB
    12  4096  P    12 MB  4331  M     4  S    16 MB    64 MB    76 MB
    13  8192  P    25 MB  2166  M     2  S    32 MB    64 MB    89 MB
    14    16 kP    50 MB  1083  M     1  S    64 MB    64 MB   114 MB
    15    32 kP   101 MB   542  M     1  S   128 MB   128 MB   229 MB
    16    64 kP   202 MB   271  M     1  S   256 MB   256 MB   458 MB
    17   128 kP   405 MB   136  M     1  S   512 MB   512 MB   917 MB
    18   256 kP   810 MB    68  M     1  S  1024 MB  1024 MB  1834 MB
    19   512 kP  1620 MB    34  M     1  S  2048 MB  2048 MB  3668 MB


FINAL CONFIGURATION
-------------------

Estimated to require 139 MB memory out of 8192 MB allowed.
Estimated to require 2 batches.

Configured complex mode for 0.136 GB memory per batch, and up to 2 batches.

Start counting with THREADED method.
Used 0.270 GB / 7.992 GB to store      2093287 kmers; need 0.000 GB to sort        15804 kmers

Input complete.  Writing results to 'read-db.meryl', using 1 thread.
finishIteration()--

Finished counting.

Cleaning up.

Bye.

Standard Output:

```
K-mer size: 21
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4b2400e6b87211f08270000d3a55ec24"`
chromInfo	`"/tmp/tmpwfmm7c9p/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Other invocation details
- history_id
  - b8063cf2aceec048
- history_state
  - error
- invocation_id
  - b8063cf2aceec048
- invocation_state
  - scheduled
- workflow_id
  - 76a148a6005dc244

…to 0.7

gxydevbot · 2025-11-10T07:20:12Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2025-11-10T07:36:53Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ kmer-profiling-hifi-VGP1.ga_0

Execution Problem:

Upload job [a3919ed58a692500] produced output [2: Collection%20of%20Pacbio%20Data_m54306U_210521_004211.hifi_reads.fastq.gz.fastqsanger.gz] in state [error]

Removed input parameters from multiple tools in the workflow.

github-actions · 2025-11-12T20:50:05Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ kmer-profiling-hifi-VGP1.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 21 requires a dataset created by step 40, but dataset entered a failed state.

Steps

Step 1: Species Name:
- step_state: scheduled
Step 2: Assembly Name:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 1, "component_value": "21", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 12: Unlabelled step:
- step_state: new
- Subworkflow Steps

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
groups_operations	`"union-sum"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 15: toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
advanced_options	`{"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": true, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""}`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_length	`"21"`
lambda	`None`
max_kmercov	`None`
output_options	`{"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]}`
ploidy	`"2"`

Step 16: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Genomescope model:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f23c00811f0bb737c1e5241bb97"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-G"`
url_paste	`"kmercov [0-9]"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f23c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": true, "find_pattern": "\\s+", "global": true, "is_regex": true, "replace_pattern": ",", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6ccc5f23c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"C"`

Step 17: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: GenomeScope summary:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f24c00811f0bb737c1e5241bb97"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-G"`
url_paste	`"Haploid"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f24c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": "bp", "replace_pattern": null, "sed_options": null}, {"__index__": 1, "find_pattern": ",", "replace_pattern": null, "sed_options": null}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2", "sed_options": null}]`

Step 4: Convert characters1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f24c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
condense	`true`
convert_from	`"s"`
dbkey	`"?"`
strip	`true`

Step 5: Estimated Genome Size File:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6ccc5f24c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: Homozygous Read Coverage:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"float"`
remove_newlines	`true`

Step 19: Estimated Genome Size:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 20: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 3: Collection of Pacbio Data:
- step_state: scheduled
Step 21: Rdeval Stats:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 4: K-mer length:
- step_state: scheduled
Step 5: Ploidy:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is error

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
images	`[{"__index__": 0, "input": {"__class__": "ConnectedValue"}}, {"__index__": 1, "input": {"__class__": "ConnectedValue"}}]`
input	`None`
label_options	`{"__current_case__": 0, "label": "true", "label_indexes": false}`
pointsize	`"14"`
resize	`"60"`
title	`None`
width	`"2"`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

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__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Test Species", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

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__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "toLidId", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 9: Unlabelled step:

step_state: new

Subworkflow Steps

Step 1: Unlabelled step:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmpepqfoyrp/job_working_directory/000/9/configs/tmp32aind6l' '/tmp/tmpepqfoyrp/job_working_directory/000/9/outputs/dataset_eda33000-9696-4636-8d7a-e8ed37576899.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastq.gz"`
__workflow_invocation_uuid__	`"6ccc5f21c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: wc_gnu:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

echo "#lines	words	characters" > /tmp/tmpepqfoyrp/job_working_directory/000/10/outputs/dataset_e9622d10-3564-4bc8-9965-9f1a04327455.dat &&  cat '/tmp/tmpepqfoyrp/files/e/d/a/dataset_eda33000-9696-4636-8d7a-e8ed37576899.dat' | wc -l -w -m | awk '{ print $1"\t"$2"\t"$3 }' >> /tmp/tmpepqfoyrp/job_working_directory/000/10/outputs/dataset_e9622d10-3564-4bc8-9965-9f1a04327455.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"6ccc5f21c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`true`
options	`["lines", "words", "characters"]`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"6ccc5f21c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1"`
dbkey	`"?"`
delimiter	`"T"`

Step 5: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f21c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 6: Unlabelled step:
- step_state: new
Step 7: Unlabelled step:
- step_state: new
Step 8: Unlabelled step:
- step_state: new

