TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
License: Other
During Confidence metrics, previously, we call depth on alignment file(s) then indicate how many positions in the chromosome(s) or contigs have an x of coverage. This was broken when pushing the new update for aggregate assemblies.
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Currently, the final confidences are reported per alignment stat for all references for a given sample and taxa. We need to aggregate and generate stats (like breadth of coverage, depth, etc.) for a given taxa, including stats across all reference from alignment
Kelly asked me to try this workflow on some metagenomic samples that we recently sequenced. The test ran okay, but it seems there are several *.view() statements and other irregularities that get printed to the screen.
Also, I'm unsure what usage to use. I currently have something running, but I thought I would share one of the warning messages that gets printed to the screen.
WARN: Access to undefined parameter `skip_assembly` -- Initialise it to a default value eg. `params.skip_assembly = some_value`No response
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Split the acc column on taxid then sample name then reference (aligned). Add a new column that is just the row count. Consider hiding the index number in the final table by editing the multiqc_config.yml file
Currently, Kraken2 reports a relatively large number of positives that are false for certain bacteria in messy sample types like stool. Consider adding GFF's into the mix for ensuring that CDS regions are being properly mapped and that there is enough breadth in coverage. Also consider filtering down to only important annotations such as AMR, virulence, pathogenicity etc.
Right now, these are missing from the report and must be manually searched for in the output folders. Add it to the Reports tab for NF Tower runs
Post-alignment, implement minmapq for minmap2 and bowtie2 BAM files before sorting
Use samtools coverage histogram (new in 1.18) as a submodule in alignment
Hello,
I am testing TaxTriage and running into an issue that I am having trouble resolving.
I have two samples, below is my sample sheet:
sample,single_end,fastq_1,fastq_2,barcode,from,trim,platform,sequencing_summary
004,FALSE,/home/centos/Desktop/TASS/004.k2dh_1.fastq.gz,/home/centos/Desktop/TASS/004.k2dh_2.fastq.gz,FALSE,,TRUE,ILLUMINA,
005,FALSE,/home/centos/Desktop/TASS/005.k2dh_1.fastq.gz,/home/centos/Desktop/TASS/005.k2dh_2.fastq.gz,FALSE,,TRUE,ILLUMINA,
It doesn't look like it's getting very far, seems like the issue might be related to Nextflow starting up. Log files and env are below, let me know if there is any other info I can provide to help troubleshoot.
Thanks,
Jake
In Basestack:
**Inputs**
Samplesheet: /home/centos/Desktop/TASS/sample_sheet.csv
Input Samplesheet contents: **Populates correctly**
Maximum CPUs: 3
Lag Time: 5
Maximum Memory: 12
Classifier database: Minikraken2
Skip De Novo Assemly: Yes
Skip QC Plotting: Yes
Resume Nextflow: Yes
Assembly File Option: NCBI Refseq Assembly
Automatically Pull Latest Code from Git Hub: Yes
Filter Database: **No selection**
Run Directory: **No selection**
Samplesheet: **No selection**
Profile: DockerclientError.log
docker.log
client.log
serverError.log
server.log
Version: 20.10.17
Kernel: 3.10.0-1160.71.1.el7.x86_64
Driver: overlay2
Running Containers: 0
Data: /var/lib/docker/1001.1001
Socket: /var/run/docker.sock
MemAvailable (GB): 33.57
Memory
Total Mem (GB): 33.57
Using Mem (GB): 2.78
Available Mem (GB): 30.79
Processor
CPU Brand: Xeon® E5-2680 v4
Cores: 16
Physical Cores: 16
Manufacturer: Intel®
Virtualization Support: false
System
Kernel: 3.10.0-1160.71.1.el7.x86_64
Platform: linux
Distro: CentOS Linux
Release: 7
TaxTriage
Version: v1.1
I'm trying to run TaxTriage and have encountered a bug involving the channels passed to the SPades module. The TaxTriage workflow trying to run SPADES_ILLUMINA but this channel hasn't been assigned.
It looks like there is a config variable called spades_hmm that defaults to null. I don't need to run SPades with a custom hmm, if that's useful.
