Comments (10)
Hi @hoelzer ,
I don't know what happened, chromomap not working ):.
from emg-viral-pipeline.
Hi @NailouZhang,
Thank you for the extensive error report. I'll try to look at this next week, I'm busy at the moment.
@hoelzer I'll update the docker container for Chromomap.
Cheers
from emg-viral-pipeline.
It tool long... but I finally added those lines to the container and pushed a new version of it.
TBH, I wasn't able to test it. I will
from emg-viral-pipeline.
Hi @NailouZhang ! Thanks for your interest in the pipeline.
It seems that the Python script filter_contigs_len.py
which is located in the bin
folder of the cloned repository can not be found correctly via your execution of the pipeline (https://github.com/EBI-Metagenomics/emg-viral-pipeline/blob/master/bin/filter_contigs_len.py). The bin
folder should be located here:
~/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline
Can you please try the following: just install the pipeline code directly via Nextflow:
# pull pipeline code
nextflow pull EBI-Metagenomics/emg-viral-pipeline
# test run w/ latest release
nextflow run EBI-Metagenomics/emg-viral-pipeline -r v0.4.0 --help
# execute your data using the latest release version
nextflow run -resume \
EBI-Metagenomics/emg-viral-pipeline -r v0.4.0 \
--fasta "/home/stone/20T/SraDownload/Genome/TBEV/NC_001672.1_sequence.fasta" \
--cores 4 \
--output /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27 \
--workdir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work \
--databases ~/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline/DATABASES \
--cachedir ~/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline/SINGULARITY \
-profile local,singularity
from emg-viral-pipeline.
Thanks! but I failed with as fellow:
#-----------------------------------------------------------------------------------------------------------------------------------------#
~/Softwares/Miniconda3/nextflow-21.03.0-edge/nextflow run -resume
/home/stone/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/virify.nf
--fasta "/home/stone/20T/SraDownload/Genome/TBEV/NC_001672.1_sequence.fasta"
--cores 4
--output /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27
--workdir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work
--databases /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/DATABASES
--cachedir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/SINGULARITY
-profile local,docker
Error executing process > 'preprocess:rename (1)'
Caused by:
Process preprocess:rename (1)
terminated with an error exit status (125)
Command executed:
if [[ NC_001672.1_sequence.fasta =~ .gz$ ]]; then
zcat NC_001672.1_sequence.fasta > tmp.fasta
else
cp NC_001672.1_sequence.fasta tmp.fasta
fi
rename_fasta.py -i tmp.fasta -m NC_001672_map.tsv -o NC_001672_renamed.fasta rename
Command exit status:
125
Command output:
(empty)
Command error:
Unable to find image 'microbiomeinformatics/emg-viral-pipeline-python3:v1' locally
docker: Error response from daemon: Head https://registry-1.docker.io/v2/microbiomeinformatics/emg-viral-pipeline-python3/manifests/v1: dial tcp: lookup registry-1.docker.io on 127.0.1.1:53: read udp 127.0.0.1:46714->127.0.1.1:53: i/o timeout.
See 'docker run --help'.
Work dir:
/home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work/b1/e3cb5d7670f844cb08409030003257
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
#-----------------------------------------------------------------------------------------------------------------------------------------#
but I work well with https://github.com/hoelzer/virify
the INSTALL and WORK as fellow:
#-----------------------------------------------------------------------------------------------------------------------------------------#
#安装virify
git clone --recursive https://github.com/hoelzer/virify.git
cd virify
docker build -t mhoelzer/prodigal_viral:0.1 -f docker/prodigal/Dockerfile .
docker build -t mhoelzer/hmmscan:0.1 -f docker/hmmscan/Dockerfile .
cp bin/* docker/annotation/
cd docker/annotation/
docker build -t mhoelzer/annotation_viral_contigs:0.1 -f Dockerfile .
cd ..
cp bin/* docker/assign/
cd docker/assign/
docker build -t mhoelzer/assign_taxonomy:0.1 -f Dockerfile .
cd ..