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpepqfoyrp/files/c/f/1/dataset_cf12b24f-55f6-49b8-8c54-d82f7de1bb9d.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 2:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpepqfoyrp/files/d/6/0/dataset_d6076daa-132a-4efb-b89b-88ebfef46452.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 3:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpepqfoyrp/files/b/f/e/dataset_bfe605ba-c021-44b0-8bc2-42637ab8a87b.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 4:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpepqfoyrp/files/b/5/e/dataset_b5e80270-3c3b-4203-a7f8-d071cf60974f.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 5:

Job state is queued

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmpepqfoyrp/files/d/8/6/dataset_d865c689-d7a3-46cf-b52b-837f06cce6e6.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"6ccc5f20c00811f0bb737c1e5241bb97"`
chromInfo	`"/tmp/tmpepqfoyrp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 751493c1b6eeeee6
- history_state
  - running
- invocation_id
  - 751493c1b6eeeee6
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 39, 'hda_id': 'ed389e8b137454c7', 'reason': 'dataset_failed', 'workflow_step_id': 20}]
- workflow_id
  - f84c3941bfd3f2c1

github-actions · 2025-11-13T01:42:02Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

❌ kmer-profiling-hifi-VGP1.ga_0

Execution Problem:

Failed to run workflow, invocation ended in [failed] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 21 requires a dataset created by step 40, but dataset entered a failed state.

Steps

Step 1: Species Name:
- step_state: scheduled
Step 2: Assembly Name:
- step_state: scheduled
Step 11: Unlabelled step:
- step_state: new
- Subworkflow Steps

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/meryl_groups_kmers/meryl_groups_kmers/1.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
groups_operations	`"union-sum"`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/meryl_histogram_kmers/meryl_histogram_kmers/1.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
advanced_options	`{"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": true, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""}`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_length	`"21"`
lambda	`None`
max_kmercov	`None`
output_options	`{"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]}`
ploidy	`"2"`

Step 15: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Genomescope model:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee717c03111f0bb73002248272a95"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-G"`
url_paste	`"kmercov [0-9]"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee717c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": true, "find_pattern": "\\s+", "global": true, "is_regex": true, "replace_pattern": ",", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"34bee717c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c2"`
dbkey	`"?"`
delimiter	`"C"`

Step 16: toolshed.g2.bx.psu.edu/repos/bgruening/imagemagick_image_montage/imagemagick_image_montage/7.1.2-2+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label_options	`{"__current_case__": 1, "label": "false"}`
pointsize	`"14"`
resize	`"60"`
title	`None`
width	`"2"`

Step 17: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: GenomeScope summary:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee718c03111f0bb73002248272a95"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`""`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-G"`
url_paste	`"Haploid"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.5+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee718c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
replacements	`[{"__index__": 0, "find_pattern": "bp", "replace_pattern": null, "sed_options": null}, {"__index__": 1, "find_pattern": ",", "replace_pattern": null, "sed_options": null}, {"__index__": 2, "find_pattern": "([a-z])\\s+([A-Z])", "replace_pattern": "\\1_\\2", "sed_options": null}]`

Step 4: Convert characters1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee718c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
condense	`true`
convert_from	`"s"`
dbkey	`"?"`
strip	`true`

Step 5: Estimated Genome Size File:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"34bee718c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c3"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: Homozygous Read Coverage:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"float"`
remove_newlines	`true`

Step 19: Estimated Genome Size:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 20: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 3: Collection of Pacbio Data:
- step_state: scheduled
Step 21: Rdeval Stats:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 4: K-mer length:
- step_state: scheduled
Step 5: Ploidy:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

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__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Test Species", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

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__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "toLidId", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 8: Unlabelled step:

step_state: new

Subworkflow Steps

Step 1: Unlabelled step:
- step_state: scheduled

Step 2: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mv '/tmp/tmplgxl8kdb/job_working_directory/000/8/configs/tmptt0qhngf' '/tmp/tmplgxl8kdb/job_working_directory/000/8/outputs/dataset_0b925c29-853f-40c0-9acd-a4c27c6228cc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fastq.gz"`
__workflow_invocation_uuid__	`"34bee715c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_collection	`{"values": [{"id": 1, "src": "hdca"}]}`

Step 3: wc_gnu:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

echo "#lines	words	characters" > /tmp/tmplgxl8kdb/job_working_directory/000/9/outputs/dataset_d8e4c85e-6de7-4392-b1b2-ca3b278b3912.dat &&  cat '/tmp/tmplgxl8kdb/files/0/b/9/dataset_0b925c29-853f-40c0-9acd-a4c27c6228cc.dat' | wc -l -w -m | awk '{ print $1"\t"$2"\t"$3 }' >> /tmp/tmplgxl8kdb/job_working_directory/000/9/outputs/dataset_d8e4c85e-6de7-4392-b1b2-ca3b278b3912.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"txt"`
__workflow_invocation_uuid__	`"34bee715c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
include_header	`true`
options	`["lines", "words", "characters"]`

Step 4: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"34bee715c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1"`
dbkey	`"?"`
delimiter	`"T"`

Step 5: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee715c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 6: Unlabelled step:
- step_state: new
Step 7: Unlabelled step:
- step_state: new
Step 8: Unlabelled step:
- step_state: new

Step 9: toolshed.g2.bx.psu.edu/repos/iuc/meryl_count_kmers/meryl_count_kmers/1.4.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmplgxl8kdb/files/a/0/b/dataset_a0baf04e-f4cc-4c4d-8990-1a5a3a6fcb51.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 2:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmplgxl8kdb/files/9/2/e/dataset_92e6668a-c754-4fe5-b4a1-26591a4716ac.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 3:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmplgxl8kdb/files/9/d/6/dataset_9d66466e-6a63-4b37-91b6-2563b22dabfa.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 4:

Job state is error

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmplgxl8kdb/files/b/1/d/dataset_b1dbb83f-5b97-43d0-b752-b86950ff5b6c.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Exit Code:

```
127
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Job 5:

Job state is queued

Command Line:

export GALAXY_MEMORY_GB=$((${GALAXY_MEMORY_MB:-8192}/1024)) && ln -s '/tmp/tmplgxl8kdb/files/0/a/b/dataset_0ab8e24e-bbde-4f7d-b7eb-b6e523752fb4.dat' ./input.fastq.gz &&  meryl count k=21 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastq.gz output read-db.meryl && echo 'K-mer size: 21' && tar -cf read-db.meryldb --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" read-db.meryl

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "21", "kmer_size": "provide"}`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is running

Command Line:

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

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"34bee714c03111f0bb73002248272a95"`
chromInfo	`"/tmp/tmplgxl8kdb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 1, "component_value": "21", "select_param_type": "integer"}}]`
dbkey	`"?"`

Other invocation details
- error_message
  - Failed to run workflow, invocation ended in [failed] state.
- history_id
  - 2f745e1d8b14c6da
- history_state
  - running
- invocation_id
  - 2f745e1d8b14c6da
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': 39, 'hda_id': '1c607b940ac147ae', 'reason': 'dataset_failed', 'workflow_step_id': 20}]
- workflow_id
  - 0a935f1fc67f1080

gxydevbot · 2025-11-17T06:44:14Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2025-11-24T05:02:48Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2025-11-24T09:57:39Z

There are new updates, if you want to integrate them, close the PR and delete branch.

Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.6 …

0068852

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gxydevbot force-pushed the workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 branch from 849deaa to 0068852 Compare November 10, 2025 07:20

gxydevbot changed the title ~~Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.6 to 0.7~~ Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.6 to 0.7 Nov 10, 2025

Remove input parameters from workflow tools

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Removed input parameters from multiple tools in the workflow.

Delphine-L approved these changes Nov 12, 2025

View reviewed changes

Fix broken connection

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Delphine-L approved these changes Nov 13, 2025

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Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.6 to 0.7 #1013

Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.6 to 0.7 #1013

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Updating workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1 from 0.6 to 0.7 #1013

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