Thanks!
nextflow run ./main.nf --input data/Samplesheet.csv --db data/databases/minikraken2_v2_8GB_201904_UPDATE --outdir tmp --remove_taxids "9606" --max_memory 8GB --max_cpus 3 -profile singularity -with-report --skip-assembly
N E X T F L O W ~ version 21.10.6
Launching `./main.nf` [nasty_babbage] - revision: ac98c18eda
WARN: Found unexpected parameters:
* --max_time: 240.h
* --config_profile_name: null
* --config_profile_url: null
* --config_profile_contact: null
* --config_profile_description: null
* --custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
* --custom_config_version: master
* --enable_conda: false
* --show_hidden_params: false
* --validate_params: true
* --help: false
* --monochrome_logs: false
* --plaintext_email: false
* --email_on_fail: null
* --publish_dir_mode: copy
* --tracedir: tmp/pipeline_info
* --skip-assembly: true
* --max_cpus: 3
* --max_memory: 8GB
* --max_multiqc_email_size: 25.MB
* --igenomes_ignore: false
* --igenomes_base: s3://ngi-igenomes/igenomes
* --genome: null
* --skip_variants: null
* --skip_consensus: null
* --subsample: null
* --top_hits_counts: null
* --spades_hmm: null
* --low_memory: null
- Ignore this warning: params.schema_ignore_params = "max_time,config_profile_name,config_profile_url,config_profile_contact,config_profile_description,custom_config_base,custom_config_version,enable_conda,show_hidden_params,validate_params,help,monochrome_logs,plaintext_email,email_on_fail,publish_dir_mode,tracedir,skip-assembly,max_cpus,max_memory,max_multiqc_email_size,igenomes_ignore,igenomes_base,genome,skip_variants,skip_consensus,subsample,top_hits_counts,spades_hmm,low_memory"
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/taxtriage v1.0dev
------------------------------------------------------
Core Nextflow options
runName : nasty_babbage
containerEngine: singularity
launchDir : /panfs/jay/groups/32/mdh/kuner010/taxtriage
workDir : /panfs/jay/groups/32/mdh/kuner010/taxtriage/work
projectDir : /panfs/jay/groups/32/mdh/kuner010/taxtriage
userName : kuner010
profile : singularity
configFiles : /panfs/jay/groups/32/mdh/kuner010/taxtriage/nextflow.config
Input/output options
input : data/Samplesheet.csv
db : data/databases/minikraken2_v2_8GB_201904_UPDATE
trim : null
outdir : tmp
remove_taxids : 9606
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/taxtriage for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/taxtriage/blob/master/CITATIONS.md
------------------------------------------------------
WARN: Access to undefined parameter `reference` -- Initialise it to a default value eg. `params.reference = some_value`
WARN: Access to undefined parameter `top_hits_count` -- Initialise it to a default value eg. `params.top_hits_count = some_value`
Top hits not specified, defaulting to 10 per rank level in taxonomy tree for database for kraken2
No assembly file given, downloading the standard ncbi one
WARN: Access to undefined parameter `assembly_file_type` -- Initialise it to a default value eg. `params.assembly_file_type = some_value`
/panfs/jay/groups/32/mdh/kuner010/taxtriage/data/Samplesheet.csv
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTQC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:NANOPLOT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MOVE_NANOPLOT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2 -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:REMOVETAXIDSCLASSIFICATION -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:TOP_HITS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_ASSEMBLY -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PULL_FASTA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BWA_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BWA_MEM -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:MINIMAP2_ALIGN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_OXFORD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_STATS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_CONSENSUS -
empty
No such variable: ch_spades_hmm
-- Check script './workflows/taxtriage.nf' at line: 318 or see '.nextflow.log' file for more detailsNo response
N E X T F L O W ~ version 21.10.6
HPC
slurm eventually, but was running locally here
Singularity/apptainer
NAME="CentOS Linux"
VERSION="7 (Core)"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="7"
PRETTY_NAME="CentOS Linux 7 (Core)"
nf-core/taxtriage v1.0.0
Currently, the main multiqc is too unwieldy. Users will want a simplistic table with as little information as needed for meaningful results
If a sample doesn't contain any trimmable reads, the file remains the same and the output is not emitted. This makes the pipeline fail. Make the output optional if it fails so the workflow can continue by reverting the next step to use the original fastq file
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Currently, the NCBI reference pull step for an assembly for each taxa only happens once. If it fails it skips. Can we do a re-attempt somewhere around here: https://github.com/jhuapl-bio/taxtriage/blob/main/bin/download_fastas.py#L257
Currently, only Docker or Singularity are capable as profiles for launching the pipeline. Try to get conda up to date
I ran a test (cmd below) where the outfile "BC05_flu.confidences.tsv" had the header but no second line content inside. So the python script failed with error:
Command error:
Traceback (most recent call last):
File "/my-local/.nextflow/assets/jhuapl-bio/taxtriage/bin/merge_assemblies_conf.py", line 108, in <module>
main()
File "/my-local/.nextflow/assets/jhuapl-bio/taxtriage/bin/merge_assemblies_conf.py", line 102, in main
writer = csv.DictWriter(f, fieldnames=aggregated[0].keys(), delimiter='\t')
IndexError: list index out of range
A test in this script prior to parsing it, or perhaps a QA test prior to it might be able to kill the wf reporting the error.
