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View Code? Open in Web Editor NEWCAMITAX: Taxon labels for microbial genomes
Home Page: https://doi.org/10.1101/532473
License: Apache License 2.0
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Upload DBs to zenodo
Don't distribute the DBs with the repo, but upload a snapshot to zenodo.
Then, provide a shell script within /db (?) to streamline their download.
Review final taxID assignments
RTLpath is maybe a bit too aggressive, but Lowest seems to be too conservative. Maybe use iuLCA again?
checkM fails when using Singularity
Hi!
The first checkM step that defines the root dir does not work when using Singularity as those containers are read only, and that command tries to change a config file. A workaround is using the current biocontainer for checkM quay.io/biocontainers/checkm-genome:1.1.2--py_1, which includes the database. This however breaks the camitaxonomy.py script as the output is slightly different in this version of checkM I think. This in turn can be fixed by skipping lines starting with [ or Bin, for example by changing the code from line 199 onwards like this:
with open(args.checkm) as f:
next(f)
for line in f:
li=line.strip()
if ( not li.startswith("[") ) and ( not li.startswith("Bin") ):
(_, name, _, _, _, completeness, contamination, strain_heterogeneity, genome_size, _, _, contigs, _, N50_contigs, _, _, _, _, gc_content, _, coding_density, _, predicted_genes, *_) = line.split('\t')
sname = name[3:-(len(name)-name.index(" (UID"))]
checkm_taxon_list.append(getTaxID(sname))Fails to download chekm databases
Dear Andreas,
I am trying to install CAMITAX with Nextflow, but it cannot download chekm databases because of certificates:
Command executed:
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar xfv checkm_*.tar.gz && rm checkm_*.tar.gz*
ERROR: The certificate of `data.ace.uq.edu.au' is not trusted.
ERROR: The certificate of `data.ace.uq.edu.au' hasn't got a known issuer.
I downloaded it manually, then tried "nextflow run CAMI-challenge/CAMITAX/init.nf --db /path/to/db/folder" with -resume flag, but it didn't help.
Fix ownership of files in work
Files in data are just fine, but the temporary files in work belong to root – which is quite annoying. Maybe I need to specify these as proper (dynamic) output files, for Nextflow's fixOwnership to properly work? Alternatively, delete unneeded files and oly keep (and specify as output) essential output files?
Installation and running
Dear Andreas,
I'm trying to install your package, but it keeps throwing errors at me. Maybe there's something I got wrong in your installation procedures.
First, I activated docker on my terminal and cloned this repository in my home.
Then, I entered the new repository directory and installed nextflow using the command provided at their homepage ("curl -s https://get.nextflow.io | bash ").
But when I enter your pull command, the program throws this error at me:
N E X T F L O W ~ version 19.01.0 ERROR ~ Project config file is malformed -- Cause: No signature of method: nextflow.config.ConfigParser$_parse_closure5.memory() is applicable for argument types: (String) values: [16 GB] Possible solutions: every(), every(), every(groovy.lang.Closure), every(groovy.lang.Closure), getAt(java.lang.String), getAt(java.lang.String)
I went to check for some typos in the nextflow.config file, and found that the program doesn't seem to like these lines:
memory '24 GB'
I tried to fix the typo by inserting all the required "="s and removed the ''s, but then, as I re-run the program, it throws the following error:
ERROR ~ Project config file is malformed -- Cause: No signature of method: java.lang.Integer.call() is applicable for argument types: (ConfigObject) values: [[:]]
What am I doing wrong? How should I install CAMITAX?
Best regards
Best ANI hit
Report highest ANI value to any sequenced genome – whatever that's worth, as I'm not aware of any reliable ANI thresholds relating to taxonomic levels other than 95% = species boundary.
Silva files don't work in dada2 Docker container
Silva files result in cryptic error message if executed within Docker...
Executing dada2 with Silva files outside of the container works just fine.
RDP files work fine, no matter what, inside and outside of the container.
Change SSU search strategy
Currently, we use Barrnap (which is great and simple to use), but always assume domain Bacteria. This results in suboptimal annotations for e.g. Archaea. Either:
- Check other annotation results for most likely domain and adjust the command line call, or
- Use CheckM's ssuFinder module, which searches for all three domains and merges annotations.