#copy emg-viral-pipeline/docker/krona to virify/docker/
cp -R ../emg-viral-pipeline/docker/krona docker/
cd docker/krona
docker build -t nanozoo/krona:2.7.1--658845d -f Dockerfile .
cd ..
cp -R ../emg-viral-pipeline/docker/bioruby docker/
cd docker/bioruby
docker build -t nanozoo/bioruby:2.0.1--1f8a188 -f Dockerfile .
cd ..
cd ~/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27
~/Softwares/Miniconda3/nextflow-20.04.1/nextflow run -resume
~/20T/DataBase/SoftwaresEnsembel/MAG/virify
--fasta "/home/stone/20T/SraDownload/Genome/TBEV/NC_001672.1_sequence.fasta"
--cores 4
--output /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27
--workdir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work
--databases ~/20T/DataBase/SoftwaresEnsembel/MAG/virify/DATABASES
--cachedir ~/20T/DataBase/SoftwaresEnsembel/MAG/virify/SINGULARITY
-profile standard
[skipped ] process > download_pprmeta:pprmetaGet [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_model_meta:metaGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_virsorter_db:virsorterGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_viphog_db:viphogGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_rvdb_db:rvdbGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_pvogs_db:pvogsGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_vogdb_db:vogdbGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_vpf_db:vpfGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_ncbi_db:ncbiGetDB [100%] 1 of 1, stored: 1 ✔
[75/59a1d0] process > download_imgvr_db:imgvrGetDB [100%] 1 of 1, failed: 1 ✘
[eb/369861] process > detect:rename (1) [100%] 1 of 1, cached: 1 ✔
[68/35b2d4] process > detect:length_filtering (1) [100%] 1 of 1, cached: 1 ✔
[e3/917400] process > detect:virsorter (1) [100%] 1 of 1, cached: 1 ✔
[e7/acbd25] process > detect:virfinder (1) [100%] 1 of 1, cached: 1 ✔
[81/471160] process > detect:pprmeta (1) [100%] 1 of 1, cached: 1 ✔
[8f/a392d7] process > detect:parse (1) [100%] 1 of 1, cached: 1 ✔
[47/da27cb] process > detect:restore (1) [100%] 1 of 1, cached: 1 ✔
[9c/37108a] process > annotate:prodigal (1) [100%] 1 of 1, cached: 1 ✔
[48/5bb7ed] process > annotate:hmmscan_viphogs (1) [100%] 1 of 1, cached: 1 ✔
[d5/0c94fe] process > annotate:hmm_postprocessing (1) [100%] 1 of 1, cached: 1 ✔
[40/dca0b6] process > annotate:ratio_evalue (1) [100%] 1 of 1, cached: 1 ✔
[89/db331a] process > annotate:annotation (1) [100%] 1 of 1, cached: 1 ✔
[08/54d4d4] process > annotate:plot_contig_map (1) [100%] 1 of 1 ✔
[de/cbe75b] process > annotate:assign (1) [100%] 1 of 1, cached: 1 ✔
[d0/6e23ba] process > plot:generate_krona_table (2) [100%] 2 of 2, cached: 2 ✔
[1e/876ef6] process > plot:krona (2) [100%] 2 of 2, cached: 2 ✔
[39/617798] process > plot:generate_sankey_table (1) [100%] 2 of 2 ✔
[6d/bc9086] process > plot:sankey (1) [100%] 2 of 2 ✔
Error executing process > 'download_imgvr_db:imgvrGetDB'
Error executing process > 'download_imgvr_db:imgvrGetDB'
Caused by:
Process download_imgvr_db:imgvrGetDB
terminated with an error exit status (4)
Command executed:
wget -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/IMG_VR_2018-07-01_4.tar.gz && tar zxvf IMG_VR_2018-07-01_4.tar.gz
Command exit status:
4
Command output:
#-----------------------------------------------------------------------------------------------------------------------------------------#
from emg-viral-pipeline.
Hi @NailouZhang !
Okay, so for your first command that failed it seems that you again used the manually cloned repository instead of the installation via Nextflow
. Can you please try once more:
# pull pipeline code
~/Softwares/Miniconda3/nextflow-21.03.0-edge/nextflow pull EBI-Metagenomics/emg-viral-pipeline
# test run w/ latest release
~/Softwares/Miniconda3/nextflow-21.03.0-edge/nextflow run EBI-Metagenomics/emg-viral-pipeline -r v0.4.0 --help
# execute your data using the latest release version
~/Softwares/Miniconda3/nextflow-21.03.0-edge/nextflow run -resume \
EBI-Metagenomics/emg-viral-pipeline -r v0.4.0 \
--fasta "/home/stone/20T/SraDownload/Genome/TBEV/NC_001672.1_sequence.fasta" \
--cores 4 \
--output /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27 \
--workdir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work \
--databases /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/DATABASES \
--cachedir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/SINGULARITY \
-profile local,docker
Does this work?
If not, the error you got
Command error:
Unable to find image 'microbiomeinformatics/emg-viral-pipeline-python3:v1' locally
docker: Error response from daemon: Head https://registry-1.docker.io/v2/microbiomeinformatics/emg-viral-pipeline-python3/manifests/v1: dial tcp: lookup registry-1.docker.io on 127.0.1.1:53: read udp 127.0.0.1:46714->127.0.1.1:53: i/o timeout.
