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jhuapl-bio / taxtriage

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.
MIT License
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Issue running TaxTriage in basestack #6

Closed garfinjm closed 1 year ago

garfinjm commented 2 years ago

Description of the bug

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

Command used and terminal output

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: Docker

Relevant files

clientError.log docker.log client.log serverError.log server.log

System information

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

Merritt-Brian commented 2 years ago

@garfinjm There seems to be an issue with looking at the .nextflow/history.lock file looking at the logs. Can you attempt to uncheck the resume flag in Basestack and reattempt? Also, if you run into any permissions issues can you uncheck the field to run as a your own user?

garfinjm commented 2 years ago

Unchecking resume didnt work (log files below). Unchecking the field to run as my user allowed nextflow to start, but it looks like I got an error during the first step.

Log files from unchecking resume: client.log server.log serverError.log

When I uncheck the run as own user box I dont get any logfiles in the directory that opens up when I click Open Log Folder (/home/centos/.config/Basestack/Basestack/data/userdata/logs). Below is copy and pasted out of the basestack Log Viewer:

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stdout: e is 65537 (0x010001)

stdout: -Signature ok subject=CN = docker:dind server

stdout: Getting CA Private Key

stdout: /certs/server/cert.pem: OK

stdout: -Signature ok subject=CN = docker:dind client

stdout: Getting CA Private Key

stdout: /certs/client/cert.pem: OK

stdout: <[WARN tini (99)] Tini is not running as PID 1 and isn't registered as a child subreaper. Zombie processes will not be re-parented to Tini, so zombie reaping won't work. To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.

stdout: time="2022-09-15T13:40:15.223145329Z" level=info msg="Starting up"

stdout: �time="2022-09-15T13:40:15.224991906Z" level=warning msg="could not change group /var/run/docker.sock to docker: group docker not found"

stdout: time="2022-09-15T13:40:15.227253640Z" level=info msg="libcontainerd: started new containerd process" pid=175

stdout: �time="2022-09-15T13:40:15.227316403Z" level=info msg="parsed scheme: \"unix\"" module=grpc time="2022-09-15T13:40:15.227329939Z" level=info msg="scheme \"unix\" not registered, fallback to default scheme" module=grpc time="2022-09-15T13:40:15.227377651Z" level=info msg="ccResolverWrapper: sending update to cc: {[{unix:///var/run/docker/containerd/containerd.sock <nil> 0 <nil>}] <nil> <nil>}" module=grpc time="2022-09-15T13:40:15.227398577Z" level=info msg="ClientConn switching balancer to \"pick_first\"" module=grpc

stdout: time="2022-09-15T13:40:15Z" level=warning msg="deprecated version : `1`, please switch to version `2`"

stdout: �time="2022-09-15T13:40:15.243007346Z" level=info msg="starting containerd" revision=3df54a852345ae127d1fa3092b95168e4a88e2f8 version=v1.5.11

stdout: �time="2022-09-15T13:40:15.266433808Z" level=info msg="loading plugin \"io.containerd.content.v1.content\"..." type=io.containerd.content.v1 �time="2022-09-15T13:40:15.266507406Z" level=info msg="loading plugin \"io.containerd.snapshotter.v1.aufs\"..." type=io.containerd.snapshotter.v1

stdout: �time="2022-09-15T13:40:15.277464607Z" level=info msg="skip loading plugin \"io.containerd.snapshotter.v1.aufs\"..." error="aufs is not supported (modprobe aufs failed: exit status 1 \"ip: can't find device 'aufs'\\nmodprobe: can't change directory to '/lib/modules': No such file or directory\\n\"): skip plugin" type=io.containerd.snapshotter.v1 time="2022-09-15T13:40:15.277501298Z" level=info msg="loading plugin \"io.containerd.snapshotter.v1.btrfs\"..." type=io.containerd.snapshotter.v1

