Added flye assembly workflow #199

AnnaSyme · 2023-07-15T00:34:23Z

Added a new folder, and then also a subfolder in here, as I will add some more.

workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye-tests.yml

mvdbeek · 2023-09-15T11:14:30Z

@AnnaSyme can we do something to help you out with this ?

AnnaSyme · 2023-09-28T11:45:54Z

@mvdbeek do you know why this would be failing at the "combine chunked test results" step? I've run this on Galaxy Au via planemo and tests pass.

mvdbeek · 2023-09-28T13:15:38Z

Sure, if you go to the summary page of the results (https://github.com/galaxyproject/iwc/actions/runs/5560862657?pr=199) you can download a report, in there you see the final state and all the workflow steps. This one is failing because the Bandage docker container is broken, and we're already working on a fix for this.

bgruening · 2023-11-07T08:01:42Z

Bandage container should be available. Lets see what the tests say.

mvdbeek · 2023-11-07T08:55:23Z

gnuplot: error while loading shared libraries: libGL.so.1: cannot open shared object file: No such file or directory

bgruening · 2023-11-07T09:05:57Z

You are using Singularity images from depot? I have seen the error and syncing building the Singularity images. But I guess Nate needs to sync the CVMFS? I can not trigger that part.

https://github.com/BioContainers/singularity-build-bot/actions/runs/6780748920/job/18433157940

mvdbeek · 2023-11-07T09:07:02Z

No, this is a broken docker image. No singularity

mvdbeek · 2023-11-07T09:07:23Z

Ah, I guess that wasn't clear, it's not bandage

bgruening · 2023-11-07T09:12:44Z

Which container is it? I fixed bandage and the container should work now.

mvdbeek · 2023-11-07T09:17:30Z

BioContainers/multi-package-containers#2813 also did the trick, we merged Delphine's workflow last week that also used bandage.

https://github.com/mvdbeek/galaxy/blob/520fa4a233145d18e3b2a53f49549ea9e4a65cc0/tools/plotting/bar_chart.xml#L1
which doesn't use any dependency at all. Do you know if we have a modern replacement ? barchart seems to be missing from ggplot2?

AnnaSyme · 2023-11-07T09:19:06Z

barchart probably isn't essential. it was just to show contig sizes.

workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye-tests.yml

workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye.ga

workflows/genome-assembly/assembly-with-flye/README.md

…ith-Flye-tests.yml Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

…ith-Flye.ga Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

github-actions · 2024-02-14T14:00:16Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ Genome-assembly-with-Flye.ga_0

Problems:

Output with path /tmp/tmp73ggqym6/Quast on data 2 HTML report__364ec7a9-e219-42b2-977e-3912fa50aee0 different than expected, difference (using sim_size):
( /home/runner/work/iwc/iwc/workflows/genome-assembly/assembly-with-flye/test-data/Quast_report.html v. /tmp/tmpnvtmfnmaQuast_report.html )
Files /home/runner/work/iwc/iwc/workflows/genome-assembly/assembly-with-flye/test-data/Quast_report.html=369176b but /tmp/tmpnvtmfnmaQuast_report.html=280775b - compare by size (delta=10000) failed

Workflow invocation details

Invocation Messages

Steps

Step 1: Input sequence reads:
- step_state: scheduled

Step 2: Flye: assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpnh8mci8f/files/d/6/a/dataset_d6a562a4-66cb-46b4-b8ea-68522b9bcf13.dat' ./input_0.fastq.gz && flye --nano-raw ./input_0.fastq.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 1

Exit Code:

```
0
```

Standard Error:

[2024-02-14 13:53:29] INFO: Starting Flye 2.9.1-b1780
[2024-02-14 13:53:29] INFO: >>>STAGE: configure
[2024-02-14 13:53:29] INFO: Configuring run
[2024-02-14 13:53:29] INFO: Total read length: 1047156
[2024-02-14 13:53:29] INFO: Reads N50/N90: 10457 / 5908
[2024-02-14 13:53:29] INFO: Minimum overlap set to 6000
[2024-02-14 13:53:29] INFO: >>>STAGE: assembly
[2024-02-14 13:53:29] INFO: Assembling disjointigs
[2024-02-14 13:53:29] INFO: Reading sequences
[2024-02-14 13:53:30] INFO: Counting k-mers:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 13:54:23] INFO: Filling index table (1/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 13:54:23] INFO: Filling index table (2/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 13:54:24] INFO: Extending reads
[2024-02-14 13:54:24] INFO: Overlap-based coverage: 1
[2024-02-14 13:54:24] INFO: Median overlap divergence: 0.238094
0% 10% 20% 30% 40% 50% 70% 80% 90% 100% 
[2024-02-14 13:54:24] INFO: Assembled 12 disjointigs
[2024-02-14 13:54:24] INFO: Generating sequence
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 13:54:24] INFO: Filtering contained disjointigs
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 13:54:24] INFO: Contained seqs: 0
[2024-02-14 13:54:24] INFO: >>>STAGE: consensus
[2024-02-14 13:54:24] INFO: Running Minimap2
[2024-02-14 13:54:25] INFO: Computing consensus
[2024-02-14 13:54:26] INFO: Alignment error rate: 0.150049
[2024-02-14 13:54:26] INFO: >>>STAGE: repeat
[2024-02-14 13:54:26] INFO: Building and resolving repeat graph
[2024-02-14 13:54:26] INFO: Parsing disjointigs
[2024-02-14 13:54:26] INFO: Building repeat graph
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 13:54:26] INFO: Median overlap divergence: 0
[2024-02-14 13:54:26] INFO: Parsing reads
[2024-02-14 13:54:26] INFO: Aligning reads to the graph
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 13:54:27] INFO: Aligned read sequence: 809934 / 936572 (0.864786)
[2024-02-14 13:54:27] INFO: Median overlap divergence: 0.107473
[2024-02-14 13:54:27] INFO: Mean edge coverage: 2
[2024-02-14 13:54:27] INFO: Simplifying the graph
[2024-02-14 13:54:27] INFO: >>>STAGE: contigger
[2024-02-14 13:54:27] INFO: Generating contigs
[2024-02-14 13:54:27] INFO: Reading sequences
[2024-02-14 13:54:27] INFO: Generated 3 contigs
[2024-02-14 13:54:27] INFO: Added 0 scaffold connections
[2024-02-14 13:54:27] INFO: >>>STAGE: polishing
[2024-02-14 13:54:27] INFO: Polishing genome (1/1)
[2024-02-14 13:54:27] INFO: Running minimap2
[2024-02-14 13:54:27] INFO: Separating alignment into bubbles
[2024-02-14 13:54:27] INFO: Alignment error rate: 0.118021
[2024-02-14 13:54:27] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 80% 90% 100% 
[2024-02-14 13:54:41] INFO: >>>STAGE: finalize
[2024-02-14 13:54:41] INFO: Assembly statistics:

	Total length:	83456
	Fragments:	3
	Fragments N50:	42654
	Largest frg:	42654
	Scaffolds:	0
	Mean coverage:	3

[2024-02-14 13:54:41] INFO: Final assembly: /tmp/tmpnh8mci8f/job_working_directory/000/2/working/out_dir/assembly.fasta

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4c80fc45cb4011eea2da8df54510c1d6"`
asm	`{"__current_case__": 1, "asm_select": "false"}`
chromInfo	`"/tmp/tmpnh8mci8f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
generate_log	`false`
i	`"1"`
iterations	`"1"`
keep_haplotypes	`false`
m	`None`
meta	`false`
min_overlap	`None`
mode	`"--nano-raw"`
mode_conditional	`{"__current_case__": 0, "mode": "--nano-raw"}`
no_alt_contigs	`false`
no_trestle	`"false"`
plasmids	`"false"`
scaffold	`false`

Step 3: Quast genome report:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo Flye_on_data_1__consensus &&    quast  --labels 'Flye_on_data_1__consensus' -o 'outputdir'   --min-identity 95.0 --min-contig 500  --large      --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmpnh8mci8f/files/f/3/4/dataset_f3424365-49bf-4157-b34c-c5d0d73d5c64.dat' --threads ${GALAXY_SLOTS:-1}  && mkdir -p '/tmp/tmpnh8mci8f/job_working_directory/000/3/outputs/dataset_364ec7a9-e219-42b2-977e-3912fa50aee0_files' && cp outputdir/*.html '/tmp/tmpnh8mci8f/job_working_directory/000/3/outputs/dataset_364ec7a9-e219-42b2-977e-3912fa50aee0_files' && cp -R outputdir/icarus_viewers '/tmp/tmpnh8mci8f/job_working_directory/000/3/outputs/dataset_364ec7a9-e219-42b2-977e-3912fa50aee0_files'

Exit Code:

```
0
```

Standard Output:

Flye_on_data_1__consensus
/usr/local/bin/quast --labels Flye_on_data_1__consensus -o outputdir --min-identity 95.0 --min-contig 500 --large --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmpnh8mci8f/files/f/3/4/dataset_f3424365-49bf-4157-b34c-c5d0d73d5c64.dat --threads 1

Version: 5.2.0

System information:
  OS: Linux-6.2.0-1019-azure-x86_64-with-glibc2.28 (linux_64)
  Python version: 3.9.13
  CPUs number: 4

Started: 2024-02-14 13:55:12

Logging to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/quast.log
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /tmp/tmpnh8mci8f/job_working_directory/000/3/working
Main parameters: 
  MODE: large, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \
  min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmpnh8mci8f/files/f/3/4/dataset_f3424365-49bf-4157-b34c-c5d0d73d5c64.dat ==> Flye_on_data_1__consensus

2024-02-14 13:55:13
Running Basic statistics processor...
  Contig files: 
    Flye_on_data_1__consensus
  Calculating N50 and L50...
    Flye_on_data_1__consensus, N50 = 42654, L50 = 1, auN = 32760.6, Total length = 83456, GC % = 51.86, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing Flye_on_data_1__consensus GC content plot...
    saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/basic_stats/Flye_on_data_1__consensus_GC_content_plot.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2024-02-14 13:55:14
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2024-02-14 13:55:14
RESULTS:
  Text versions of total report are saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/icarus.html
  Log is saved to /tmp/tmpnh8mci8f/job_working_directory/000/3/working/outputdir/quast.log

Finished: 2024-02-14 13:55:14
Elapsed time: 0:00:02.285189
NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"4c80fc45cb4011eea2da8df54510c1d6"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}`
al	`{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "fragmented_max_indent": "50", "min_alignment": "65", "min_identity": "95.0", "upper_bound_assembly": false, "upper_bound_min_con": "2", "use_all_alignments": false}`
alignments	`{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}`
assembly	`{"__current_case__": 0, "min_identity": "95.0", "orga_type": "", "ref": {"__current_case__": 1, "est_ref_size": null, "use_ref": "false"}, "type": "genome"}`
chromInfo	`"/tmp/tmpnh8mci8f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circos	`"false"`
contig_thresholds	`"0,1000"`
dbkey	`"?"`
extensive_mis_size	`"1000"`
genes	`{"conserved_genes_finding": false, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}`
in	`{"__current_case__": 1, "custom": "false", "inputs": {"__class__": "RuntimeValue"}}`
k_mer	`{"__current_case__": 1, "k_mer_stats": ""}`
large	`true`
min_contig	`"500"`
mode	`{"__current_case__": 1, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 2, "src": "hda"}]}}, "mode": "co", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`"html"`
scaffold_gap_max_size	`"1000"`
skip_unaligned_mis_contigs	`"false"`
split_scaffolds	`false`
strict_NA	`"false"`
unaligned_part_size	`"500"`

Step 4: Fasta statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmpnh8mci8f/files/f/3/4/dataset_f3424365-49bf-4157-b34c-c5d0d73d5c64.dat' --stats_output '/tmp/tmpnh8mci8f/job_working_directory/000/4/outputs/dataset_2a59195f-62cb-420b-9cf9-d1cc9e24fe91.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4c80fc45cb4011eea2da8df54510c1d6"`
chromInfo	`"/tmp/tmpnh8mci8f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dataset	`{"__class__": "ConnectedValue"}`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 5: Bandage image: Flye assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmpnh8mci8f/files/2/e/8/dataset_2e8e9e12-e59b-4966-942b-251f172fb77d.dat' input.gfa &&  export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.jpg' --height '1000'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"4c80fc45cb4011eea2da8df54510c1d6"`
chromInfo	`"/tmp/tmpnh8mci8f/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fontsize	`None`
height	`"1000"`
lengths	`false`
names	`false`
nodewidth	`None`
output_format	`"jpg"`
width	`None`

Other invocation details
- history_id
  - 7c2c45c30e2312b7
- history_state
  - ok
- invocation_id
  - 7c2c45c30e2312b7
- invocation_state
  - scheduled
- workflow_id
  - 7c2c45c30e2312b7

github-actions · 2024-02-14T15:20:53Z

Test Results (powered by Planemo)

Test Summary

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

Failed Tests

❌ Genome-assembly-with-Flye.ga_0

Problems:

Output with path /tmp/tmpfdocymdd/Flye on data 1 consensus__cce38151-52f2-4571-bcb3-af47acb70b00 different than expected
Expected file size to be in [86k:inf] found 84878

