Closed arianccbasile closed 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Thank you, @arianccbasile – I was using an outdated Nextflow version.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
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 directive
centrifugefor process
mash WARN: Unknown directive
checkmfor process
mash WARN: Unknown directive
dada2for process
mash WARN: Unknown directive
kaijufor process
mash WARN: Unknown directive
mashfor process
mash WARN: Unknown directive
prodigalfor process
mash [warm up] executor > local WARN: Unknown directive
centrifugefor process
checkm WARN: Unknown directive
checkmfor process
checkm WARN: Unknown directive
dada2for process
checkm WARN: Unknown directive
kaijufor process
checkm WARN: Unknown directive
mashfor process
checkm WARN: Unknown directive
prodigalfor process
checkm WARN: Unknown directive
centrifugefor process
dada2 WARN: Unknown directive
checkmfor process
dada2 WARN: Unknown directive
dada2for process
dada2 WARN: Unknown directive
kaijufor process
dada2 WARN: Unknown directive
mashfor process
dada2 WARN: Unknown directive
prodigalfor process
dada2 WARN: Unknown directive
centrifugefor process
prodigal WARN: Unknown directive
checkmfor process
prodigal WARN: Unknown directive
dada2for process
prodigal WARN: Unknown directive
kaijufor process
prodigal WARN: Unknown directive
mashfor process
prodigal WARN: Unknown directive
prodigalfor process
prodigal WARN: Unknown directive
centrifugefor process
centrifuge WARN: Unknown directive
checkmfor process
centrifuge WARN: Unknown directive
dada2for process
centrifuge WARN: Unknown directive
kaijufor process
centrifuge WARN: Unknown directive
mashfor process
centrifuge WARN: Unknown directive
prodigalfor process
centrifuge WARN: Unknown directive
centrifugefor process
kaiju WARN: Unknown directive
checkmfor process
kaiju WARN: Unknown directive
dada2for process
kaiju WARN: Unknown directive
kaijufor process
kaiju WARN: Unknown directive
mashfor process
kaiju WARN: Unknown directive
prodigalfor process
kaiju WARN: Unknown directive
centrifugefor process
taxonomy WARN: Unknown directive
checkmfor process
taxonomy WARN: Unknown directive
dada2for process
taxonomy WARN: Unknown directive
kaijufor process
taxonomy WARN: Unknown directive
mashfor process
taxonomy WARN: Unknown directive
prodigalfor process
taxonomy WARN: Unknown directive
centrifugefor process
summary WARN: Unknown directive
checkmfor process
summary WARN: Unknown directive
dada2for process
summary WARN: Unknown directive
kaijufor process
summary WARN: Unknown directive
mashfor process
summary WARN: Unknown directive
prodigalfor process
summary`
[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:
echo CAMITAX_db/checkm/ | checkm data setRoot CAMITAX_db/checkm/
checkm ssu_finder -t 8 -x fa bin.26.fa . ssu_finder 2>&1 ln -s ssu_finder/ssu.fna bin.26.ssu.fna
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:
echo CAMITAX_db/checkm/ | checkm data setRoot CAMITAX_db/checkm/
checkm ssu_finder -t 8 -x fa bin.38.fa . ssu_finder 2>&1 ln -s ssu_finder/ssu.fna bin.38.ssu.fna
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!!
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/
Tested the current version of CAMITAX with Nextflow 19.01.0, it was running on a Debian 8.10 machine without error or warning
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...
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
Great to hear! If you have any questions or feedback, @arianccbasile, please feel free to drop me an email or write here. 👍
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 $processName has been deprecated -- Replaceprocess.$checkm = <value>
with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replaceprocess.$dada2 = <value>
with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replaceprocess.$prodigal = <value>
with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replaceprocess.$centrifuge = <value>
with a process selector WARN: Process configuration syntax $processName has been deprecated -- Replaceprocess.$kaiju = <value>
with a process selector