stdout: �time="2022-09-15T13:40:15.277718857Z" level=info msg="skip loading plugin \"io.containerd.snapshotter.v1.btrfs\"..." error="path /var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.btrfs (ext4) must be a btrfs filesystem to be used with the btrfs snapshotter: skip plugin" type=io.containerd.snapshotter.v1 time="2022-09-15T13:40:15.277739151Z" level=info msg="loading plugin \"io.containerd.snapshotter.v1.devmapper\"..." type=io.containerd.snapshotter.v1 time="2022-09-15T13:40:15.277762381Z" level=warning msg="failed to load plugin io.containerd.snapshotter.v1.devmapper" error="devmapper not configured" time="2022-09-15T13:40:15.277773318Z" level=info msg="loading plugin \"io.containerd.snapshotter.v1.native\"..." type=io.containerd.snapshotter.v1 time="2022-09-15T13:40:15.277799412Z" level=info msg="loading plugin \"io.containerd.snapshotter.v1.overlayfs\"..." type=io.containerd.snapshotter.v1 time="2022-09-15T13:40:15.277942188Z" level=info msg="loading plugin \"io.containerd.snapshotter.v1.zfs\"..." type=io.containerd.snapshotter.v1 time="2022-09-15T13:40:15.278133917Z" level=info msg="skip loading plugin \"io.containerd.snapshotter.v1.zfs\"..." error="path /var/lib/docker/containerd/daemon/io.containerd.snapshotter.v1.zfs must be a zfs filesystem to be used with the zfs snapshotter: skip plugin" type=io.containerd.snapshotter.v1 time="2022-09-15T13:40:15.278150768Z" level=info msg="loading plugin \"io.containerd.metadata.v1.bolt\"..." type=io.containerd.metadata.v1 time="2022-09-15T13:40:15.278170348Z" level=warning msg="could not use snapshotter devmapper in metadata plugin" error="devmapper not configured" time="2022-09-15T13:40:15.278182087Z" level=info msg="metadata content store policy set" policy=shared time="2022-09-15T13:40:15.278311654Z" level=info msg="loading plugin \"io.containerd.differ.v1.walking\"..." type=io.containerd.differ.v1 time="2022-09-15T13:40:15.278332590Z" level=info msg="loading plugin \"io.containerd.gc.v1.scheduler\"..." type=io.containerd.gc.v1 time="2022-09-15T13:40:15.278385279Z" level=info msg="loading plugin \"io.containerd.service.v1.introspection-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278421340Z" level=info msg="loading plugin \"io.containerd.service.v1.containers-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278455528Z" level=info msg="loading plugin \"io.containerd.service.v1.content-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278474705Z" level=info msg="loading plugin \"io.containerd.service.v1.diff-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278491039Z" level=info msg="loading plugin \"io.containerd.service.v1.images-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278515581Z" level=info msg="loading plugin \"io.containerd.service.v1.leases-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278532257Z" level=info msg="loading plugin \"io.containerd.service.v1.namespaces-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278545737Z" level=info msg="loading plugin \"io.containerd.service.v1.snapshots-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.278560937Z" level=info msg="loading plugin \"io.containerd.runtime.v1.linux\"..." type=io.containerd.runtime.v1 time="2022-09-15T13:40:15.278721110Z" level=info msg="loading plugin \"io.containerd.runtime.v2.task\"..." type=io.containerd.runtime.v2 time="2022-09-15T13:40:15.278846607Z" level=info msg="loading plugin \"io.containerd.monitor.v1.cgroups\"..." type=io.containerd.monitor.v1 time="2022-09-15T13:40:15.279239797Z" level=info msg="loading plugin \"io.containerd.service.v1.tasks-service\"..." type=io.containerd.service.v1 time="2022-09-15T13:40:15.279268494Z" level=info msg="loading plugin \"io.containerd.internal.v1.restart\"..." type=io.containerd.internal.v1 time="2022-09-15T13:40:15.279331075Z" level=info msg="loading plugin \"io.containerd.grpc.v1.containers\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279347133Z" level=info msg="loading plugin \"io.containerd.grpc.v1.content\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279365021Z" level=info msg="loading plugin \"io.containerd.grpc.v1.diff\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279377755Z" level=info msg="loading plugin \"io.containerd.grpc.v1.events\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279389067Z" level=info msg="loading plugin \"io.containerd.grpc.v1.healthcheck\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279401909Z" level=info msg="loading plugin \"io.containerd.grpc.v1.images\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279449216Z" level=info msg="loading plugin \"io.containerd.grpc.v1.leases\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279465435Z" level=info msg="loading plugin \"io.containerd.grpc.v1.namespaces\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279480516Z" level=info msg="loading plugin \"io.containerd.internal.v1.opt\"..." type=io.containerd.internal.v1 time="2022-09-15T13:40:15.279713242Z" level=info msg="loading plugin \"io.containerd.grpc.v1.snapshots\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279759731Z" level=info msg="loading plugin \"io.containerd.grpc.v1.tasks\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279776193Z" level=info msg="loading plugin \"io.containerd.grpc.v1.version\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.279787047Z" level=info msg="loading plugin \"io.containerd.grpc.v1.introspection\"..." type=io.containerd.grpc.v1 time="2022-09-15T13:40:15.280051930Z" level=info msg=serving... address=/var/run/docker/containerd/containerd-debug.sock time="2022-09-15T13:40:15.280149572Z" level=info msg=serving... address=/var/run/docker/containerd/containerd.sock.ttrpc time="2022-09-15T13:40:15.280242417Z" level=info msg=serving... address=/var/run/docker/containerd/containerd.sock time="2022-09-15T13:40:15.280269085Z" level=info msg="containerd successfully booted in 0.038801s"