Output with path /tmp/tmplv3blcey/Quast on data 2 HTML report__a9f63622-76b3-4202-9b30-693f09c0d35c different than expected
Expected file size to be in [300k:400k] found 280775

Workflow invocation details

Invocation Messages

Steps

Step 1: Input sequence reads:
- step_state: scheduled

Step 2: Flye: assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp8s_wc0a5/files/7/6/7/dataset_7679172e-3f60-4ae4-b873-803ef7d84d62.dat' ./input_0.fastq.gz && flye --nano-raw ./input_0.fastq.gz -o out_dir -t ${GALAXY_SLOTS:-4} -i 1

Exit Code:

```
0
```

Standard Error:

[2024-02-14 15:17:59] INFO: Starting Flye 2.9.1-b1780
[2024-02-14 15:17:59] INFO: >>>STAGE: configure
[2024-02-14 15:17:59] INFO: Configuring run
[2024-02-14 15:17:59] INFO: Total read length: 1047156
[2024-02-14 15:17:59] INFO: Reads N50/N90: 10457 / 5908
[2024-02-14 15:17:59] INFO: Minimum overlap set to 6000
[2024-02-14 15:17:59] INFO: >>>STAGE: assembly
[2024-02-14 15:17:59] INFO: Assembling disjointigs
[2024-02-14 15:17:59] INFO: Reading sequences
[2024-02-14 15:18:00] INFO: Counting k-mers:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 15:18:52] INFO: Filling index table (1/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 15:18:52] INFO: Filling index table (2/2)
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 15:18:54] INFO: Extending reads
[2024-02-14 15:18:54] INFO: Overlap-based coverage: 1
[2024-02-14 15:18:54] INFO: Median overlap divergence: 0.238094
0% 10% 20% 30% 40% 50% 70% 80% 90% 100% 
[2024-02-14 15:18:54] INFO: Assembled 12 disjointigs
[2024-02-14 15:18:54] INFO: Generating sequence
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 15:18:54] INFO: Filtering contained disjointigs
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 15:18:54] INFO: Contained seqs: 0
[2024-02-14 15:18:54] INFO: >>>STAGE: consensus
[2024-02-14 15:18:54] INFO: Running Minimap2
[2024-02-14 15:18:54] INFO: Computing consensus
[2024-02-14 15:18:56] INFO: Alignment error rate: 0.150049
[2024-02-14 15:18:56] INFO: >>>STAGE: repeat
[2024-02-14 15:18:56] INFO: Building and resolving repeat graph
[2024-02-14 15:18:56] INFO: Parsing disjointigs
[2024-02-14 15:18:56] INFO: Building repeat graph
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 15:18:56] INFO: Median overlap divergence: 0
[2024-02-14 15:18:56] INFO: Parsing reads
[2024-02-14 15:18:56] INFO: Aligning reads to the graph
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[2024-02-14 15:18:56] INFO: Aligned read sequence: 809934 / 936572 (0.864786)
[2024-02-14 15:18:56] INFO: Median overlap divergence: 0.107473
[2024-02-14 15:18:56] INFO: Mean edge coverage: 2
[2024-02-14 15:18:56] INFO: Simplifying the graph
[2024-02-14 15:18:56] INFO: >>>STAGE: contigger
[2024-02-14 15:18:56] INFO: Generating contigs
[2024-02-14 15:18:56] INFO: Reading sequences
[2024-02-14 15:18:56] INFO: Generated 3 contigs
[2024-02-14 15:18:56] INFO: Added 0 scaffold connections
[2024-02-14 15:18:56] INFO: >>>STAGE: polishing
[2024-02-14 15:18:56] INFO: Polishing genome (1/1)
[2024-02-14 15:18:56] INFO: Running minimap2
[2024-02-14 15:18:56] INFO: Separating alignment into bubbles
[2024-02-14 15:18:57] INFO: Alignment error rate: 0.118021
[2024-02-14 15:18:57] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 80% 90% 100% 
[2024-02-14 15:19:10] INFO: >>>STAGE: finalize
[2024-02-14 15:19:10] INFO: Assembly statistics:

	Total length:	83456
	Fragments:	3
	Fragments N50:	42654
	Largest frg:	42654
	Scaffolds:	0
	Mean coverage:	3

[2024-02-14 15:19:10] INFO: Final assembly: /tmp/tmp8s_wc0a5/job_working_directory/000/2/working/out_dir/assembly.fasta

