Add annotation for vgp1 kmer profiling workflow #640

dannon · 2024-12-17T14:57:41Z

FOR CONTRIBUTOR:

I have read the Adding workflows guidelines
License permits unrestricted use (educational + commercial)
Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

.dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
Changelog contains appropriate entries
Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

github-actions · 2024-12-17T15:10:55Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ kmer-profiling-hifi-VGP1.ga_0

Problems:

Output with path /tmp/tmp15amyt33/GenomeScope on data 7 Summary__4b82e937-ae55-4e2d-b9d5-4dc2b68c0081 different than expected
Expected text '35,913 bp' in output ('GenomeScope version 2.0
input file = /tmp/tmpikfn99fz/files/d/e/b/dataset_debd9e9d-54b5-4416-8d54-4f9386e9310d.dat
output directory = .
p = 1
k = 8
TESTING set to TRUE

property                      min               max               
Homozygous (a)                100%              100%              
Genome Haploid Length         33,671 bp         43,432 bp         
Genome Repeat Length          5,829 bp          7,519 bp          
Genome Unique Length          27,842 bp         35,914 bp         
Model Fit                     91.9682%          94.5609%          
Read Error Rate               3.33067e-13%      3.33067e-13%      
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Collection of Pacbio Data:
- step_state: scheduled
**Step 2: K-mer length **:
- step_state: scheduled
Step 3: Ploidy:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_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__	`"b05ffac8bc8811ef8af67c1e526e05bb"`
chromInfo	`"/tmp/tmpikfn99fz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 1, "default_value": "21", "param_type": "integer", "pick_from": [{"__index__": 0, "value": "8"}]}}`

Step 5: 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/tmpikfn99fz/files/a/d/9/dataset_ad93c5fc-cde5-408f-b39e-9d07d80f0050.dat' ./input.fastqsanger &&  meryl count k=8 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastqsanger output read-db.meryl && echo 'K-mer size: 8' && 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 2047 (estimated) thousand canonical 8-mers from 1 input file:
    sequence-file: ./input.fastqsanger


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

  8-mers
    -> 65536 entries for counts up to 65535.
    -> 1024 kbits memory used

  2096311 input bases
    -> expected max count of 8385, needing 0 extra bits.
    -> no memory used

  128 kB memory needed


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

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P    10 kB   511 kM   240  S  8192  B  1920 kB  1930 kB
     2     4  P    16 kB   255 kM   112  S    16 kB  1792 kB  1808 kB
     3     8  P    28 kB   127 kM    52  S    32 kB  1664 kB  1692 kB
     4    16  P    53 kB    63 kM    24  S    64 kB  1536 kB  1589 kB
     5    32  P   103 kB    31 kM    11  S   128 kB  1408 kB  1511 kB
     6    64  P   204 kB    15 kM     5  S   256 kB  1280 kB  1484 kB
     7   128  P   407 kB  8189  M     3  S   512 kB  1536 kB  1943 kB
     8   256  P   810 kB  4095  M     1  S  1024 kB  1024 kB  1834 kB
     9   512  P  1620 kB  2048  M     1  S  2048 kB  2048 kB  3668 kB
    10  1024  P  3240 kB  1024  M     1  S  4096 kB  4096 kB  7336 kB  Best Value!
    11  2048  P  6480 kB   512  M     1  S  8192 kB  8192 kB    14 MB
    12  4096  P    12 MB   256  M     1  S    16 MB    16 MB    28 MB
    13  8192  P    25 MB   128  M     1  S    32 MB    32 MB    57 MB
    14    16 kP    50 MB    64  M     1  S    64 MB    64 MB   114 MB


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

Estimated to require 128 kB memory out of 8192 MB allowed.
Estimated to require 2 batches.

Configured simple mode for 0.000 GB memory per batch, and up to 2 batches.

Start counting with SIMPLE method.
Loading kmers from './input.fastqsanger' into buckets.