I'm slightly leaning towards CheckM at the moment, which will also eliminate the dependencies on Barrnap and Bedtools, but this needs proper testing obviously!
Confidence values
It might be useful to have some kind of confidence values of the tools (if they provide it internally).
I have seen the following example for one of the (new) genomes:
The LCA of tools was bacteria (TaxID 2), which was caused by a single conflicting assignment:
Mash, Kaiju as well as Centrifuge all predicted a Psychrobacter, CheckM predicted bacteria, only dada2 predicted a Chryseobacterium which is of a different phylum than Psychrobacter. If the dada2 prediction is not really confident, one could decide to go with the matching prediction of the other 3.
Update CAMITAX db
Test local database snapshots, then update the Zenodo ones (and the download links in init.nf).
Suggestion : Run checkm on more than 1 MAG at a time
Hi,
I have a few hundred MAGs that I want to taxonomically check and I realized that the checkm software is run MAG per MAG as are all the other steps. However, the pplacer step in checkm takes quite some time as it needs to put the tree in memory to place the MAG each time. When running it by itself, I think that it's much faster to do it with all the MAGS at the same time.
Using the default 8 cores, the checkm software is using only 2 cores at a time and the other 6 are not used as soon as prodigal and mash are finished
Would it be possible to implement this in the pipeline or maybe doing 20-30 at once?
Best
Greg
Using CAMITAX without an internet connection
Is there any way to install/run CAMITAX on a machine with no connection to the internet (data can be transferred via external hard drive)?
not working with singularity
I have followed the instructions in the readme for downloading the databases but now I'm trying to run camitax on real genomes and I get a lot of errors:
nextflow run CAMI-challenge/CAMITAX -profile singularity --db db --i input --x fasta
...
Error executing process > 'prodigal (Sdev_DM33A01_acrmy.spades.pilon)'
Caused by:ror:
Process `prodigal (Sdev_DM33A01_acrmy.spades.pilon)` terminated with an error exit status (1)f doesn't exist in conta
iner
Command executed: 0: cd: /gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6: No
such file or directory
prodigal -a Sdev_DM33A01_acrmy.spades.pilon.genes.faa -d Sdev_DM33A01_acrmy.spades.pilon.genes.fna -i Sdev_DM33A01_acrmy.spades.pilon.fasta
grep -c "^>" Sdev_DM33A01_acrmy.spades.pilon.genes.faa > Sdev_DM33A01_acrmy.spades.pilon.genes.cnt
/gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6
Command exit status:
1: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Command output:
(empty)
Command error:
WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
/bin/bash: line 0: cd: /gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6: No such file or directory
/bin/bash: .command.sh: No such file or directory
Work dir:
/gpfs/gsfs10/users/Segrelab/conlans/sandbox/camitax/work/96/da102cca5ee73b371511f6b4e610b6
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Yesterday, I was getting errors like:
Error executing process > 'mash (Scap_DM24H05_acrog.spades.pilon)'
FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://q
Caused by:containers/mash:2.0--gsl2.2_2: pinging container registry quay.io: Get "https://quay.io/v2/": EOF
Failed to pull singularity image
command: singularity pull --name quay.io-biocontainers-mash-2.0--gsl2.2_2.img.pulling.1647808897118 docker://quay.io/biocontainers/mash:2.0--gsl2.2_2 > /dev/null
status : 255
message:ing pending tasks (2)
FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://quay.io/biocontainers/mash:2.0--gsl2.2_2: pinging container registry quay.io: Get "https://quay.io/v2/": EOF
Has something changes in the containers or container host? I'm using nextflow 21.10.5
Check for Nextflow version
Triggered by #15, I think we should check for a required Nextflow version.
https://www.nextflow.io/docs/latest/metadata.html#nextflow-metadata
In #15, a deprecated container definition syntax caused CAMITAX to fail now.
Not sure how to handle this other than specifying the tested (and working) version.
