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CAMI-challenge / CAMITAX

CAMITAX: Taxon labels for microbial genomes
https://doi.org/10.1101/532473
Apache License 2.0
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warning process name deprecated #15

Closed arianccbasile closed 5 years ago

arianccbasile commented 5 years ago

Dear Andreas, I have installed CAMITAX usin "nextflow /docker". Installation completed successfully but the process stops with the warning reported below. Thanks in advance

Input genomes: WARN: Process configuration syntax $processName has been deprecated -- Replace process.$mash = <value> with a process selector [warm up] executor > local WARN: Process configuration syntax $processName has been deprecated -- Replace process.$checkm = <value> with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replace process.$dada2 = <value> with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replace process.$prodigal = <value> with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replace process.$centrifuge = <value> with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replace process.$kaiju = <value> with a process selector

abremges commented 5 years ago

Thank you, @arianccbasile – I was using an outdated Nextflow version.

Apparently, the containers definitions changed recently, as described here: https://www.nextflow.io/docs/latest/docker.html#multiple-containers

I just applied a hotfix, hopefully this solved the issue. Please try again. Unfortunately I couldn't test it, yet, but will do so first thing tomorrow.

Thanks again! /A

arianccbasile commented 5 years ago

Dear Andreas, I fixed the nextflow.config file as suggested. Using the command line NXF_VER=0.28.0 nextflow run abremges/CAMITAX --db /mnt/data_HDD/databases/CAMITAX_db/ --i /mnt/data_HDD/stefano/progetto_yifeng_rusen/BIN_REFINEMENT/metaWRAP_bins/ --x fa I have the following error:

WARN: Unknown directivecentrifugefor processmash WARN: Unknown directivecheckmfor processmash WARN: Unknown directivedada2for processmash WARN: Unknown directivekaijufor processmash WARN: Unknown directivemashfor processmash WARN: Unknown directiveprodigalfor processmash [warm up] executor > local WARN: Unknown directivecentrifugefor processcheckm WARN: Unknown directivecheckmfor processcheckm WARN: Unknown directivedada2for processcheckm WARN: Unknown directivekaijufor processcheckm WARN: Unknown directivemashfor processcheckm WARN: Unknown directiveprodigalfor processcheckm WARN: Unknown directivecentrifugefor processdada2 WARN: Unknown directivecheckmfor processdada2 WARN: Unknown directivedada2for processdada2 WARN: Unknown directivekaijufor processdada2 WARN: Unknown directivemashfor processdada2 WARN: Unknown directiveprodigalfor processdada2 WARN: Unknown directivecentrifugefor processprodigal WARN: Unknown directivecheckmfor processprodigal WARN: Unknown directivedada2for processprodigal WARN: Unknown directivekaijufor processprodigal WARN: Unknown directivemashfor processprodigal WARN: Unknown directiveprodigalfor processprodigal WARN: Unknown directivecentrifugefor processcentrifuge WARN: Unknown directivecheckmfor processcentrifuge WARN: Unknown directivedada2for processcentrifuge WARN: Unknown directivekaijufor processcentrifuge WARN: Unknown directivemashfor processcentrifuge WARN: Unknown directiveprodigalfor processcentrifuge WARN: Unknown directivecentrifugefor processkaiju WARN: Unknown directivecheckmfor processkaiju WARN: Unknown directivedada2for processkaiju WARN: Unknown directivekaijufor processkaiju WARN: Unknown directivemashfor processkaiju WARN: Unknown directiveprodigalfor processkaiju WARN: Unknown directivecentrifugefor processtaxonomy WARN: Unknown directivecheckmfor processtaxonomy WARN: Unknown directivedada2for processtaxonomy WARN: Unknown directivekaijufor processtaxonomy WARN: Unknown directivemashfor processtaxonomy WARN: Unknown directiveprodigalfor processtaxonomy WARN: Unknown directivecentrifugefor processsummary WARN: Unknown directivecheckmfor processsummary WARN: Unknown directivedada2for processsummary WARN: Unknown directivekaijufor processsummary WARN: Unknown directivemashfor processsummary WARN: Unknown directiveprodigalfor processsummary` [93/f2c001] Submitted process > checkm (bin.26) [eb/55232c] Submitted process > checkm (bin.27) [39/409739] Submitted process > checkm (bin.19) [fa/c80ed6] Submitted process > mash (bin.33) [d4/3422f0] Submitted process > prodigal (bin.12) [bb/ce711a] Submitted process > mash (bin.11) [0c/4cb763] Submitted process > mash (bin.14) [4a/41782a] Submitted process > checkm (bin.16) [f3/462545] Submitted process > mash (bin.18) [55/456fa3] Submitted process > prodigal (bin.10) [46/198e5f] Submitted process > mash (bin.32) [6c/c16449] Submitted process > prodigal (bin.23) [e7/2c93dd] Submitted process > mash (bin.8) [f0/253456] Submitted process > prodigal (bin.20) [4a/570345] Submitted process > mash (bin.30) [31/c884e1] Submitted process > prodigal (bin.36) [7a/a1dd46] Submitted process > prodigal (bin.3) [90/9c1dbb] Submitted process > mash (bin.17) [62/b6c2f0] Submitted process > mash (bin.36) [90/1053e3] Submitted process > mash (bin.40) ERROR ~ Error executing process > 'checkm (bin.26)'