stdout: time="2022-09-15T13:40:15.291536574Z" level=info msg="parsed scheme: \"unix\"" module=grpc time="2022-09-15T13:40:15.291568604Z" level=info msg="scheme \"unix\" not registered, fallback to default scheme" module=grpc time="2022-09-15T13:40:15.291588723Z" level=info msg="ccResolverWrapper: sending update to cc: {[{unix:///var/run/docker/containerd/containerd.sock <nil> 0 <nil>}] <nil> <nil>}" module=grpc time="2022-09-15T13:40:15.291598110Z" level=info msg="ClientConn switching balancer to \"pick_first\"" module=grpc

stdout: time="2022-09-15T13:40:15.292290567Z" level=info msg="parsed scheme: \"unix\"" module=grpc time="2022-09-15T13:40:15.292314221Z" level=info msg="scheme \"unix\" not registered, fallback to default scheme" module=grpc time="2022-09-15T13:40:15.292331185Z" level=info msg="ccResolverWrapper: sending update to cc: {[{unix:///var/run/docker/containerd/containerd.sock <nil> 0 <nil>}] <nil> <nil>}" module=grpc time="2022-09-15T13:40:15.292346309Z" level=info msg="ClientConn switching balancer to \"pick_first\"" module=grpc

stdout: time="2022-09-15T13:40:15.356252855Z" level=info msg="[graphdriver] using prior storage driver: overlay2"

stdout: time="2022-09-15T13:40:15.379499084Z" level=info msg="Loading containers: start."

stdout: �time="2022-09-15T13:40:15.400417778Z" level=warning msg="Running modprobe bridge br_netfilter failed with message: ip: can't find device 'bridge'\nbridge 151336 1 br_netfilter\nstp 12976 2 bridge,garp\nllc 14552 3 bridge,garp,stp\nip: can't find device 'br_netfilter'\nbr_netfilter 22256 0 \nbridge 151336 1 br_netfilter\nmodprobe: can't change directory to '/lib/modules': No such file or directory\n, error: exit status 1"

stdout: �time="2022-09-15T13:40:15.482946739Z" level=info msg="Default bridge (docker0) is assigned with an IP address 172.17.0.0/16. Daemon option --bip can be used to set a preferred IP address"

stdout: time="2022-09-15T13:40:15.514277956Z" level=info msg="Loading containers: done."

stdout: }time="2022-09-15T13:40:15.543659897Z" level=info msg="Docker daemon" commit=87a90dc graphdriver(s)=overlay2 version=20.10.14 [time="2022-09-15T13:40:15.543831357Z" level=info msg="Daemon has completed initialization"

stdout: time="2022-09-15T13:40:15.564411020Z" level=info msg="API listen on /var/run/docker.sock"

stdout: time="2022-09-15T13:40:15.568494577Z" level=info msg="API listen on [::]:2376"

stdout: tty: ignoring all arguments

stdout: `13:40:21.547 [main] DEBUG nextflow.cli.Launcher - Oops .. not a valid $COLUMNS value: not a tty

stdout: $N E X T F L O W ~ version 22.04.3

stdout: Launching `/opt/code/main.nf` [adoring_stallman] DSL2 - revision: ac98c18eda

stdout:

stdout: 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: /opt/output/pipeline_info * --demux: true * --skip_assembly: true * --skip_plots: true * --max_cpus: 3 * --max_memory: 12GB * --outdir: /opt/output �* --max_multiqc_email_size: 25.MB * --multiqc_config: null * --igenomes_ignore: false * --igenomes_base: s3://ngi-igenomes/igenomes * --genome: null * --low_memory: null

stdout: �- 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,demux,skip_assembly,skip_plots,max_cpus,max_memory,outdir,max_multiqc_email_size,multiqc_config,igenomes_ignore,igenomes_base,genome,low_memory"

stdout: ------------------------------------------------------ � ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/taxtriage v1.0dev ------------------------------------------------------ Core Nextflow options runName : adoring_stallman containerEngine: docker launchDir : /opt/code workDir : /opt/code/work projectDir : /opt/code userName : root profile : docker configFiles : /opt/code/nextflow.config Input/output options input : /opt/samplesheet/Samplesheet.csv db : /opt/databases/minikraken2 � assembly : /opt/code/assembly_summary_refseq.txt !! 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

stdout: ------------------------------------------------------

stdout: WARN: Access to undefined parameter `reference` -- Initialise it to a default value eg. `params.reference = some_value`

stdout: �WARN: Access to undefined parameter `top_hits_count` -- Initialise it to a default value eg. `params.top_hits_count = some_value`

stdout: Top hits not specified, defaulting to 10 per rank level in taxonomy tree for database for kraken2

stdout: ^Assembly file present, using it to pull genomes from... /opt/code/assembly_summary_refseq.txt

stdout: �WARN: Access to undefined parameter `assembly_file_type` -- Initialise it to a default value eg. `params.assembly_file_type = some_value`

stdout: !/opt/samplesheet/Samplesheet.csv

stdout: [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... -

stdout:

stdout: �[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - �[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - DataflowBroadcast around DataflowStream[?] �WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value` WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value` �WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value` WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value`

stdout:

stdout: �[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - �[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - DataflowBroadcast around DataflowStream[?] WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value` WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value` WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value` WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value` WARN: There's no process matching config selector: RUN_BLAST WARN: There's no process matching config selector: BWAMEM2_MEM -- Did you mean: BWA_MEM? �WARN: There's no process matching config selector: GUNZIP_SCAFFOLDS WARN: There's no process matching config selector: GUNZIP_GFA

stdout:

stdout: �executor > local (1) [1f/21a9d7] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... [ 0%] 0 of 1 [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - DataflowBroadcast around DataflowStream[?] �WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value` WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value` WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value` WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value` WARN: There's no process matching config selector: RUN_BLAST WARN: There's no process matching config selector: BWAMEM2_MEM -- Did you mean: BWA_MEM? WARN: There's no process matching config selector: GUNZIP_SCAFFOLDS >WARN: There's no process matching config selector: GUNZIP_GFA

stdout: time="2022-09-15T13:40:34.486140284Z" level=info msg="No non-localhost DNS nameservers are left in resolv.conf. Using default external servers: [nameserver 8.8.8.8 nameserver 8.8.4.4]" time="2022-09-15T13:40:34.486189802Z" level=info msg="IPv6 enabled; Adding default IPv6 external servers: [nameserver 2001:4860:4860::8888 nameserver 2001:4860:4860::8844]"

stdout: �time="2022-09-15T13:40:34.527760359Z" level=info msg="starting signal loop" namespace=moby path=/run/docker/containerd/daemon/io.containerd.runtime.v2.task/moby/99a17eb08ed4f47f863b7923581fb1a54e8f130bb54a70ea7e1069da30e46c64 pid=524

stdout: ntime="2022-09-15T13:40:34.849352879Z" level=info msg="ignoring event" container=99a17eb08ed4f47f863b7923581fb1a54e8f130bb54a70ea7e1069da30e46c64 module=libcontainerd namespace=moby topic=/tasks/delete type="*events.TaskDelete" time="2022-09-15T13:40:34.849372520Z" level=info msg="shim disconnected" id=99a17eb08ed4f47f863b7923581fb1a54e8f130bb54a70ea7e1069da30e46c64 time="2022-09-15T13:40:34.849434685Z" level=warning msg="cleaning up after shim disconnected" id=99a17eb08ed4f47f863b7923581fb1a54e8f130bb54a70ea7e1069da30e46c64 namespace=moby time="2022-09-15T13:40:34.849453436Z" level=info msg="cleaning up dead shim"