Users could then resort to the NXF_VER thingy, if future changes break stuff again:
https://www.nextflow.io/docs/latest/faq.html#how-do-i-use-a-specific-version-of-nextflow
Incorrect RTLpath
Example, with 2 phylum-level assignments, yet RTLpath favours one (because of weird intermediate NCBI Taxonomy levels):
Genome taxID Mash Dada2 Centrifuge Kaiju CheckM
TARA_IOS_MAG_00022 1239 1 1 1239 2 28890
Either go for the "RealDepth" or switch to lowest assignment w/o conflict, as discussed.
State if 16S was found
Presence/absence of 16S gene in assembly, e.g. as a new column in the summary.
Collect individual taxon assignments
The goal is to have exactly one taxon label per input genome. As the individual approaches (Fig. 1A–D) are complementary and quite conservative, the maximal root-to-leaf path is appropriate here (Fig. 1E).
Issues installing docker
Hello,
I was trying to use CAMITAX with docker. All the databases have been successfully downloaded. However, I'm having issues with downloading and installing docker.
conda install -c conda-forge/label/cf202003 docker
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- docker
Finally, when I do run CAMITAX I just get a blank run. Is it because docker isn't installed? Any suggestions to solve this is appreciated.
picture.pdf
We also ran the same command with singularity installed and get the exact same response as the attached picture. Command to run CAMITAX with singularity is below
run CAMI-challenge/CAMITAX -profile singularity --db ~/cami_dat/ --i PLS/1_11.fasta --x fasta
Novelty category
Given the final taxID, determine the full lineage, go from lower to higher taxIDs, and look up whether a sequenced isolate is available in RefSeq (Mash sketches contain all sequenced microbial genomes, i.e. simply hash their full lineages and check if the query taxID exists).
start with conda
Hello
Can you please provide some help on how to run camitax with conda? How to config the nextflow config file to do this?
Neither Docker nor singularity is an option for me at the moment.
I have created a conda env, activated it, installed the requirements, cloned the repo and I have all the dbs and nextflow as well.
Thanks. Cheers, Balazs.
Scientific name
Small QoL improvement would to also print out the scientific name corresponding to the NCBI tax ID
error running camitax
Dear Andreas,
I have a problem while running camitax. After installation it was working, but after some trials it is no more working, and it is giving an error after few steps. We don't understand if the problem is associated to the docker or to another reason.
I have attached below the ".nextflow.log" in order for you to have an idea of the problem.
I hope you can help.
Thanks in advance.
Sincerely
Stefano
giu-07 14:53:51.403 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 19.01.0
giu-07 14:53:52.319 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/stefano/.nextflow/assets/CAMI-challenge/CAMITAX/.git/config; branch: master; remote: origin; url: https://github.com/CAMI-challenge/CAMITAX.git
giu-07 14:53:52.331 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/stefano/.nextflow/assets/CAMI-challenge/CAMITAX/.git/config; branch: master; remote: origin; url: https://github.com/CAMI-challenge/CAMITAX.git
giu-07 14:53:52.437 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/stefano/.nextflow/assets/CAMI-challenge/CAMITAX/.git/config; branch: master; remote: origin; url: https://github.com/CAMI-challenge/CAMITAX.git
giu-07 14:53:52.437 [main] INFO nextflow.cli.CmdRun - Launching `CAMI-challenge/CAMITAX` [big_hodgkin] - revision: 1ed2ac92cc [master]
giu-07 14:53:53.539 [main] INFO nextflow.scm.AssetManager - NOTE: Your local project version looks outdated - a different revision is available in the remote repository [f7e4933900]
giu-07 14:53:53.557 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/stefano/.nextflow/assets/CAMI-challenge/CAMITAX/nextflow.config
giu-07 14:53:53.558 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/stefano/.nextflow/assets/CAMI-challenge/CAMITAX/nextflow.config
giu-07 14:53:53.578 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
giu-07 14:53:53.718 [main] DEBUG nextflow.Session - Session uuid: 20ac1238-b64b-4bfd-a8dd-9939a1ae20ff
giu-07 14:53:53.718 [main] DEBUG nextflow.Session - Run name: big_hodgkin
giu-07 14:53:53.719 [main] DEBUG nextflow.Session - Executor pool size: 40
giu-07 14:53:53.731 [main] DEBUG nextflow.cli.CmdRun -
Version: 19.01.0 build 5050
Modified: 22-01-2019 11:19 UTC (12:19 CEST)
System: Linux 4.4.0-150-generic
Runtime: Groovy 2.5.5 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_201-b09
Encoding: UTF-8 (UTF-8)
Process: 65738@loki [127.0.1.1]
CPUs: 40 - Mem: 251,8 GB (230,9 GB) - Swap: 255,9 GB (255,9 GB)
giu-07 14:53:53.753 [main] DEBUG nextflow.Session - Work-dir: /mnt/data_HDD/stefano/progetto_proteins_nanopore/annotation/work [xfs]