Writing results to 'read-db.meryl', using 1 threads.
             [ file ][  prefix ][  suffix ][ count-suffix ]
   widths    [    6 ][       0 ][      10 ][            0 ]
   number    [   64 ][       1 ][    1024 ][              ]

thread  0 working on block 0x00000000<0x00000000<0x00000000     1024 kmers between 0x0000000000000000 and 0x00000000000003ff
thread  0 working on block 0x00000001<0x00000001<0x00000001     1024 kmers between 0x0000000000000400 and 0x00000000000007ff
thread  0 working on block 0x00000002<0x00000002<0x00000002     1024 kmers between 0x0000000000000800 and 0x0000000000000bff
thread  0 working on block 0x00000003<0x00000003<0x00000003     1024 kmers between 0x0000000000000c00 and 0x0000000000000fff
thread  0 working on block 0x00000004<0x00000004<0x00000004     1024 kmers between 0x0000000000001000 and 0x00000000000013ff
thread  0 working on block 0x00000005<0x00000005<0x00000005     1024 kmers between 0x0000000000001400 and 0x00000000000017ff
thread  0 working on block 0x00000006<0x00000006<0x00000006     1024 kmers between 0x0000000000001800 and 0x0000000000001bff
thread  0 working on block 0x00000007<0x00000007<0x00000007     1024 kmers between 0x0000000000001c00 and 0x0000000000001fff
thread  0 working on block 0x00000008<0x00000008<0x00000008     1024 kmers between 0x0000000000002000 and 0x00000000000023ff
thread  0 working on block 0x00000009<0x00000009<0x00000009     1024 kmers between 0x0000000000002400 and 0x00000000000027ff
thread  0 working on block 0x0000000a<0x0000000a<0x0000000a     1024 kmers between 0x0000000000002800 and 0x0000000000002bff
thread  0 working on block 0x0000000b<0x0000000b<0x0000000b     1024 kmers between 0x0000000000002c00 and 0x0000000000002fff
thread  0 working on block 0x0000000c<0x0000000c<0x0000000c     1024 kmers between 0x0000000000003000 and 0x00000000000033ff
thread  0 working on block 0x0000000d<0x0000000d<0x0000000d     1024 kmers between 0x0000000000003400 and 0x00000000000037ff
thread  0 working on block 0x0000000e<0x0000000e<0x0000000e     1024 kmers between 0x0000000000003800 and 0x0000000000003bff
thread  0 working on block 0x0000000f<0x0000000f<0x0000000f     1024 kmers between 0x0000000000003c00 and 0x0000000000003fff
thread  0 working on block 0x00000010<0x00000010<0x00000010     1024 kmers between 0x0000000000004000 and 0x00000000000043ff
thread  0 working on block 0x00000011<0x00000011<0x00000011     1024 kmers between 0x0000000000004400 and 0x00000000000047ff
thread  0 working on block 0x00000012<0x00000012<0x00000012     1024 kmers between 0x0000000000004800 and 0x0000000000004bff
thread  0 working on block 0x00000013<0x00000013<0x00000013     1024 kmers between 0x0000000000004c00 and 0x0000000000004fff
thread  0 working on block 0x00000014<0x00000014<0x00000014     1024 kmers between 0x0000000000005000 and 0x00000000000053ff
thread  0 working on block 0x00000015<0x00000015<0x00000015     1024 kmers between 0x0000000000005400 and 0x00000000000057ff
thread  0 working on block 0x00000016<0x00000016<0x00000016     1024 kmers between 0x0000000000005800 and 0x0000000000005bff
thread  0 working on block 0x00000017<0x00000017<0x00000017     1024 kmers between 0x0000000000005c00 and 0x0000000000005fff
thread  0 working on block 0x00000018<0x00000018<0x00000018     1024 kmers between 0x0000000000006000 and 0x00000000000063ff
thread  0 working on block 0x00000019<0x00000019<0x00000019     1024 kmers between 0x0000000000006400 and 0x00000000000067ff
thread  0 working on block 0x0000001a<0x0000001a<0x0000001a     1024 kmers between 0x0000000000006800 and 0x0000000000006bff
thread  0 working on block 0x0000001b<0x0000001b<0x0000001b     1024 kmers between 0x0000000000006c00 and 0x0000000000006fff
thread  0 working on block 0x0000001c<0x0000001c<0x0000001c     1024 kmers between 0x0000000000007000 and 0x00000000000073ff
thread  0 working on block 0x0000001d<0x0000001d<0x0000001d     1024 kmers between 0x0000000000007400 and 0x00000000000077ff
thread  0 working on block 0x0000001e<0x0000001e<0x0000001e     1024 kmers between 0x0000000000007800 and 0x0000000000007bff