stdout: �time="2022-09-15T13:40:34.861362664Z" level=warning msg="cleanup warnings time=\"2022-09-15T13:40:34Z\" level=info msg=\"starting signal loop\" namespace=moby pid=670\n"

stdout:

stdout: ~executor > local (1) [1f/21a9d7] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... [ 0%] 0 of 1 [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - DataflowBroadcast around DataflowStream[?] WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value` WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value` WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value` WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value` WARN: There's no process matching config selector: RUN_BLAST WARN: There's no process matching config selector: BWAMEM2_MEM -- Did you mean: BWA_MEM? WARN: There's no process matching config selector: GUNZIP_SCAFFOLDS WARN: There's no process matching config selector: GUNZIP_GFA

stdout: �Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)' Caused by: Process `NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)` terminated with an error exit status (1) Command executed: check_samplesheet.py \ Samplesheet.csv \ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONS Command exit status: 1 Command output: (empty) Command error: [CRITICAL] FASTQ pairs must have the same file extensions. On line 2. Work dir: /opt/code/work/1f/21a9d7a27345a0b42ecdd9b20fcbf2 � 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`

stdout:

stdout: �executor > local (1) [1f/21a9d7] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - �[- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... [ 0%] 0 of 1 DataflowBroadcast around DataflowStream[?] Execution cancelled -- Finishing pending tasks before exit

stdout: tWARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value` WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value` WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value` WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value` WARN: There's no process matching config selector: RUN_BLAST WARN: There's no process matching config selector: BWAMEM2_MEM -- Did you mean: BWA_MEM? WARN: There's no process matching config selector: GUNZIP_SCAFFOLDS WARN: There's no process matching config selector: GUNZIP_GFA Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)' Caused by: Process `NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)` terminated with an error exit status (1) Command executed: check_samplesheet.py \ Samplesheet.csv \ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml � "NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONS Command exit status: 1 Command output: (empty) Command error: [CRITICAL] FASTQ pairs must have the same file extensions. On line 2. Work dir: /opt/code/work/1f/21a9d7a27345a0b42ecdd9b20fcbf2 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`

stdout:

stdout: �executor > local (1) [1f/21a9d7] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... - [- ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:... [ 0%] 0 of 1 DataflowBroadcast around DataflowStream[?] Execution cancelled -- Finishing pending tasks before exit WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value` WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value` WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value` WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value` WARN: There's no process matching config selector: RUN_BLAST WARN: There's no process matching config selector: BWAMEM2_MEM -- Did you mean: BWA_MEM? WARN: There's no process matching config selector: GUNZIP_SCAFFOLDS WARN: There's no process matching config selector: GUNZIP_GFA WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info. Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)' Caused by: Process `NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)` terminated with an error exit status (1) Command executed: check_samplesheet.py \ Samplesheet.csv \ samplesheet.valid.csv cat <<-END_VERSIONS > versions.yml "NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK": python: $(python --version | sed 's/Python //g') END_VERSIONS Command exit status: 1 Command output: (empty) Command error: [CRITICAL] FASTQ pairs must have the same file extensions. On line 2. Work dir: /opt/code/work/1f/21a9d7a27345a0b42ecdd9b20fcbf2 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`

stdout:
Merritt-Brian commented 2 years ago

Cuplrit looks like it is here: 

python: $(python --version | sed 's/Python //g') END_VERSIONS 
Command exit status: 1 Command output: (empty) Command error: [CRITICAL] FASTQ pairs must have the same file extensions. 
On line 2. Work dir: /opt/code/work/1f/21a9d7a27345a0b42ecdd9b20fcbf2 
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`

Do you see a mytax2/Samplesheet.csv file in the same dir as your uploaded samplesheet file? If so, what are the contents?

Any luck with running Taxtriage using the same samplesheet with nextflow natively?

For example 

nextflow run 'https://github.com/jhuapl-bio/taxtriage '<rest of arguments>`
Merritt-Brian commented 1 year ago

Adding a new issue https://github.com/jhuapl-bio/Basestack/issues/149 for Basestack to handle native nextflow installations. This will also include Singularity support through the automated nextflow containerization standards

garfinjm commented 1 year ago

Do you see a mytax2/Samplesheet.csv file in the same dir as your uploaded samplesheet file? If so, what are the contents?