See 'docker run --help'.
sounds like some issue with Docker. Does this work:
docker pull microbiomeinformatics/emg-viral-pipeline-python3:v1
Second, you then used an discontinued code repository from the early days of the Nextflow
version of the pipeline (https://github.com/hoelzer/virify). I don't recommend to use this code because it is not maintained anymore. However, it seems that you build here all the necessary Docker images manually and then executed the pipeline which will work (should also work for the EBI-Metagenomics/emg-viral-pipeline code). But: actually this is not necessary because Nextflow
should take care of pulling the Docker images automatically when you use -profile docker,local
for example.
So best would be that you get the code from this repository running, using the nextflow pull
option and a provided -r
release version in combination with the -profile docker,local
that should then download the necessary dependencies automatically - if Docker is configured correctly.
from emg-viral-pipeline.
Hi @hoelzer ,
Thanks for your suggestion. Now I can run well with emg-viral-pipeline-0.4.0/tests/parse_viral_fixtures/base_fixtures/input.fasta with :
work well
/home/stone/Softwares/Miniconda3/nextflow-21.03.0-edge/nextflow run -resume ~/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/virify.nf
--fasta "tests/parse_viral_fixtures/base_fixtures/input.fasta"
--cores 4 --output /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27
--workdir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work
--databases ~/20T/DataBase/SoftwaresEnsembel/MAG/virify/DATABASES
--cachedir ~/20T/DataBase/SoftwaresEnsembel/MAG/virify/SINGULARITY
--virome
--hmmextend
--blastextend
--length 1
-profile local,docker
however, When I add --chromomap --balloon , I work errors
I found that the microbiomeinformatics/r_chromomap:v0.1 installed by docker pull cant run well with errors "no chromomap packages", I did some modifications with docker/r_chromomap/Dockerfile
FROM rocker/r-ver:3.5.0
LABEL base_image="rocker/verse:3.5.0"
LABEL version="1"
LABEL about.summary="r visualization packages"
LABEL about.license="SPDX:Apache-2.0"
LABEL about.tags="r, visualization"
LABEL about.home="https://cran.r-project.org/web/packages/chromoMap/, https://cran.r-project.org/web/packages/ggplot2/, https://cran.r-project.org/web/packages/plotly/"
LABEL software="r packages chromoMap, ggplot2, plotly"
LABEL software.version="3.15"
LABEL maintainer="MGnify team https://www.ebi.ac.uk/support/metagenomics"
#I added
RUN apt update && apt install libcurl4-openssl-dev libssl-dev -y
RUN Rscript -e "install.packages('httr', repos = 'http://cran.us.r-project.org')" &&
Rscript -e "install.packages('curl', repos = 'http://cran.us.r-project.org')" &&
Rscript -e "install.packages('chromoMap')" &&
Rscript -e "install.packages('ggplot2', repos = 'http://cran.us.r-project.org')" &&
Rscript -e "install.packages('plotly', repos = 'http://cran.us.r-project.org')" &&
rm -rf /tmp/downloaded_packages/ /tmp/*.rds
#and then run:
docker build -t microbiomeinformatics/r_chromomap:v0.1 -f docker/r_chromomap/Dockerfile .