thread  0 working on block 0x0000001f<0x0000001f<0x0000001f     1024 kmers between 0x0000000000007c00 and 0x0000000000007fff
thread  0 working on block 0x00000020<0x00000020<0x00000020     1024 kmers between 0x0000000000008000 and 0x00000000000083ff
thread  0 working on block 0x00000021<0x00000021<0x00000021     1024 kmers between 0x0000000000008400 and 0x00000000000087ff
thread  0 working on block 0x00000022<0x00000022<0x00000022     1024 kmers between 0x0000000000008800 and 0x0000000000008bff
thread  0 working on block 0x00000023<0x00000023<0x00000023     1024 kmers between 0x0000000000008c00 and 0x0000000000008fff
thread  0 working on block 0x00000024<0x00000024<0x00000024     1024 kmers between 0x0000000000009000 and 0x00000000000093ff
thread  0 working on block 0x00000025<0x00000025<0x00000025     1024 kmers between 0x0000000000009400 and 0x00000000000097ff
thread  0 working on block 0x00000026<0x00000026<0x00000026     1024 kmers between 0x0000000000009800 and 0x0000000000009bff
thread  0 working on block 0x00000027<0x00000027<0x00000027     1024 kmers between 0x0000000000009c00 and 0x0000000000009fff
thread  0 working on block 0x00000028<0x00000028<0x00000028     1024 kmers between 0x000000000000a000 and 0x000000000000a3ff
thread  0 working on block 0x00000029<0x00000029<0x00000029     1024 kmers between 0x000000000000a400 and 0x000000000000a7ff
thread  0 working on block 0x0000002a<0x0000002a<0x0000002a     1024 kmers between 0x000000000000a800 and 0x000000000000abff
thread  0 working on block 0x0000002b<0x0000002b<0x0000002b     1024 kmers between 0x000000000000ac00 and 0x000000000000afff
thread  0 working on block 0x0000002c<0x0000002c<0x0000002c     1024 kmers between 0x000000000000b000 and 0x000000000000b3ff
thread  0 working on block 0x0000002d<0x0000002d<0x0000002d     1024 kmers between 0x000000000000b400 and 0x000000000000b7ff
thread  0 working on block 0x0000002e<0x0000002e<0x0000002e     1024 kmers between 0x000000000000b800 and 0x000000000000bbff
thread  0 working on block 0x0000002f<0x0000002f<0x0000002f     1024 kmers between 0x000000000000bc00 and 0x000000000000bfff
thread  0 working on block 0x00000030<0x00000030<0x00000030     1024 kmers between 0x000000000000c000 and 0x000000000000c3ff
thread  0 working on block 0x00000031<0x00000031<0x00000031     1024 kmers between 0x000000000000c400 and 0x000000000000c7ff
thread  0 working on block 0x00000032<0x00000032<0x00000032     1024 kmers between 0x000000000000c800 and 0x000000000000cbff
thread  0 working on block 0x00000033<0x00000033<0x00000033     1024 kmers between 0x000000000000cc00 and 0x000000000000cfff
thread  0 working on block 0x00000034<0x00000034<0x00000034     1024 kmers between 0x000000000000d000 and 0x000000000000d3ff
thread  0 working on block 0x00000035<0x00000035<0x00000035     1024 kmers between 0x000000000000d400 and 0x000000000000d7ff
thread  0 working on block 0x00000036<0x00000036<0x00000036     1024 kmers between 0x000000000000d800 and 0x000000000000dbff
thread  0 working on block 0x00000037<0x00000037<0x00000037     1024 kmers between 0x000000000000dc00 and 0x000000000000dfff
thread  0 working on block 0x00000038<0x00000038<0x00000038     1024 kmers between 0x000000000000e000 and 0x000000000000e3ff
thread  0 working on block 0x00000039<0x00000039<0x00000039     1024 kmers between 0x000000000000e400 and 0x000000000000e7ff
thread  0 working on block 0x0000003a<0x0000003a<0x0000003a     1024 kmers between 0x000000000000e800 and 0x000000000000ebff
thread  0 working on block 0x0000003b<0x0000003b<0x0000003b     1024 kmers between 0x000000000000ec00 and 0x000000000000efff
thread  0 working on block 0x0000003c<0x0000003c<0x0000003c     1024 kmers between 0x000000000000f000 and 0x000000000000f3ff
thread  0 working on block 0x0000003d<0x0000003d<0x0000003d     1024 kmers between 0x000000000000f400 and 0x000000000000f7ff
thread  0 working on block 0x0000003e<0x0000003e<0x0000003e     1024 kmers between 0x000000000000f800 and 0x000000000000fbff
thread  0 working on block 0x0000003f<0x0000003f<0x0000003f     1024 kmers between 0x000000000000fc00 and 0x000000000000ffff
finishIteration()--