I don't get a mytax2 dir made in the directory my samplesheet is in, I am now getting a file named Samplesheet.target.csv Samplesheet.target.csv

Any luck with running Taxtriage using the same samplesheet with nextflow natively?

No luck, I might not be getting the params quite right though.

[centos@basestack TASS]$ nextflow run https://github.com/jhuapl-bio/taxtriage --input /home/centos/Desktop/TASS/Samplesheet.csv --db /home/centos/Desktop/TASS/resources/minikraken2_v2_8GB_201904_UPDATE --outdir /home/centos/Desktop/TASS/output --max_memory 12GB --max_cpus 3 -profile docker --skip_plots --skip_assembly --demux
NOTE: Nextflow is not tested with Java 1.8.0_332 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.5
Project `jhuapl-bio/taxtriage` currently is sticked on revision: 0113e8549f228d47b7e80184811cca869d836cac -- you need to specify explicitly a revision with the option `-r` to use it
Merritt-Brian commented 1 year ago

Ah, you need to append the -r main argument to specify you want the main branch of the repo to be pulled. Also call -latest to pull latest repo changes (if any) each run

garfinjm commented 1 year ago

I'm still having some issues.

Here's the stdout when I add -r main and -latest

[centos@basestack TASS]$ nextflow run https://github.com/jhuapl-bio/taxtriage --input /home/centos/Desktop/TASS/Samplesheet.csv --db /home/centos/Desktop/TASS/resources/minikraken2_v2_8GB_201904_UPDATE --outdir /home/centos/Desktop/TASS/output --max_memory 12GB --max_cpus 3 -profile docker --skip_plots --skip_assembly --demux -r main -latest
NOTE: Nextflow is not tested with Java 1.8.0_332 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.5
Pulling jhuapl-bio/taxtriage ...
 Already-up-to-date
Launching `https://github.com/jhuapl-bio/taxtriage` [marvelous_poisson] DSL2 - revision: 82d023f527 [main]

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: /home/centos/Desktop/TASS/output/pipeline_info
* --max_cpus: 3
* --max_memory: 12GB
* --max_multiqc_email_size: 25.MB
* --igenomes_ignore: false
* --igenomes_base: s3://ngi-igenomes/igenomes
* --genome: 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,max_cpus,max_memory,max_multiqc_email_size,igenomes_ignore,igenomes_base,genome,low_memory" 

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/taxtriage v1.0dev
------------------------------------------------------
Core Nextflow options
  revision       : main
  runName        : marvelous_poisson
  containerEngine: docker
  launchDir      : /home/centos/Desktop/TASS
  workDir        : /home/centos/Desktop/TASS/work
  projectDir     : /home/centos/.nextflow/assets/jhuapl-bio/taxtriage
  userName       : centos
  profile        : docker
  configFiles    : /home/centos/.nextflow/assets/jhuapl-bio/taxtriage/nextflow.config

Input/output options
  input          : /home/centos/Desktop/TASS/Samplesheet.csv
  db             : /home/centos/Desktop/TASS/resources/minikraken2_v2_8GB_201904_UPDATE
  skip_plots     : true
  skip_assembly  : true
  demux          : true
  outdir         : /home/centos/Desktop/TASS/output