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"20e11807cb4c11ee866da7b7687d9f2a"`
asm	`{"__current_case__": 1, "asm_select": "false"}`
chromInfo	`"/tmp/tmp8s_wc0a5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
generate_log	`false`
i	`"1"`
iterations	`"1"`
keep_haplotypes	`false`
m	`None`
meta	`false`
min_overlap	`None`
mode	`"--nano-raw"`
mode_conditional	`{"__current_case__": 0, "mode": "--nano-raw"}`
no_alt_contigs	`false`
no_trestle	`"false"`
plasmids	`"false"`
scaffold	`false`

Step 3: Quast genome report:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo Flye_on_data_1__consensus &&    quast  --labels 'Flye_on_data_1__consensus' -o 'outputdir'   --min-identity 95.0 --min-contig 500  --large      --min-alignment 65 --ambiguity-usage 'one' --ambiguity-score 0.99   --local-mis-size 200   --contig-thresholds '0,1000'  --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500   --x-for-Nx 90  '/tmp/tmp8s_wc0a5/files/c/c/e/dataset_cce38151-52f2-4571-bcb3-af47acb70b00.dat' --threads ${GALAXY_SLOTS:-1}  && mkdir -p '/tmp/tmp8s_wc0a5/job_working_directory/000/3/outputs/dataset_a9f63622-76b3-4202-9b30-693f09c0d35c_files' && cp outputdir/*.html '/tmp/tmp8s_wc0a5/job_working_directory/000/3/outputs/dataset_a9f63622-76b3-4202-9b30-693f09c0d35c_files' && cp -R outputdir/icarus_viewers '/tmp/tmp8s_wc0a5/job_working_directory/000/3/outputs/dataset_a9f63622-76b3-4202-9b30-693f09c0d35c_files'

Exit Code:

```
0
```

Standard Output:

Flye_on_data_1__consensus
/usr/local/bin/quast --labels Flye_on_data_1__consensus -o outputdir --min-identity 95.0 --min-contig 500 --large --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmp8s_wc0a5/files/c/c/e/dataset_cce38151-52f2-4571-bcb3-af47acb70b00.dat --threads 1

Version: 5.2.0

System information:
  OS: Linux-6.2.0-1019-azure-x86_64-with-glibc2.28 (linux_64)
  Python version: 3.9.13
  CPUs number: 4

Started: 2024-02-14 15:19:42

Logging to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/quast.log
WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /tmp/tmp8s_wc0a5/job_working_directory/000/3/working
Main parameters: 
  MODE: large, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \
  min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000

Contigs:
  Pre-processing...
  /tmp/tmp8s_wc0a5/files/c/c/e/dataset_cce38151-52f2-4571-bcb3-af47acb70b00.dat ==> Flye_on_data_1__consensus

2024-02-14 15:19:42
Running Basic statistics processor...
  Contig files: 
    Flye_on_data_1__consensus
  Calculating N50 and L50...
    Flye_on_data_1__consensus, N50 = 42654, L50 = 1, auN = 32760.6, Total length = 83456, GC % = 51.86, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing Flye_on_data_1__consensus GC content plot...
    saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/basic_stats/Flye_on_data_1__consensus_GC_content_plot.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.

2024-02-14 15:19:43
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating PDF with all tables and plots...
  2 of 2: Creating Icarus viewers...
Done

2024-02-14 15:19:44
RESULTS:
  Text versions of total report are saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) is saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/report.pdf
  Icarus (contig browser) is saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/icarus.html
  Log is saved to /tmp/tmp8s_wc0a5/job_working_directory/000/3/working/outputdir/quast.log

Finished: 2024-02-14 15:19:44
Elapsed time: 0:00:02.217822
NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0

Thank you for using QUAST!