Cleaning up.

Bye.

Standard Output:

```
K-mer size: 8
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b05ffac8bc8811ef8af67c1e526e05bb"`
chromInfo	`"/tmp/tmpikfn99fz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "8", "kmer_size": "provide"}`

Step 6: 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/tmpikfn99fz/files/c/f/a/dataset_cfa39e2a-f2b0-471d-91b4-696ced4a0f75.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_0 && mv ./tmp_folder_0/* db_'0'.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
    output to read-db.meryl

Cleaning up.

Bye.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b05ffac8bc8811ef8af67c1e526e05bb"`
chromInfo	`"/tmp/tmpikfn99fz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
groups_operations	`"union-sum"`

Step 7: 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/tmpikfn99fz/files/6/f/0/dataset_6f08b967-d112-48d6-8a5d-85a3f532eca1.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__	`"b05ffac8bc8811ef8af67c1e526e05bb"`
chromInfo	`"/tmp/tmpikfn99fz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 8: 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/tmpikfn99fz/files/d/e/b/dataset_debd9e9d-54b5-4416-8d54-4f9386e9310d.dat' --output . --kmer_length 8  --testing  --ploidy 1

Exit Code:

```
0
```

Standard Output:

GenomeScope analyzing /tmp/tmpikfn99fz/files/d/e/b/dataset_debd9e9d-54b5-4416-8d54-4f9386e9310d.dat p=1 k=8 outdir=.
a:100%
Model converged het:0 kcov:27.4 err:3.33e-15 model fit:10.1 len:37934

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"b05ffac8bc8811ef8af67c1e526e05bb"`
advanced_options	`{"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": true, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""}`
chromInfo	`"/tmp/tmpikfn99fz/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_length	`"8"`
lambda	`None`
max_kmercov	`None`
output_options	`{"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]}`
ploidy	`"1"`

Other invocation details
- history_id
  - c3422836f625a2da
- history_state
  - ok
- invocation_id
  - c3422836f625a2da
- invocation_state
  - scheduled
- workflow_id
  - c3422836f625a2da

github-actions · 2024-12-17T16:24:23Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ kmer-profiling-hifi-VGP1.ga_0

Problems:

Output with path /tmp/tmp741n0ha9/GenomeScope on data 7 Summary__e0c0c017-d416-4183-abe0-d01f46bdb69e different than expected
Expected text '35,913 bp' in output ('GenomeScope version 2.0
input file = /tmp/tmpczmv6ehb/files/9/d/9/dataset_9d926d93-922f-4c7d-860e-cf97270015dc.dat
output directory = .
p = 1
k = 8
TESTING set to TRUE

property                      min               max               
Homozygous (a)                100%              100%              
Genome Haploid Length         33,671 bp         43,432 bp         
Genome Repeat Length          5,829 bp          7,519 bp          
Genome Unique Length          27,842 bp         35,914 bp         
Model Fit                     91.9682%          94.5609%          
Read Error Rate               3.33067e-13%      3.33067e-13%      
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Collection of Pacbio Data:
- step_state: scheduled
**Step 2: K-mer length **:
- step_state: scheduled
Step 3: Ploidy:
- step_state: scheduled

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_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__	`"ddb56224bc9211ef899e6045bdd9c6c6"`
chromInfo	`"/tmp/tmpczmv6ehb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 1, "default_value": "21", "param_type": "integer", "pick_from": [{"__index__": 0, "value": "8"}]}}`