!! 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
WARN: Access to undefined parameter `assembly` -- Initialise it to a default value eg. `params.assembly = some_value`
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`
/home/centos/Desktop/TASS/Samplesheet.csv
executor >  local (1)
[7f/3147ea] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv) [  0%] 0 of 1
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX                                 -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC                                          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES                                  -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2                                 -
[-        ] 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:BAM_TO_SAM                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC                               -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC                                         -
empty
DataflowBroadcast around DataflowStream[?]
WARN: Access to undefined parameter `subsample` -- Initialise it to a default value eg. `params.subsample = some_value`
WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value`
WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value`
WARN: Access to undefined parameter `remove_taxids` -- Initialise it to a default value eg. `params.remove_taxids = some_value`
WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value`
WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value`
executor >  local (1)
[7f/3147ea] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX                                 -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC                                          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES                                  -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2                                 -
[-        ] 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:BAM_TO_SAM                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC                               -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC                                         [  0%] 0 of 1
empty
DataflowBroadcast around DataflowStream[?]
Execution cancelled -- Finishing pending tasks before exit
WARN: Access to undefined parameter `subsample` -- Initialise it to a default value eg. `params.subsample = some_value`
WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value`
WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value`
WARN: Access to undefined parameter `remove_taxids` -- Initialise it to a default value eg. `params.remove_taxids = some_value`
WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value`
WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value`
executor >  local (1)
[7f/3147ea] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX                                 -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC                                          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES                                  -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2                                 -
[-        ] 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:BAM_TO_SAM                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC                               -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC                                         [  0%] 0 of 1
empty
DataflowBroadcast around DataflowStream[?]
Execution cancelled -- Finishing pending tasks before exit
WARN: Access to undefined parameter `subsample` -- Initialise it to a default value eg. `params.subsample = some_value`
WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value`
WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value`
WARN: Access to undefined parameter `remove_taxids` -- Initialise it to a default value eg. `params.remove_taxids = some_value`
WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value`
WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value`
WARN: There's no process matching config selector: RUN_BLAST
WARN: There's no process matching config selector: BWAMEM2_MEM -- Did you mean: BWA_MEM?
WARN: There's no process matching config selector: GUNZIP_SCAFFOLDS
WARN: There's no process matching config selector: GUNZIP_GFA
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)'

Caused by:
  Process `NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)` terminated with an error exit status (126)

Command executed:

  check_samplesheet.py \
      Samplesheet.csv \
      samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: .command.run: Permission denied

Work dir:
  /home/centos/Desktop/TASS/work/7f/3147ea96f4cdd251fe29cd163ece29

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

[centos@basestack TASS]$

That looks like a docker permisisons issue to me, if I add docker.userEmulation = false to an extra configruation file I get an error that looks a lot like what I was getting in basestack:

[centos@basestack TASS]$ nextflow run https://github.com/jhuapl-bio/taxtriage --input /home/centos/Desktop/TASS/Samplesheet.csv --db /home/centos/Desktop/TASS/resources/minikraken2_v2_8GB_201904_UPDATE --outdir /home/centos/Desktop/TASS/output --max_memory 12GB --max_cpus 3 -profile docker --skip_plots --skip_assembly --demux -r main -latest -c extra.config 
NOTE: Nextflow is not tested with Java 1.8.0_332 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.5
Pulling jhuapl-bio/taxtriage ...
 Already-up-to-date
Launching `https://github.com/jhuapl-bio/taxtriage` [drunk_heyrovsky] DSL2 - revision: e6b2489b45 [main]

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: /home/centos/Desktop/TASS/output/pipeline_info
* --max_cpus: 3
* --max_memory: 12GB
* --max_multiqc_email_size: 25.MB
* --igenomes_ignore: false
* --igenomes_base: s3://ngi-igenomes/igenomes
* --genome: 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,max_cpus,max_memory,max_multiqc_email_size,igenomes_ignore,igenomes_base,genome,low_memory" 

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/taxtriage v1.0dev
------------------------------------------------------
Core Nextflow options
  revision       : main
  runName        : drunk_heyrovsky
  containerEngine: docker
  launchDir      : /home/centos/Desktop/TASS
  workDir        : /home/centos/Desktop/TASS/work
  projectDir     : /home/centos/.nextflow/assets/jhuapl-bio/taxtriage
  userName       : centos
  profile        : docker
  configFiles    : /home/centos/.nextflow/assets/jhuapl-bio/taxtriage/nextflow.config, /home/centos/Desktop/TASS/extra.config

Input/output options
  input          : /home/centos/Desktop/TASS/Samplesheet.csv
  db             : /home/centos/Desktop/TASS/resources/minikraken2_v2_8GB_201904_UPDATE
  skip_plots     : true
  skip_assembly  : true
  demux          : true
  outdir         : /home/centos/Desktop/TASS/output