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"20e11807cb4c11ee866da7b7687d9f2a"`
advanced	`{"contig_thresholds": "0,1000", "extensive_mis_size": "1000", "fragmented_max_indent": null, "report_all_metrics": false, "scaffold_gap_max_size": "1000", "skip_unaligned_mis_contigs": true, "strict_NA": false, "unaligned_part_size": "500", "x_for_Nx": "90"}`
al	`{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "fragmented_max_indent": "50", "min_alignment": "65", "min_identity": "95.0", "upper_bound_assembly": false, "upper_bound_min_con": "2", "use_all_alignments": false}`
alignments	`{"ambiguity_score": "0.99", "ambiguity_usage": "one", "fragmented": false, "local_mis_size": "200", "min_alignment": "65", "upper_bound_assembly": false, "upper_bound_min_con": null, "use_all_alignments": false}`
assembly	`{"__current_case__": 0, "min_identity": "95.0", "orga_type": "", "ref": {"__current_case__": 1, "est_ref_size": null, "use_ref": "false"}, "type": "genome"}`
chromInfo	`"/tmp/tmp8s_wc0a5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
circos	`"false"`
contig_thresholds	`"0,1000"`
dbkey	`"?"`
extensive_mis_size	`"1000"`
genes	`{"conserved_genes_finding": false, "gene_finding": {"__current_case__": 0, "tool": "none"}, "rna_finding": false}`
in	`{"__current_case__": 1, "custom": "false", "inputs": {"__class__": "RuntimeValue"}}`
k_mer	`{"__current_case__": 1, "k_mer_stats": ""}`
large	`true`
min_contig	`"500"`
mode	`{"__current_case__": 1, "in": {"__current_case__": 1, "custom": "false", "inputs": {"values": [{"id": 2, "src": "hda"}]}}, "mode": "co", "reads": {"__current_case__": 0, "reads_option": "disabled"}}`
output_files	`"html"`
scaffold_gap_max_size	`"1000"`
skip_unaligned_mis_contigs	`"false"`
split_scaffolds	`false`
strict_NA	`"false"`
unaligned_part_size	`"500"`

Step 4: Fasta statistics:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmp8s_wc0a5/files/c/c/e/dataset_cce38151-52f2-4571-bcb3-af47acb70b00.dat' --stats_output '/tmp/tmp8s_wc0a5/job_working_directory/000/4/outputs/dataset_f0ceff54-7df6-4f3e-91ca-6a2779f35a1f.dat'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"20e11807cb4c11ee866da7b7687d9f2a"`
chromInfo	`"/tmp/tmp8s_wc0a5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dataset	`{"__class__": "ConnectedValue"}`
dbkey	`"?"`
gaps_option	`false`
genome_size	`None`

Step 5: Bandage image: Flye assembly:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp8s_wc0a5/files/3/4/d/dataset_34d35b54-b676-4cff-b3ce-1e4733f0eede.dat' input.gfa &&  export QT_QPA_PLATFORM='offscreen' && Bandage image input.gfa 'out.jpg' --height '1000'

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"20e11807cb4c11ee866da7b7687d9f2a"`
chromInfo	`"/tmp/tmp8s_wc0a5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fontsize	`None`
height	`"1000"`
lengths	`false`
names	`false`
nodewidth	`None`
output_format	`"jpg"`
width	`None`

Other invocation details
- history_id
  - 48574035fa9b433f
- history_state
  - ok
- invocation_id
  - 48574035fa9b433f
- invocation_state
  - scheduled
- workflow_id
  - 48574035fa9b433f

mvdbeek · 2024-02-14T16:31:05Z

Thank you @AnnaSyme!

bgruening reviewed Jul 15, 2023

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AnnaSyme and others added 5 commits February 14, 2024 14:57

Added new assembly workflow

a8dd9c6

Removed white space from file names

a01b390

dockstore.yml

9c58570

json prettify

d24a912

Update workflows/genome-assembly/assembly-with-flye/Genome-assembly-w…

b919f8b

…ith-Flye-tests.yml Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

AnnaSyme and others added 8 commits February 14, 2024 14:57

Update workflows/genome-assembly/assembly-with-flye/Genome-assembly-w…

2a005f3

…ith-Flye.ga Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

Update workflows/genome-assembly/assembly-with-flye/README.md

3754a78

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>

Update README.md - take out bar chart mentions

db4f78d

Delete unused test data

c5994ec

Update README.md - add info for input reads

b4f3480

Update README.md - add in intro

10b266d

Fix workflow formatting

2ebc60b

Tweak labels a little

6b2e00c

mvdbeek force-pushed the assembly-wfs branch 5 times, most recently from 0fa84dc to 0bc7958 Compare February 14, 2024 15:09

Use asserts statements instead of file comparisons

b6cefa4

mvdbeek force-pushed the assembly-wfs branch from 0bc7958 to b6cefa4 Compare February 14, 2024 15:39

mvdbeek changed the title ~~Added new assembly workflow~~ Added flye assembly workflow Feb 14, 2024

mvdbeek merged commit 5d9e8ee into galaxyproject:main Feb 14, 2024
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Added flye assembly workflow #199

Added flye assembly workflow #199

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Workflow invocation details

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Added flye assembly workflow #199

Added flye assembly workflow #199

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