nextflow run https://github.com/jhuapl-bio/taxtriage \
--outdir tmp_viral \
-resume \
--input examples/Samplesheet.csv \
--taxtab "default" \
-r main \
-latest \
-profile local,singularity \
--db /my-local/reference/kraken-databases/minusB[21/6fb402] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMEN... [100%] 3 of 3
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMEN... -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMEN... -
[5e/c55e0d] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMEN... [100%] 3 of 3 ✔
[a8/909432] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMEN... [100%] 4 of 4 ✔
[82/97500c] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDEN... [100%] 4 of 4 ✔
[03/1f58a6] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDEN... [100%] 4 of 4, failed: 1 ✘
[4a/13073e] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_... [100%] 3 of 3 ✔
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGE_CO... [ 0%] 0 of 1
[01/01eeeb] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_D... [100%] 1 of 1 ✔
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/taxtriage] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_MERGE (BC05_flu)'
Caused by:
Process NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_MERGE (BC05_flu) terminated with an error exit status (1)
Command executed:
merge_assemblies_conf.py
-i BC05_flu.confidences.tsv
-o BC05_flu.fullconfidences.tsv
cat <<-END_VERSIONS > versions.yml
"NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_MERGE":
python3: $(python3 --version | sed 's/Python //g')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/my-local/.nextflow/assets/jhuapl-bio/taxtriage/bin/merge_assemblies_conf.py", line 108, in
main()
File "/my-local/.nextflow/assets/jhuapl-bio/taxtriage/bin/merge_assemblies_conf.py", line 102, in main
writer = csv.DictWriter(f, fieldnames=aggregated[0].keys(), delimiter='\t')
IndexError: list index out of range
N E X T F L O W
version 23.10.0 build 5889
created 15-10-2023 15:07 UTC (11:07 EDT)
cite doi:10.1038/nbt.3820
http://nextflow.io
local (no job scheduler)
singularity version 3.8.7-1.el7
Operating System: CentOS Stream 8
CPE OS Name: cpe:/o:centos:centos:8
Kernel: Linux 4.18.0-536.el8.x86_64
Architecture: x86-64
https://github.com/jhuapl-bio/taxtriage main branch version but also tested v1.2.2 tag with git checkout tags/v1.2.2
Currently, in singularity, Nanoplot fails when using longreads test file
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Alignment results are displayed in the sample specific .tsv files in "convert" directory and subsequently are incorporated into the "confidences.merged_mqc.tsv" in the "merge" directory. The data is not being incorporated into the MultiQC report which only displays the explanations for headers in the table.
The pipeline was run by cloning of the repository main branch and running the command below.