Caused by: Process checkm (bin.26) terminated with an error exit status (127)

Command executed:

Set CheckM root data location

echo CAMITAX_db/checkm/ | checkm data setRoot CAMITAX_db/checkm/

Extract 16S rRNA gene sequences with Nhmmer

checkm ssu_finder -t 8 -x fa bin.26.fa . ssu_finder 2>&1 ln -s ssu_finder/ssu.fna bin.26.ssu.fna

Phylogenetic placement onto reduced reference tree

checkm lineage_wf -t 8 --reduced_tree -x fa . checkm checkm qa -o 2 --tab_table checkm/lineage.ms checkm > bin.26.checkm.tsv

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 3: checkm: command not found

Work dir: /mnt/data_HDD/databases/CAMITAX_db/work/93/f2c0012f5c9c694e2924f50e25116f

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

-- Check '.nextflow.log' file for details WARN: Killing pending tasks (19)`

using "nextflow version 19.01.0.5050" and running the command line below: nextflow run abremges/CAMITAX --db /mnt/data_HDD/databases/CAMITAX_db/ --i /mnt/data_HDD/stefano/progetto_yifeng_rusen/BIN_REFINEMENT/metaWRAP_bins/ --x fa

the error is the following: `[warm up] executor > local [7d/7cbea0] Submitted process > checkm (bin.38) [77/2530d3] Submitted process > checkm (bin.13) [33/3e1d4a] Submitted process > checkm (bin.29) [73/476716] Submitted process > prodigal (bin.22) [c2/bbdec8] Submitted process > checkm (bin.25) [71/78cc90] Submitted process > prodigal (bin.8) [d6/65a3f8] Submitted process > mash (bin.17) [ee/a139fa] Submitted process > prodigal (bin.28) [fd/b6cf73] Submitted process > mash (bin.13) [05/d7ec33] Submitted process > prodigal (bin.11) [80/4dba73] Submitted process > mash (bin.32) [60/0bfb7c] Submitted process > mash (bin.9) [f9/1543ae] Submitted process > checkm (bin.8) ERROR ~ Error executing process > 'checkm (bin.38)'

Caused by: Process checkm (bin.38) terminated with an error exit status (126)

Command executed:

Set CheckM root data location

echo CAMITAX_db/checkm/ | checkm data setRoot CAMITAX_db/checkm/

Extract 16S rRNA gene sequences with Nhmmer

checkm ssu_finder -t 8 -x fa bin.38.fa . ssu_finder 2>&1 ln -s ssu_finder/ssu.fna bin.38.ssu.fna

Phylogenetic placement onto reduced reference tree

checkm lineage_wf -t 8 --reduced_tree -x fa . checkm checkm qa -o 2 --tab_table checkm/lineage.ms checkm > bin.38.checkm.tsv

Command exit status: 126

Command output: (empty)

Command error: docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.35/containers/create?name=nxf-0kcjDa9jjL0JByGyefmrGN8K: dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'.

Work dir: /mnt/data_HDD/databases/CAMITAX_db/work/7d/7cbea047c081cc0a1109144c40f56d

Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option -resume

-- Check '.nextflow.log' file for details WARN: Killing pending tasks (11)`

Thanks in advance for your support!!

abremges commented 5 years ago

Thank you, @arianccbasile. It indeed shouldn't work when using NXF_VER=0.28.0, because the container definitions were changed thereafter (this should work with the older CAMITAX version, by the way, before I applied the hotfix). Anyway...

The second issue, running on Nextflow v19.01.0.5050, sounds like a more general Docker issue. Please try to execute a simple docker run hello-world on your machine. If this works, I'll have to further investigate. Else it appears to be a Docker problem on your end, please check for instance: https://techoverflow.net/2017/03/01/solving-docker-permission-denied-while-trying-to-connect-to-the-docker-daemon-socket/

AlphaSquad commented 5 years ago

Tested the current version of CAMITAX with Nextflow 19.01.0, it was running on a Debian 8.10 machine without error or warning

abremges commented 5 years ago

Thank you, @AlphaSquad, for testing and confirming that everything works (again).

I'm closing this issue now, @arianccbasile, please re-open if you feel so. If Docker continues to cause trouble, use Singularity or install all dependencies using bioconda. Both options are outlined in the README but note that you need to provide a local nextflow.config then: https://www.nextflow.io/docs/latest/config.html

Thanks again, @arianccbasile, for this issue. I definitely learned something new again, based on that we can improve CAMITAX in future versions...

arianccbasile commented 5 years ago

Thank you @abremges and @AlphaSquad for all the support. It was indeed a problem of Docker, we solved it with https://techoverflow.net/2017/03/01/solving-docker-permission-denied-while-trying-to-connect-to-the-docker-daemon-socket/ help and after that it worked properly.

Sincerely, Arianna Basile

abremges commented 5 years ago

Great to hear! If you have any questions or feedback, @arianccbasile, please feel free to drop me an email or write here. 👍