giu-07 14:53:53.969 [main] DEBUG nextflow.Session - Session start invoked
giu-07 14:53:53.976 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
giu-07 14:53:53.977 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
giu-07 14:53:54.529 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
giu-07 14:53:54.570 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /mnt/data_HDD/stefano/progetto_proteins_nanopore/selected_MAGs/; pattern: *.fa; options: [:]
giu-07 14:53:54.886 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:mash` matches process mash
giu-07 14:53:54.891 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:54.891 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:54.899 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:54.902 [main] INFO nextflow.executor.Executor - [warm up] executor > local
giu-07 14:53:54.907 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=40; memory=251,8 GB; capacity=40; pollInterval=100ms; dumpInterval=5m
giu-07 14:53:54.912 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
giu-07 14:53:54.914 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
giu-07 14:53:54.916 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
giu-07 14:53:54.963 [main] DEBUG nextflow.Session - >>> barrier register (process: mash)
giu-07 14:53:54.967 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > mash -- maxForks: 40
giu-07 14:53:54.999 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:checkm` matches process checkm
giu-07 14:53:55.000 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:55.000 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:55.000 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:55.005 [main] DEBUG nextflow.Session - >>> barrier register (process: checkm)
giu-07 14:53:55.008 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > checkm -- maxForks: 40
giu-07 14:53:55.043 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:dada2` matches process dada2
giu-07 14:53:55.045 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:55.045 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:55.045 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:55.046 [main] DEBUG nextflow.Session - >>> barrier register (process: dada2)
giu-07 14:53:55.046 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > dada2 -- maxForks: 40
giu-07 14:53:55.059 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:prodigal` matches process prodigal
giu-07 14:53:55.060 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:55.060 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:55.060 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:55.061 [main] DEBUG nextflow.Session - >>> barrier register (process: prodigal)
giu-07 14:53:55.061 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > prodigal -- maxForks: 40
giu-07 14:53:55.123 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:centrifuge` matches process centrifuge
giu-07 14:53:55.141 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:55.141 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:55.141 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:55.149 [main] DEBUG nextflow.Session - >>> barrier register (process: centrifuge)
giu-07 14:53:55.149 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > centrifuge -- maxForks: 40
giu-07 14:53:55.192 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:kaiju` matches process kaiju
giu-07 14:53:55.204 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:55.204 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:55.205 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:55.211 [main] DEBUG nextflow.Session - >>> barrier register (process: kaiju)
giu-07 14:53:55.233 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > kaiju -- maxForks: 40
giu-07 14:53:55.492 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:55.492 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:55.492 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:55.511 [main] DEBUG nextflow.Session - >>> barrier register (process: taxonomy)
giu-07 14:53:55.511 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > taxonomy -- maxForks: 40
giu-07 14:53:55.602 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
giu-07 14:53:55.603 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
giu-07 14:53:55.603 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
giu-07 14:53:55.806 [main] DEBUG nextflow.Session - >>> barrier register (process: summary)
giu-07 14:53:55.807 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > summary -- maxForks: 40
giu-07 14:53:55.813 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
giu-07 14:53:55.815 [main] DEBUG nextflow.Session - Session await
giu-07 14:53:56.190 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.196 [Task submitter] INFO nextflow.Session - [c9/a016cd] Submitted process > checkm (bin_33_unycicler)