See the screenshot of MultiQC report below:
nextflow run main.nf -profile singularity,sge -work-dir /scicomp/scratch/ukm9/taxtriage -c /scicomp/reference/nextflow/configs/cdc.config --input data/Validation_data/0343_samples.csv --db /scicomp/groups/OID/NCEZID/DSR/BCFB/by-project/ukm9_TaxTriage/kraken2db/kraken2_MinusB --outdir output/Validation_data_0343_MinusB --remove_taxids '"9606"' --demux --skip_assemblyNo response
Nextflow - version 22.10.06
Hardware - HPC
Executor - SGE
Container - Singularity
OS - CentOS
If you get VCF stats for scaffolds (usually 80+ accessions) this part becomes unwieldy. Remove it entirely for now as it is not necessary in general
I am testing taxtriage on CLI with ONT metagenomics data and having issues with porechop. 4/5 samples were pre-processed (low complexity and quality filtering, adaptor clipping) using another pipeline and I left one sample unprocessed to test with taxtriage. The pipeline fails at the porechop step for the unprocessed sample (Sample65). The pipeline works fine when trim is set to "FALSE" for all samples.
Nextflow command:
run jhuapl-bio/taxtriage --input samplesheet.csv --outdir taxtriage_out2 -profile docker --db /Volumes/IDGenomics_NAS/Data/kraken2_plus_pf16gb/k2_pluspf_16gb_20231009 -r main -latest --reference_assembly --remove_taxids \'9606\' -resume
Samplesheet:
sample,platform,fastq_1,fastq_2,sequencing_summary,trim
Sample14_UT-P2S01293-240126,OXFORD,taxprofiler/taxprofiler_out/analysis_ready_fastqs/Sample14_UT-P2S01293-240126_run1_filtered.fastq.gz,,,TRUE
Sample15_UT-P2S01293-240126,OXFORD,taxprofiler/taxprofiler_out/analysis_ready_fastqs/Sample15_UT-P2S01293-240126_run1_filtered.fastq.gz,,,TRUE
Sample59_UT-P2S01293-240126,OXFORD,taxprofiler/taxprofiler_out/analysis_ready_fastqs/Sample59_UT-P2S01293-240126_run1_filtered.fastq.gz,,,TRUE
Sample62_UT-P2S01293-240126,OXFORD,taxprofiler/taxprofiler_out/analysis_ready_fastqs/Sample62_UT-P2S01293-240126_run1_filtered.fastq.gz,,,TRUE
Sample65_UT-P2S01293-240126,OXFORD,combined/Sample65_UT-P2S01293-240126.fastq.gz,,,TRUE
Error:
Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:PORECHOP (Sample65_UT-P2S01293-240126)'
Caused by:
Process `NFCORE_TAXTRIAGE:TAXTRIAGE:PORECHOP (Sample65_UT-P2S01293-240126)` terminated with an error exit status (137)
Command executed:
porechop \
-i Sample65_UT-P2S01293-240126.fastq.gz \
-t 12 \
\
-o Sample65_UT-P2S01293-240126.fastq.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_TAXTRIAGE:TAXTRIAGE:PORECHOP":
porechop: $( porechop --version )
END_VERSIONS
Command exit status:
137
Command output:
[1m[4mLoading reads[0m
Sample65_UT-P2S01293-240126.fastq.gz
Command error:
[1m[4mLoading reads[0m
Sample65_UT-P2S01293-240126.fastq.gz
.command.sh: line 6: 29 Killed porechop -i Sample65_UT-P2S01293-240126.fastq.gz -t 12 -o Sample65_UT-P2S01293-240126.fastq.gz
Work dir:
/Volumes/BioNGS_1/UT-P2S01293-240126/UT-P2S01293-240126/20240126_2026_P2S-01293-A_PAS21742_bded1596/work/ea/e089eaf142e00437c60686780fa8de
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`No response
Nextflow version (version 23.04.1)
bin/split_vcf.py decompresses the singulary channel output vcf.gz file, then splits them on the kraken taxid in the accession columnd (second index of split on "|") into individual files. Python3 is too slow, consider changing to gawk
Previously, BLAST was functional at the end of the pipeline (post top hits/re-alignment) but computationally expensive. Consider automated subsampling by hit-type and diversity of sequences for tuning purposes on final reporting metrics.
