WtP terminal execution:
In this section we want to explain what you see in the Terminal when you execute WtP:
I'm currently writing on this part
Let's do a Testrun
Open your terminal, move to a directory where you want to execute WtP and type/copy the following command
nextflow run phage.nf -profile smalltest,local,docker --work-dir work --cores 16
A lot of stuff will pop up but we will quide you through it:
N E X T F L O W ~ version 20.07.1
Launching `phage.nf` [admiring_pesquet] - revision: 1b76c726d3
_____ _____ ____ ____ ___ ___ __ __ _ _
__ _______________________
/ \ / \__ ___/\______ \
\ \/\/ / | | | ___/
\ / | | | |
\__/\ / |____| |____|
\/
_____ _____ ____ ____ ___ ___ __ __ _ _
Profile: smalltest,local,docker
Current User: mike
Nextflow-version: 20.07.1
WtP intended for Nextflow-version: 20.01.0
Starting time: 24-07-2020 15:18 UTC
Workdir location [--workdir]:
/home/mike/bioinformatics/What_the_Phage/cores=16
Output location [--output]:
results
Database location [--databases]:
nextflow-autodownload-databases
CPUs to use: 8, maximal CPUs to use: 20
- this is the first thing that will pop up and will give you some basic workflow information: eg where output is stored or how many cores you are using for computing
- An overview about all the WtP processes will show up and looks like this:
[6b/79564a] process > identify_fasta_MSF:fasta_validation_wf:input_suffix_check (1) [100%] 1 of 1 ✔
[c7/d34016] process > identify_fasta_MSF:fasta_validation_wf:seqkit (1) [100%] 1 of 1 ✔
[- ] process > identify_fasta_MSF:virsorter_wf:virsorter [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:virsorter_wf:filter_virsorter -
[- ] process > identify_fasta_MSF:virsorter_wf:virsorter_collect_data -
[ff/f698ec] process > identify_fasta_MSF:virsorter2_wf:virsorter2 (1) [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:virsorter2_wf:filter_virsorter2 -
*
*
*
executor > local (9)
[skipped ] process > phage_references:download_references [100%] 1 of 1, stored: 1 ✔
[skipped ] process > phage_blast_DB:phage_references_blastDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > ppr_dependecies:ppr_download_dependencies [100%] 1 of 1, stored: 1 ✔
[skipped ] process > vibrant_database:vibrant_download_DB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > virsorter_database:virsorter_download_DB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > pvog_database:pvog_DB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > vogtable_database:vogtable_DB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > vog_database:vog_DB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > rvdb_database:rvdb_DB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > checkV_database:download_checkV_DB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > sourmash_database:sourmash_download_DB [100%] 1 of 1, stored: 1 ✔
[6b/79564a] process > identify_fasta_MSF:fasta_validation_wf:input_suffix_check (1) [100%] 1 of 1 ✔
[c7/d34016] process > identify_fasta_MSF:fasta_validation_wf:seqkit (1) [100%] 1 of 1 ✔
[- ] process > identify_fasta_MSF:virsorter_wf:virsorter [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:virsorter_wf:filter_virsorter -
[- ] process > identify_fasta_MSF:virsorter_wf:virsorter_collect_data -
[ff/f698ec] process > identify_fasta_MSF:virsorter2_wf:virsorter2 (1) [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:virsorter2_wf:filter_virsorter2 -
[- ] process > identify_fasta_MSF:virsorter2_wf:virsorter2_collect_data -
*
*
*
[fc/e0fcc7] process > identify_fasta_MSF:pprmeta_wf:pprmeta (1) [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:pprmeta_wf:filter_PPRmeta -
[- ] process > identify_fasta_MSF:pprmeta_wf:pprmeta_collect_data -