I can run well with 103 flavivirus
However, The taxonomy in sankey plot and krona can't class these virus fasta
I run as follow:
cd ~/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/
/home/stone/Softwares/Miniconda3/nextflow-21.03.0-edge/nextflow run -resume
~/20T/DataBase/SoftwaresEnsembel/MAG/emg-viral-pipeline-0.4.0/virify.nf
--fasta "/home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/Flavivirus.fasta"
--cores 4
--output /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27
--workdir /home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work
--databases ~/20T/DataBase/SoftwaresEnsembel/MAG/virify/DATABASES
--cachedir ~/20T/DataBase/SoftwaresEnsembel/MAG/virify/SINGULARITY
--virome
--hmmextend
--blastextend
--length 1
-profile local,docker
[skipped ] process > download_pprmeta:pprmetaGet [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_virsorter_db:virsorterGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_virfinder_db:virfinderGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_model_meta:metaGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_viphog_db:viphogGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_rvdb_db:rvdbGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_pvogs_db:pvogsGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_vogdb_db:vogdbGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_vpf_db:vpfGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_ncbi_db:ncbiGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_imgvr_db:imgvrGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_checkv_db:checkvGetDB [100%] 1 of 1, stored: 1 ✔
[d3/0ade86] process > preprocess:rename (1) [100%] 1 of 1 ✔
[ac/b56dc6] process > preprocess:length_filtering (1) [100%] 1 of 1 ✔
[a8/c75806] process > detect:virsorter (1) [100%] 1 of 1 ✔
[92/9ea9f6] process > detect:virfinder (1) [100%] 1 of 1 ✔
[60/1ef0a9] process > detect:pprmeta (1) [100%] 1 of 1 ✔
[f0/82185a] process > detect:parse (1) [100%] 1 of 1 ✔
[f5/8abf7d] process > postprocess:restore (1) [100%] 1 of 1 ✔
[92/98ab09] process > annotate:prodigal (1) [100%] 1 of 1 ✔
[e2/713785] process > annotate:hmmscan_viphogs (1) [100%] 1 of 1 ✔
[6d/1e84b5] process > annotate:hmm_postprocessing (1) [100%] 1 of 1 ✔
[88/b20eca] process > annotate:ratio_evalue (1) [100%] 1 of 1 ✔
[6e/1a15cd] process > annotate:annotation (1) [100%] 1 of 1 ✔
[40/82ec13] process > annotate:plot_contig_map (1) [100%] 1 of 1 ✔
[81/e500aa] process > annotate:assign (1) [100%] 1 of 1 ✔
[48/d831c4] process > annotate:blast (1) [100%] 1 of 1 ✔
[4f/070cf9] process > annotate:blast_filter (1) [100%] 1 of 1 ✔
[74/24cf11] process > annotate:hmmscan_rvdb (1) [100%] 1 of 1 ✔
[d5/3c537e] process > annotate:hmmscan_pvogs (1) [100%] 1 of 1 ✔
[16/373266] process > annotate:hmmscan_vogdb (1) [100%] 1 of 1 ✔
[be/8eb74f] process > annotate:hmmscan_vpf (1) [100%] 1 of 1 ✔
[64/aad264] process > annotate:checkV (1) [100%] 1 of 1 ✔
[68/7f16bd] process > plot:generate_krona_table (1) [100%] 2 of 2 ✔
[70/3ccd1f] process > plot:krona (2) [100%] 2 of 2 ✔
[9f/f9cb59] process > plot:generate_sankey_table (2) [100%] 2 of 2 ✔
[37/f2526d] process > plot:sankey (2) [100%] 2 of 2 ✔
Completed at: 31-十二月-2021 19:31:33
Duration : 13m 37s
CPU hours : 1.6
Succeeded : 29
the run results can be checked:
link: https://pan.baidu.com/s/1xiJQ8c4nsRNtg3TVw2TSUg extracte code: vabi
from emg-viral-pipeline.
Hi @NailouZhang
ok, glad it worked finally. But now you have different issues.
Chromomap
So basically you added
#I added
RUN apt update && apt install libcurl4-openssl-dev libssl-dev -y
to the Dockerfile, then you re-build the image and then it worked fine? If so, thanks for checking and reporting so we could then update the Docker image for Chromomap accordingly @mberacochea .
Taxonomy not assigned for sequence set of flaviviruses
So basically you are certain that the input sequences are flaviviruses but you don't get any taxonomy assignments, right? This requires checking your input FASTAs in more detail. Are the contigs/sequences relatively short? If so, it's hard for VIRify to assign a taxonomy bc/ the method relies on detectable ORFs. And if the sequence is short and only 1-2 informative ORFs can be found, it's difficult to assign a taxonomy with some certainty. In addition, we already saw that some RNA viruses are more difficult to assign in comparison to DNA viruses (shorter genomes, sometimes less well represented in our HMM model set, ...). Nevertheless, VIRify should find clear cases which we would need to investigate more carefully.
from emg-viral-pipeline.
Hi @hoelzer ,
Thank you for your reply. Happy New Year.