Adding 2 classifier approaches
Centrifuge and metaPhlan2
Additional classifier to add: Kaiju
If the confidences that is merged has a mismatch in columns, the table does not get populated
Due to the taxid not mapping in the merge portion
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Currently, the confidences are only run on the reads alignments that are assigned to the species or subspecies level
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It seems like some recent changes to the top hits report generation may have introduced some sort of mis-specified array:
Here's my error:
RROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingMethodException: No signature of method: Script_861716d0$_runScript_closure1$_closure2$_closure22.call() is applicable for argument types: (ArrayList) values: [[[id:230029461_WB, single_end:false, platform:ILLUMINA, fastq_1:/home/mdh/shared/taxtriage/231005_test/samples/230029461.Illumina.kraken.dehosted.1.fastq.gz, ...], ...]]
The log file truncates it but grabbing it from the slurm output:
ERROR ~ Invalid method invocation call with arguments: [[id:230029461_WB, single_end:false, platform:ILLUMINA, fastq_1:/home/mdh/shared/taxtriage/231005_test/samples/230029461.Illumina.kraken.dehosted.1.fastq.gz, fastq_2:/home/mdh/shared/taxtriage/231005_test/samples/230029461.Illumina.kraken.dehosted.2.fastq.gz, trim:false, directory:false, sequencing_summary:null], /panfs/jay/groups/32/mdh/shared/taxtriage/231005_test/work/66/89eb4288f373a6ad78f6d9d8079efd/230029461_WB.top_report.tsv, [/panfs/jay/groups/32/mdh/shared/taxtriage/231005_test/work/a0/587a499c14235a2d369c0e418fca23/230029461_WB.classified_1.fastq.gz, /panfs/jay/groups/32/mdh/shared/taxtriage/231005_test/work/a0/587a499c14235a2d369c0e418fca23/230029461_WB.classified_2.fastq.gz], /panfs/jay/groups/32/mdh/shared/taxtriage/231005_test/work/4e/923481f65a775d1ffa8f53afbea9bb/230029461_WB.output.references.fasta] (java.util.ArrayList) on _closure22 type
I haven't had a chance to do much digging, but the addition of the $2 variable in the top_hits.nf module might be breaking things?
nextflow run /home/mdh/shared/software_modules/taxtriage/1.2.0/main.nf -c /home/mdh/shared/software_modules/taxtriage/1.2.0/mdh.config --input samples//Samplesheet.csv --db /home/mdh/shared/software_modules/kraken/kraken2_databases/k2_standard_230605/ --outdir tt_out --email [email protected] --tmpdir /tmp --remove_taxids '"9606"' --max_memory 248GB --max_cpus 16 --skip_assembly FALSE --top_hits_count 50 --demux -profile singularity -with-report tt_out/tt_test_231005_report.html -with-dag ./work/tt_test_231005_taxtriage.html -resumeHere's the command.sh from the work directory where this breaks:
#!/bin/bash -euo pipefail
echo 230029460_WB "-----------------META variable------------------"
get_top_hits.py
-i "230029460_WB.filtered.report"
-o 230029460_WB.top_report.tsv
-t 50
awk -F '\t' -v id=230029460_WB
'BEGIN{OFS="\t"} { if (NR==1){ print "Sample_Taxid", $2, $1, $4, $6} else { $5 = id"_"$5; print $5, $2, $1, $4, $6 }}' 230029460_WB.top_report.tsv > 230029460_WB.krakenreport_mqc.tsv
cat <<-END_VERSIONS > versions.yml
"NFCORE_TAXTRIAGE:TAXTRIAGE:TOP_HITS":
python: $(python --version | sed 's/Python //g')
END_VERSIONS
Nextflow version 24.04.2
Hardware HPC, Desktop, Cloud
Executor slurm
Container engine: Singularity
OS CentOS Linux
Version of nf-core/taxtriage 1.2.0
I likely didn't create the sample sheet correctly or use the correct options. Sorry! I've attached the .nextflow.log as well as my sample sheet.
I ran the taxtriage test profile, and that worked okay. I decided to use it on "real" samples. They are two metagenomic samples from milk. The workflow was running until it wasn't.