giu-07 14:53:56.221 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.222 [Task submitter] INFO nextflow.Session - [02/28f124] Submitted process > mash (bin_4_metaspades)
giu-07 14:53:56.239 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.240 [Task submitter] INFO nextflow.Session - [d8/2319e6] Submitted process > prodigal (bin_33_unycicler)
giu-07 14:53:56.256 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.257 [Task submitter] INFO nextflow.Session - [c8/2c8e1d] Submitted process > mash (bin_16_metaspades)
giu-07 14:53:56.275 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.289 [Task submitter] INFO nextflow.Session - [f6/e2d9e3] Submitted process > mash (bin_4_operams)
giu-07 14:53:56.296 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.297 [Task submitter] INFO nextflow.Session - [68/5509a3] Submitted process > checkm (bin_35_metaspades)
giu-07 14:53:56.305 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.325 [Task submitter] INFO nextflow.Session - [77/bf1955] Submitted process > mash (bin_5_unycicler)
giu-07 14:53:56.339 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.340 [Task submitter] INFO nextflow.Session - [83/a3a8c3] Submitted process > prodigal (bin_35_metaspades)
giu-07 14:53:56.349 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.350 [Task submitter] INFO nextflow.Session - [f7/469646] Submitted process > checkm (bin_14_unycicler)
giu-07 14:53:56.356 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.380 [Task submitter] INFO nextflow.Session - [38/598252] Submitted process > mash (bin_9_operams)
giu-07 14:53:56.400 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.404 [Task submitter] INFO nextflow.Session - [87/1390f3] Submitted process > prodigal (bin_2_operams)
giu-07 14:53:56.425 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.433 [Task submitter] INFO nextflow.Session - [f4/10df77] Submitted process > prodigal (bin_5_unycicler)
giu-07 14:53:56.446 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.446 [Task submitter] INFO nextflow.Session - [ff/5336cf] Submitted process > prodigal (bin_10_metaspades)
giu-07 14:53:56.456 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.465 [Task submitter] INFO nextflow.Session - [c9/218269] Submitted process > mash (bin_33_unycicler)
giu-07 14:53:56.474 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.481 [Task submitter] INFO nextflow.Session - [bb/92fcc3] Submitted process > mash (bin_36_operams)
giu-07 14:53:56.503 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.504 [Task submitter] INFO nextflow.Session - [c0/d90de9] Submitted process > prodigal (bin_8_metaspades)
giu-07 14:53:56.510 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.511 [Task submitter] INFO nextflow.Session - [42/a6d15e] Submitted process > mash (bin_28_operams)
giu-07 14:53:56.528 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.528 [Task submitter] INFO nextflow.Session - [e5/54ee50] Submitted process > prodigal (bin_37_operams)
giu-07 14:53:56.533 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:53:56.534 [Task submitter] INFO nextflow.Session - [fb/fc2a3c] Submitted process > prodigal (bin_40_metaspades)
giu-07 14:54:05.662 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: checkm (bin_33_unycicler); status: COMPLETED; exit: 1; error: -; workDir: /mnt/data_HDD/stefano/progetto_proteins_nanopore/annotation/work/c9/a016cd07a3749f119b24599000c5c9]
giu-07 14:54:05.668 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
giu-07 14:54:05.677 [Task submitter] INFO nextflow.Session - [39/173609] Submitted process > checkm (bin_5_operams)
giu-07 14:54:05.757 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'checkm (bin_33_unycicler)'
Caused by:
Process `checkm (bin_33_unycicler)` terminated with an error exit status (1)
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_33_unycicler.fa . ssu_finder 2>&1
ln -s ssu_finder/ssu.fna bin_33_unycicler.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_33_unycicler.checkm.tsv
Command exit status:
1
Command output:
located at /usr/local/lib/python2.7/site-packages/checkm/DATA_CONFIG
Please try again with updated privileges. Error was:
[Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/checkm/DATA_CONFIG'
*******************************************************************************
[CheckM - ssu_finder] Identifying SSU (16S/18S) rRNAs in sequences.
*******************************************************************************
Determining bin assignment of sequences.
Identifying SSU rRNAs on sequences.
Identifying bacterial 16S.
Error: File existence/permissions problem in trying to open query file hmms_ssu/SSU_bacteria.hmm.
HMM file hmms_ssu/SSU_bacteria.hmm not found (nor an .h3m binary of it)
cat: write error: Broken pipe
Identifying archaeal 16S.
Error: File existence/permissions problem in trying to open query file hmms_ssu/SSU_archaea.hmm.