Step 5: 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/tmpczmv6ehb/files/e/a/4/dataset_ea44f4ab-a1a3-4108-b797-cbb699736255.dat' ./input.fastqsanger &&  meryl count k=8 memory=$GALAXY_MEMORY_GB threads=${GALAXY_SLOTS:-1} ./input.fastqsanger output read-db.meryl && echo 'K-mer size: 8' && 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 2047 (estimated) thousand canonical 8-mers from 1 input file:
    sequence-file: ./input.fastqsanger


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

  8-mers
    -> 65536 entries for counts up to 65535.
    -> 1024 kbits memory used

  2096311 input bases
    -> expected max count of 8385, needing 0 extra bits.
    -> no memory used

  128 kB memory needed


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

prefix     # of   struct   kmers/    segs/      min     data    total
  bits   prefix   memory   prefix   prefix   memory   memory   memory
------  -------  -------  -------  -------  -------  -------  -------
     1     2  P    10 kB   511 kM   240  S  8192  B  1920 kB  1930 kB
     2     4  P    16 kB   255 kM   112  S    16 kB  1792 kB  1808 kB
     3     8  P    28 kB   127 kM    52  S    32 kB  1664 kB  1692 kB
     4    16  P    53 kB    63 kM    24  S    64 kB  1536 kB  1589 kB
     5    32  P   103 kB    31 kM    11  S   128 kB  1408 kB  1511 kB
     6    64  P   204 kB    15 kM     5  S   256 kB  1280 kB  1484 kB
     7   128  P   407 kB  8189  M     3  S   512 kB  1536 kB  1943 kB
     8   256  P   810 kB  4095  M     1  S  1024 kB  1024 kB  1834 kB
     9   512  P  1620 kB  2048  M     1  S  2048 kB  2048 kB  3668 kB
    10  1024  P  3240 kB  1024  M     1  S  4096 kB  4096 kB  7336 kB  Best Value!
    11  2048  P  6480 kB   512  M     1  S  8192 kB  8192 kB    14 MB
    12  4096  P    12 MB   256  M     1  S    16 MB    16 MB    28 MB
    13  8192  P    25 MB   128  M     1  S    32 MB    32 MB    57 MB
    14    16 kP    50 MB    64  M     1  S    64 MB    64 MB   114 MB


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

Estimated to require 128 kB memory out of 8192 MB allowed.
Estimated to require 2 batches.

Configured simple mode for 0.000 GB memory per batch, and up to 2 batches.

Start counting with SIMPLE method.
Loading kmers from './input.fastqsanger' into buckets.

Writing results to 'read-db.meryl', using 1 threads.
             [ file ][  prefix ][  suffix ][ count-suffix ]
   widths    [    6 ][       0 ][      10 ][            0 ]
   number    [   64 ][       1 ][    1024 ][              ]

thread  0 working on block 0x00000000<0x00000000<0x00000000     1024 kmers between 0x0000000000000000 and 0x00000000000003ff
thread  0 working on block 0x00000001<0x00000001<0x00000001     1024 kmers between 0x0000000000000400 and 0x00000000000007ff
thread  0 working on block 0x00000002<0x00000002<0x00000002     1024 kmers between 0x0000000000000800 and 0x0000000000000bff
thread  0 working on block 0x00000003<0x00000003<0x00000003     1024 kmers between 0x0000000000000c00 and 0x0000000000000fff
thread  0 working on block 0x00000004<0x00000004<0x00000004     1024 kmers between 0x0000000000001000 and 0x00000000000013ff
thread  0 working on block 0x00000005<0x00000005<0x00000005     1024 kmers between 0x0000000000001400 and 0x00000000000017ff
thread  0 working on block 0x00000006<0x00000006<0x00000006     1024 kmers between 0x0000000000001800 and 0x0000000000001bff
thread  0 working on block 0x00000007<0x00000007<0x00000007     1024 kmers between 0x0000000000001c00 and 0x0000000000001fff