$ nextflow run jhuapl-bio/taxtriage --input samplesheet.csv --outdir taxtriage -profile docker -resume -with-tower --db /Volumes/IDGenomics_NAS/Data/kraken2_db/2023-06-05 -r main
# top of stdout was cutoff due to screen limitations
No assembly file given, downloading the standard ncbi one
-[nf-core/taxtriage] Pipeline completed with errors- URL: https://tower.nf/user/erin-olde/watch/2BJYwM7lmUfLva
WARN: Killing running tasks (1)
Monitor the execution with Nextflow Tower using this URL: https://tower.nf/user/erin-olde/watch/2BJYwM7lmUfLva
executor > local (10)
[6e/47237e] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB [100%] 1 of 1 ✔
Monitor the execution with Nextflow Tower using this URL: https://tower.nf/user/erin-olde/watch/2BJYwM7lmUfLva
executor > local (10)
[6e/47237e] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB [100%] 1 of 1 ✔
[3b/275b6b] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES [100%] 1 of 1 ✔
[ce/e9d577] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC -
[0d/9e27ec] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTP (sample58) [100%] 1 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FASTQC -
[b7/67ad35] process > NFCORE_TAXTRIAGE:TAXTRIAGE:NANOPLOT (sample59) [100%] 1 of 1
[98/187187] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2 (sample59) [100%] 1 of 1
[6b/8c754c] process > NFCORE_TAXTRIAGE:TAXTRIAGE:VISUALIZE_REPORTS:KRONA_KTIMPORTTAXONOMY (sample59) [100%] 1 of 1
[26/c0417b] process > NFCORE_TAXTRIAGE:TAXTRIAGE:TOP_HITS (sample59) [100%] 1 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGEDKRAKENREPORT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FILTERKRAKEN -
[fe/ee62ee] process > NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_ASSEMBLY (sample59) [100%] 1 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_FAIDX [ 0%] 0 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_BUILD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BOWTIE2_ALIGN -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:MINIMAP2_ALIGN [ 0%] 0 of 1
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_DEPTH -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SAMTOOLS_COVERAGE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_OXFORD -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_MPILEUP_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:SPLIT_VCF -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_INDEX -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_STATS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:BCFTOOLS_CONSENSUS -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ALIGNMENT:RSEQC_BAMSTAT -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MERGE_CONFIDENCE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:SPADES_ILLUMINA -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:FLYE -
[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC - ERROR ~ Invalid method invocation `call` with arguments: [[id:sample59, single_end:true, platform:OXFORD, fastq_1:combined/sample59.fastq.gz, fastq_2:, trim:true, directory:false, sequencing_summary:null], /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work/26/c0417b071c657866ebeaf1d0173dc5/sample59.top_report.tsv, [/Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work/98/187187a25512238459d3c4d3cb052c/sample59.classified.fastq.gz], /Volumes/BioNGS_1/UT-P2S01293-231116/UT-P2S01293-231116/20231116_2158_P2S-01293-B_PAS24124_ea91207e/work/fe/ee62eefbb15ce2841320b077ee4f00/sample59.output.references.fasta] (java.util.ArrayList) on _closure24 type
-- Check '.nextflow.log' file for details
WARN: Tower request field `workflow.errorMessage` exceeds expected size | offending value: `No signature of method: Script_91470e4e8cb8ea83$_runScript_closure1$_closure3$_closure24.call() is applicable for argument types: (ArrayList) values: [[[id:sample59, single_end:true, platform:OXFORD, fastq_1:combined/sample59.fastq.gz, ...], ...]]
Possible solutions: any(), any(), each(groovy.lang.Closure), tap(groovy.lang.Closure), any(groovy.lang.Closure), each(groovy.lang.Closure)`, size: 386 (max: 255)This is the .nextflow.log file:
nextflow.log
And my sample sheet:
samplesheet.csv
N E X T F L O W version 23.10.0 build 5889
Hardware : Local
Executor : local
Container engine: Docker
OS : CentOS
Version of jhuapl-bio/taxtriage : current version (pulled 11/22/2023)
Instead of only giving the option to use Kraken2 for de-hosting, provide minimap2/bowtie2 and save unaligned reads to another fastq file (.gz)
Additional parameters to add:
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