!! 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
WARN: Access to undefined parameter `assembly` -- Initialise it to a default value eg. `params.assembly = some_value`
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`
/home/centos/Desktop/TASS/Samplesheet.csv
executor >  local (1)
[60/9218a3] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv) [  0%] 0 of 1
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX                                 -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC                                          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES                                  -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2                                 -
[-        ] 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:BAM_TO_SAM                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC                               -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC                                         -
empty
DataflowBroadcast around DataflowStream[?]
WARN: Access to undefined parameter `subsample` -- Initialise it to a default value eg. `params.subsample = some_value`
WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value`
WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value`
WARN: Access to undefined parameter `remove_taxids` -- Initialise it to a default value eg. `params.remove_taxids = some_value`
WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value`
WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value`
executor >  local (1)
[60/9218a3] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX                                 -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC                                          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES                                  -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2                                 -
[-        ] 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:BAM_TO_SAM                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC                               -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC                                         [  0%] 0 of 1
empty
DataflowBroadcast around DataflowStream[?]
Execution cancelled -- Finishing pending tasks before exit
WARN: Access to undefined parameter `subsample` -- Initialise it to a default value eg. `params.subsample = some_value`
WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value`
WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value`
WARN: Access to undefined parameter `remove_taxids` -- Initialise it to a default value eg. `params.remove_taxids = some_value`
WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value`
WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value`
executor >  local (1)
[60/9218a3] process > NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv) [100%] 1 of 1, failed: 1 ✘
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:ARTIC_GUPPYPLEX                                 -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:PYCOQC                                          -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:GET_ASSEMBLIES                                  -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:KRAKEN2_KRAKEN2                                 -
[-        ] 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:BAM_TO_SAM                            -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONFIDENCE_METRIC                               -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CONVERT_CONFIDENCE                              -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:CUSTOM_DUMPSOFTWAREVERSIONS                     -
[-        ] process > NFCORE_TAXTRIAGE:TAXTRIAGE:MULTIQC                                         [  0%] 0 of 1
empty
DataflowBroadcast around DataflowStream[?]
Execution cancelled -- Finishing pending tasks before exit
WARN: Access to undefined parameter `subsample` -- Initialise it to a default value eg. `params.subsample = some_value`
WARN: Access to undefined parameter `filter` -- Initialise it to a default value eg. `params.filter = some_value`
WARN: Access to undefined parameter `trim` -- Initialise it to a default value eg. `params.trim = some_value`
WARN: Access to undefined parameter `remove_taxids` -- Initialise it to a default value eg. `params.remove_taxids = some_value`
WARN: Access to undefined parameter `skip_realignment` -- Initialise it to a default value eg. `params.skip_realignment = some_value`
WARN: Access to undefined parameter `spades_hmm` -- Initialise it to a default value eg. `params.spades_hmm = some_value`
WARN: There's no process matching config selector: RUN_BLAST
WARN: There's no process matching config selector: BWAMEM2_MEM -- Did you mean: BWA_MEM?
WARN: There's no process matching config selector: GUNZIP_SCAFFOLDS
WARN: There's no process matching config selector: GUNZIP_GFA
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)'

Caused by:
  Process `NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK (Samplesheet.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py \
      Samplesheet.csv \
      samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_TAXTRIAGE:TAXTRIAGE:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  [CRITICAL] FASTQ pairs must have the same file extensions. On line 2.

Work dir:
  /home/centos/Desktop/TASS/work/60/9218a322e911b35b5b48e886e2cdb1

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Merritt-Brian commented 1 year ago

This certainly is a specific issue with centos + Docker, were you able to follow all steps for setup of Docker for centos here https://docs.docker.com/engine/install/centos/ ?

Mainly, check if you're part of the docker group and do a quick logout and login. The pipeline also works 100% with singularity which could potentially circumvent and permission issues you might have though I'd make sure all permissions are fine on the input file(s)/dir(s) as well prior.

You can specify Singularity instead of Docker with -profile singularity. You can specify a persistent Container location in the nextflow configurations or setting the env variable appropriately

Info on installing Singularity can be found here

Nextflow caches those images in the singularity directory in the pipeline work directory by default. However it is suggest to provide a centralised caching directory by using either the NXF_SINGULARITY_CACHEDIR environment variable or the singularity.cacheDir setting in the Nextflow config file.

I usually just set it to my $HOME/singularity

In the meantime, I'm actively working on an update for Basestack (v2.4.0) to allow native running of Nextflow (or other binaries) directly from the UI so stay tuned for that in the coming month

Lastly, if interested, we have cloud support documentation using Nextflow Tower here

Merritt-Brian commented 1 year ago

Closing this as this should be resolved with v3 Basestack release when fully released