thread  0 working on block 0x00000008<0x00000008<0x00000008     1024 kmers between 0x0000000000002000 and 0x00000000000023ff
thread  0 working on block 0x00000009<0x00000009<0x00000009     1024 kmers between 0x0000000000002400 and 0x00000000000027ff
thread  0 working on block 0x0000000a<0x0000000a<0x0000000a     1024 kmers between 0x0000000000002800 and 0x0000000000002bff
thread  0 working on block 0x0000000b<0x0000000b<0x0000000b     1024 kmers between 0x0000000000002c00 and 0x0000000000002fff
thread  0 working on block 0x0000000c<0x0000000c<0x0000000c     1024 kmers between 0x0000000000003000 and 0x00000000000033ff
thread  0 working on block 0x0000000d<0x0000000d<0x0000000d     1024 kmers between 0x0000000000003400 and 0x00000000000037ff
thread  0 working on block 0x0000000e<0x0000000e<0x0000000e     1024 kmers between 0x0000000000003800 and 0x0000000000003bff
thread  0 working on block 0x0000000f<0x0000000f<0x0000000f     1024 kmers between 0x0000000000003c00 and 0x0000000000003fff
thread  0 working on block 0x00000010<0x00000010<0x00000010     1024 kmers between 0x0000000000004000 and 0x00000000000043ff
thread  0 working on block 0x00000011<0x00000011<0x00000011     1024 kmers between 0x0000000000004400 and 0x00000000000047ff
thread  0 working on block 0x00000012<0x00000012<0x00000012     1024 kmers between 0x0000000000004800 and 0x0000000000004bff
thread  0 working on block 0x00000013<0x00000013<0x00000013     1024 kmers between 0x0000000000004c00 and 0x0000000000004fff
thread  0 working on block 0x00000014<0x00000014<0x00000014     1024 kmers between 0x0000000000005000 and 0x00000000000053ff
thread  0 working on block 0x00000015<0x00000015<0x00000015     1024 kmers between 0x0000000000005400 and 0x00000000000057ff
thread  0 working on block 0x00000016<0x00000016<0x00000016     1024 kmers between 0x0000000000005800 and 0x0000000000005bff
thread  0 working on block 0x00000017<0x00000017<0x00000017     1024 kmers between 0x0000000000005c00 and 0x0000000000005fff
thread  0 working on block 0x00000018<0x00000018<0x00000018     1024 kmers between 0x0000000000006000 and 0x00000000000063ff
thread  0 working on block 0x00000019<0x00000019<0x00000019     1024 kmers between 0x0000000000006400 and 0x00000000000067ff
thread  0 working on block 0x0000001a<0x0000001a<0x0000001a     1024 kmers between 0x0000000000006800 and 0x0000000000006bff
thread  0 working on block 0x0000001b<0x0000001b<0x0000001b     1024 kmers between 0x0000000000006c00 and 0x0000000000006fff
thread  0 working on block 0x0000001c<0x0000001c<0x0000001c     1024 kmers between 0x0000000000007000 and 0x00000000000073ff
thread  0 working on block 0x0000001d<0x0000001d<0x0000001d     1024 kmers between 0x0000000000007400 and 0x00000000000077ff
thread  0 working on block 0x0000001e<0x0000001e<0x0000001e     1024 kmers between 0x0000000000007800 and 0x0000000000007bff
thread  0 working on block 0x0000001f<0x0000001f<0x0000001f     1024 kmers between 0x0000000000007c00 and 0x0000000000007fff
thread  0 working on block 0x00000020<0x00000020<0x00000020     1024 kmers between 0x0000000000008000 and 0x00000000000083ff
thread  0 working on block 0x00000021<0x00000021<0x00000021     1024 kmers between 0x0000000000008400 and 0x00000000000087ff
thread  0 working on block 0x00000022<0x00000022<0x00000022     1024 kmers between 0x0000000000008800 and 0x0000000000008bff
thread  0 working on block 0x00000023<0x00000023<0x00000023     1024 kmers between 0x0000000000008c00 and 0x0000000000008fff