HMM file hmms_ssu/SSU_archaea.hmm not found (nor an .h3m binary of it)
cat: write error: Broken pipe
Identifying eukaryotic 18S.
Error: File existence/permissions problem in trying to open query file hmms_ssu/SSU_euk.hmm.
HMM file hmms_ssu/SSU_euk.hmm not found (nor an .h3m binary of it)
cat: write error: Broken pipe
It seems that the CheckM data folder has not been set yet or has been removed. Running: 'checkm data setRoot'.
You do not seem to have permission to edit the checkm config file
located at /usr/local/lib/python2.7/site-packages/checkm/DATA_CONFIG
Please try again with updated privileges. Error was:
[Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/checkm/DATA_CONFIG'
Sorry, CheckM cannot run without a valid data folder.
Unexpected error: <type 'exceptions.IOError'>
Traceback (most recent call last):
File "/usr/local/bin/checkm", line 709, in <module>
checkmParser.parseOptions(args)
File "/usr/local/lib/python2.7/site-packages/checkm/main.py", line 1312, in parseOptions
self.ssuFinder(options)
File "/usr/local/lib/python2.7/site-packages/checkm/main.py", line 1130, in ssuFinder
ssuFinder.run(options.seq_file, binFiles, options.out_folder, options.evalue, options.concatenate)
File "/usr/local/lib/python2.7/site-packages/checkm/ssuFinder.py", line 216, in run
seqInfo = self.__readHits(os.path.join(outputDir, 'ssu' + '.' + domain + '.txt'), domain, evalueThreshold)
File "/usr/local/lib/python2.7/site-packages/checkm/ssuFinder.py", line 60, in __readHits
for line in open(resultsFile):
IOError: [Errno 2] No such file or directory: 'ssu_finder/ssu.archaea.txt'
Command error:
*******************************************************************************
[CheckM - data] Check for database updates. [setRoot]
*******************************************************************************
Data location not changed
Work dir:
/mnt/data_HDD/stefano/progetto_proteins_nanopore/annotation/work/c9/a016cd07a3749f119b24599000c5c9
Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option `-resume`
giu-07 14:54:05.830 [Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Process `checkm (bin_33_unycicler)` terminated with an error exit status (1)
giu-07 14:54:05.906 [Task monitor] DEBUG nextflow.Session - The following nodes are still active:
[process] dada2
status=ACTIVE
port 0: (value) bound ; channel: db
port 1: (queue) OPEN ; channel: -
port 2: (cntrl) - ; channel: $
[process] centrifuge
status=ACTIVE
port 0: (value) bound ; channel: db
port 1: (queue) OPEN ; channel: -
port 2: (cntrl) - ; channel: $
[process] kaiju
status=ACTIVE
port 0: (value) bound ; channel: db
port 1: (queue) OPEN ; channel: -
port 2: (cntrl) - ; channel: $
[process] taxonomy
status=ACTIVE
port 0: (value) bound ; channel: db
port 1: (queue) OPEN ; channel: -
port 2: (cntrl) - ; channel: $
[process] summary
status=ACTIVE
port 0: (value) OPEN ; channel: summaryList
port 1: (cntrl) - ; channel: $
giu-07 14:54:05.922 [main] DEBUG nextflow.Session - Session await > all process finished
giu-07 14:54:05.922 [main] DEBUG nextflow.Session - Session await > all barriers passed
giu-07 14:54:05.928 [main] WARN n.processor.TaskPollingMonitor - Killing pending tasks (19)
giu-07 14:54:05.989 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 124; name: prodigal (bin_40_metaspades); status: COMPLETED; exit: 0; error: -; workDir: /mnt/data_HDD/stefano/progetto_proteins_nanopore/annotation/work/fb/fc2a3ce441ea135a5f7063ba4c53db]
giu-07 14:54:06.316 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
giu-07 14:54:06.346 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=1; failedCount=19; ignoredCount=0; cachedCount=0; succeedDuration=9.4s; failedDuration=1m 15s; cachedDuration=0ms]
giu-07 14:54:06.480 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
giu-07 14:54:06.501 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
edited by Adrian: Fixed md formatting
Assembly statistics
Incorporate the CheckM-reported genome assembly statistics (N50 etc.) into the final CAMITAX report.
warning process name deprecated
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
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