[- ] process > identify_fasta_MSF:vibrant_wf:vibrant [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:vibrant_wf:filter_vibrant -
[- ] process > identify_fasta_MSF:vibrant_wf:vibrant_collect_data -
[- ] process > identify_fasta_MSF:vibrant_virome_wf:vibrant_virome [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:vibrant_virome_wf:filter_vibrant_virome -
[- ] process > identify_fasta_MSF:vibrant_virome_wf:vibrant_virome_collect_data -
[08/50ce71] process > identify_fasta_MSF:virnet_wf:normalize_contig_size (1) [100%] 1 of 1 ✔
[- ] process > identify_fasta_MSF:virnet_wf:virnet [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:virnet_wf:filter_virnet -
[- ] process > identify_fasta_MSF:virnet_wf:virnet_collect_data -
[4e/ca5a07] process > identify_fasta_MSF:phigaro_wf:phigaro (1) [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:phigaro_wf:phigaro_collect_data -
[- ] process > identify_fasta_MSF:seeker_wf:seeker [ 0%] 0 of 1
[- ] process > identify_fasta_MSF:seeker_wf:filter_seeker -
[- ] process > identify_fasta_MSF:seeker_wf:seeker_collect_data -
[- ] process > identify_fasta_MSF:filter_tool_names -
[- ] process > identify_fasta_MSF:r_plot -
[- ] process > identify_fasta_MSF:upsetr_plot -
[- ] process > identify_fasta_MSF:samtools -
[- ] process > phage_annotation_MSF:prodigal -
[- ] process > phage_annotation_MSF:hmmscan -
[- ] process > phage_annotation_MSF:chromomap_parser -
[- ] process > phage_annotation_MSF:chromomap -
[- ] process > checkV_wf:checkV -
[- ] process > phage_tax_classification:split_multi_fasta -
[- ] process > phage_tax_classification:sourmash_for_tax -
Started process
[4e/ca5a07] process > identify_fasta_MSF:phigaro_wf:phigaro (1) [ 0%] 0 of 1
[4e/ca5a07]: is the process folder where the tasks of this process is started/executedidentify_fasta_MSF: is one of two sub workflows (identify sequence; phage annotation)phigaro_wf:: the Phigaro identification process contains a smaller workflow with phigaro and phigaro_collect_data (raw output of Phigaro)phigaro: is the actual phage identification task[ 0%] 0 of 1: Process has not finished yet
Finished Process
- this is how a finished process will look like this:
[6b/79564a] process > identify_fasta_MSF:fasta_validation_wf:input_suffix_check (1) [100%] 1 of 1 ✔
[6b/79564a]: is the process folder where the tasks of this process (input_suffix_check) is executed-
you can access the folder:
- default:
cd /tmp/nextflow-phage-$USER/6b/79564aand tabcompletion - in our case with --work-dir :
cd work/6b/79564aand tab completion - you will see the files used/created in this process
- default:
-
identify_fasta_MSF: is one of two sub workflows (identify sequence; phage annotation) -
input_suffix_check (1): is the actual task (in this case: checks if the fasta file has the correct format) -
[100%] 1 of 1 ✔: tells you that the process is complete
Stored process
[skipped ] process > phage_blast_DB:phage_references_blastDB [100%] 1 of 1, stored: 1 ✔
- this is shown when you already e.g. downloaded the database so WtP won't execute this process again because the data is already stored
Process in Queue
[- ] process > identify_fasta_MSF:phigaro_wf:phigaro_collect_data -
- this is shows you that the process has not been started yet and is queued and waiting for execution
OnComplete
Done! Results are stored here --> results
Thank you for using What the Phage
Please cite us: https://doi.org/10.1101/2020.07.24.219899
Please also cite the other tools we use in our workflow --> results/literature
Completed at: 30-Oct-2020 10:15:27
Duration : 49m 34s
CPU hours : 5.2
Succeeded : 61
- the onComplete message is shown when WtP is done
- here you find again some basic information e.g. how long was your run, where are the results and a literature-file for citing us and the tools WtP uses