thread  0 working on block 0x00000024<0x00000024<0x00000024     1024 kmers between 0x0000000000009000 and 0x00000000000093ff
thread  0 working on block 0x00000025<0x00000025<0x00000025     1024 kmers between 0x0000000000009400 and 0x00000000000097ff
thread  0 working on block 0x00000026<0x00000026<0x00000026     1024 kmers between 0x0000000000009800 and 0x0000000000009bff
thread  0 working on block 0x00000027<0x00000027<0x00000027     1024 kmers between 0x0000000000009c00 and 0x0000000000009fff
thread  0 working on block 0x00000028<0x00000028<0x00000028     1024 kmers between 0x000000000000a000 and 0x000000000000a3ff
thread  0 working on block 0x00000029<0x00000029<0x00000029     1024 kmers between 0x000000000000a400 and 0x000000000000a7ff
thread  0 working on block 0x0000002a<0x0000002a<0x0000002a     1024 kmers between 0x000000000000a800 and 0x000000000000abff
thread  0 working on block 0x0000002b<0x0000002b<0x0000002b     1024 kmers between 0x000000000000ac00 and 0x000000000000afff
thread  0 working on block 0x0000002c<0x0000002c<0x0000002c     1024 kmers between 0x000000000000b000 and 0x000000000000b3ff
thread  0 working on block 0x0000002d<0x0000002d<0x0000002d     1024 kmers between 0x000000000000b400 and 0x000000000000b7ff
thread  0 working on block 0x0000002e<0x0000002e<0x0000002e     1024 kmers between 0x000000000000b800 and 0x000000000000bbff
thread  0 working on block 0x0000002f<0x0000002f<0x0000002f     1024 kmers between 0x000000000000bc00 and 0x000000000000bfff
thread  0 working on block 0x00000030<0x00000030<0x00000030     1024 kmers between 0x000000000000c000 and 0x000000000000c3ff
thread  0 working on block 0x00000031<0x00000031<0x00000031     1024 kmers between 0x000000000000c400 and 0x000000000000c7ff
thread  0 working on block 0x00000032<0x00000032<0x00000032     1024 kmers between 0x000000000000c800 and 0x000000000000cbff
thread  0 working on block 0x00000033<0x00000033<0x00000033     1024 kmers between 0x000000000000cc00 and 0x000000000000cfff
thread  0 working on block 0x00000034<0x00000034<0x00000034     1024 kmers between 0x000000000000d000 and 0x000000000000d3ff
thread  0 working on block 0x00000035<0x00000035<0x00000035     1024 kmers between 0x000000000000d400 and 0x000000000000d7ff
thread  0 working on block 0x00000036<0x00000036<0x00000036     1024 kmers between 0x000000000000d800 and 0x000000000000dbff
thread  0 working on block 0x00000037<0x00000037<0x00000037     1024 kmers between 0x000000000000dc00 and 0x000000000000dfff
thread  0 working on block 0x00000038<0x00000038<0x00000038     1024 kmers between 0x000000000000e000 and 0x000000000000e3ff
thread  0 working on block 0x00000039<0x00000039<0x00000039     1024 kmers between 0x000000000000e400 and 0x000000000000e7ff
thread  0 working on block 0x0000003a<0x0000003a<0x0000003a     1024 kmers between 0x000000000000e800 and 0x000000000000ebff
thread  0 working on block 0x0000003b<0x0000003b<0x0000003b     1024 kmers between 0x000000000000ec00 and 0x000000000000efff
thread  0 working on block 0x0000003c<0x0000003c<0x0000003c     1024 kmers between 0x000000000000f000 and 0x000000000000f3ff
thread  0 working on block 0x0000003d<0x0000003d<0x0000003d     1024 kmers between 0x000000000000f400 and 0x000000000000f7ff
thread  0 working on block 0x0000003e<0x0000003e<0x0000003e     1024 kmers between 0x000000000000f800 and 0x000000000000fbff
thread  0 working on block 0x0000003f<0x0000003f<0x0000003f     1024 kmers between 0x000000000000fc00 and 0x000000000000ffff
finishIteration()--

Cleaning up.

Bye.

Standard Output:

```
K-mer size: 8
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddb56224bc9211ef899e6045bdd9c6c6"`
chromInfo	`"/tmp/tmpczmv6ehb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
count_operation	`"count"`
dbkey	`"?"`
options_kmer_size	`{"__current_case__": 0, "input_kmer_size": "8", "kmer_size": "provide"}`

Step 6: 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/tmpczmv6ehb/files/3/e/2/dataset_3e26438f-e4cf-4f9a-9e8a-d44c96d348ab.dat --use-compress-program="pigz -p ${GALAXY_SLOTS:-1}" -C ./tmp_folder_0 && mv ./tmp_folder_0/* db_'0'.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
    output to read-db.meryl

Cleaning up.

Bye.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddb56224bc9211ef899e6045bdd9c6c6"`
chromInfo	`"/tmp/tmpczmv6ehb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
groups_operations	`"union-sum"`

Step 7: 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/tmpczmv6ehb/files/8/0/f/dataset_80f39fa7-90d4-4c6a-8190-b887ee1942b4.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__	`"ddb56224bc9211ef899e6045bdd9c6c6"`
chromInfo	`"/tmp/tmpczmv6ehb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`

Step 8: 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/tmpczmv6ehb/files/9/d/9/dataset_9d926d93-922f-4c7d-860e-cf97270015dc.dat' --output . --kmer_length 8  --testing  --ploidy 1

Exit Code:

```
0
```

Standard Output:

GenomeScope analyzing /tmp/tmpczmv6ehb/files/9/d/9/dataset_9d926d93-922f-4c7d-860e-cf97270015dc.dat p=1 k=8 outdir=.
a:100%
Model converged het:0 kcov:27.4 err:3.33e-15 model fit:10.1 len:37934

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"ddb56224bc9211ef899e6045bdd9c6c6"`
advanced_options	`{"initial_heterozygosities": "", "initial_repetitiveness": null, "num_rounds": null, "testing": true, "topology": null, "trace_flag": false, "transform_exp": null, "true_params": ""}`
chromInfo	`"/tmp/tmpczmv6ehb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
kmer_length	`"8"`
lambda	`None`
max_kmercov	`None`
output_options	`{"no_unique_sequence": false, "output_files": ["model_output", "summary_output"]}`
ploidy	`"1"`

Other invocation details
- history_id
  - 8c9924ebef569352
- history_state
  - ok
- invocation_id
  - 8c9924ebef569352
- invocation_state
  - scheduled
- workflow_id
  - 8c9924ebef569352

mvdbeek · 2024-12-17T17:47:42Z

Thank you!

mvdbeek · 2024-12-17T17:47:44Z

Attention: deployment skipped!

https://github.com/galaxyproject/iwc/actions/runs/12378342787

mvdbeek · 2024-12-17T17:49:31Z

Attention: deployment cancelled!

https://github.com/galaxyproject/iwc/actions/runs/12378342787

Add annotation for vgp1 kmer profiling workflow

86e1591

mvdbeek requested a review from Delphine-L December 17, 2024 14:58

Update changelog and increment version to 0.1.9; add workflow annotation

1114755

Make test slightly more lentient

6acb4bd

mvdbeek approved these changes Dec 17, 2024

View reviewed changes

dannon merged commit 3e0a792 into galaxyproject:main Dec 17, 2024
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Add annotation for vgp1 kmer profiling workflow #640

Add annotation for vgp1 kmer profiling workflow #640

dannon commented Dec 17, 2024 •

edited

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Workflow invocation details

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Workflow invocation details

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mvdbeek commented Dec 17, 2024

mvdbeek commented Dec 17, 2024

Add annotation for vgp1 kmer profiling workflow #640

Add annotation for vgp1 kmer profiling workflow #640

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dannon commented Dec 17, 2024 • edited Loading

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github-actions bot commented Dec 17, 2024

Test Results (powered by Planemo)

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Workflow invocation details

mvdbeek commented Dec 17, 2024

mvdbeek commented Dec 17, 2024

mvdbeek commented Dec 17, 2024

dannon commented Dec 17, 2024 •

edited

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