There were some errors running Chromomap, After adding the parameter -- chromomap, the following information is displayed:
[skipped ] process > download_pprmeta:pprmetaGet [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_virsorter_db:virsorterGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_virfinder_db:virfinderGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_model_meta:metaGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_viphog_db:viphogGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_rvdb_db:rvdbGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_pvogs_db:pvogsGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_vogdb_db:vogdbGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_vpf_db:vpfGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_ncbi_db:ncbiGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_imgvr_db:imgvrGetDB [100%] 1 of 1, stored: 1 ✔
[skipped ] process > download_checkv_db:checkvGetDB [100%] 1 of 1, stored: 1 ✔
[d3/0ade86] process > preprocess:rename (1) [100%] 1 of 1, cached: 1 ✔
[ac/b56dc6] process > preprocess:length_filtering (1) [100%] 1 of 1, cached: 1 ✔
[a8/c75806] process > detect:virsorter (1) [100%] 1 of 1, cached: 1 ✔
[92/9ea9f6] process > detect:virfinder (1) [100%] 1 of 1, cached: 1 ✔
[60/1ef0a9] process > detect:pprmeta (1) [100%] 1 of 1, cached: 1 ✔
[f0/82185a] process > detect:parse (1) [100%] 1 of 1, cached: 1 ✔
[f5/8abf7d] process > postprocess:restore (1) [100%] 1 of 1, cached: 1 ✔
[92/98ab09] process > annotate:prodigal (1) [100%] 1 of 1, cached: 1 ✔
[e2/713785] process > annotate:hmmscan_viphogs (1) [100%] 1 of 1, cached: 1 ✔
[6d/1e84b5] process > annotate:hmm_postprocessing (1) [100%] 1 of 1, cached: 1 ✔
[88/b20eca] process > annotate:ratio_evalue (1) [100%] 1 of 1, cached: 1 ✔
[6e/1a15cd] process > annotate:annotation (1) [100%] 1 of 1, cached: 1 ✔
[40/82ec13] process > annotate:plot_contig_map (1) [100%] 1 of 1, cached: 1 ✔
[81/e500aa] process > annotate:assign (1) [100%] 1 of 1, cached: 1 ✔
[48/d831c4] process > annotate:blast (1) [100%] 1 of 1, cached: 1 ✔
[4f/070cf9] process > annotate:blast_filter (1) [100%] 1 of 1, cached: 1 ✔
[74/24cf11] process > annotate:hmmscan_rvdb (1) [100%] 1 of 1, cached: 1 ✔
[d5/3c537e] process > annotate:hmmscan_pvogs (1) [100%] 1 of 1, cached: 1 ✔
[16/373266] process > annotate:hmmscan_vogdb (1) [100%] 1 of 1, cached: 1 ✔
[be/8eb74f] process > annotate:hmmscan_vpf (1) [100%] 1 of 1, cached: 1 ✔
[64/aad264] process > annotate:checkV (1) [100%] 1 of 1, cached: 1 ✔
[3c/b676ea] process > plot:generate_krona_table (2) [100%] 2 of 2, cached: 2 ✔
[70/3ccd1f] process > plot:krona (1) [100%] 2 of 2, cached: 2 ✔
[9f/f9cb59] process > plot:generate_sankey_table (1) [100%] 2 of 2, cached: 2 ✔
[37/f2526d] process > plot:sankey (2) [100%] 2 of 2, cached: 2 ✔
[49/af036d] process > plot:generate_chromomap_table (1) [100%] 2 of 2 ✔
[5c/20110c] process > plot:chromomap (1) [100%] 1 of 1, failed: 1
[skipping] Stored process > download_ncbi_db:ncbiGetDB
[skipping] Stored process > download_virfinder_db:virfinderGetDB
[skipping] Stored process > download_vogdb_db:vogdbGetDB
[skipping] Stored process > download_model_meta:metaGetDB
[skipping] Stored process > download_pvogs_db:pvogsGetDB
[skipping] Stored process > download_vpf_db:vpfGetDB
[skipping] Stored process > download_virsorter_db:virsorterGetDB
[skipping] Stored process > download_viphog_db:viphogGetDB
[skipping] Stored process > download_imgvr_db:imgvrGetDB
[skipping] Stored process > download_rvdb_db:rvdbGetDB
[skipping] Stored process > download_checkv_db:checkvGetDB
[skipping] Stored process > download_pprmeta:pprmetaGet
Error executing process > 'plot:chromomap (2)'
Caused by:
Process plot:chromomap (2)
terminated with an error exit status (1)
Command executed:
#!/usr/bin/env Rscript
library(chromoMap)
library(ggplot2)
library(plotly)
contigs <- list()
annos <- list()
contigs <- dir(pattern = ".contigs.txt")
annos <- dir(pattern = ".anno.txt")
for (k in 1:length(contigs)){
c = contigs[k]
a = annos[k]
# check if a file is empty
if (file.info(c)$size == 0 || file.info(a)$size == 0) {
next
}
# check how many categories we have
categories <- c("limegreen", "orange","grey")
df <- read.table(a, sep = "\t")
set <- unique(df$V5)
if ( length(set) == 2 ) {
if ( set[1] == 'High confidence' && set[2] == 'Low confidence') {
categories <- c("limegreen", "orange")
}
if ( set[1] == 'High confidence' && set[2] == 'No hit') {
categories <- c("limegreen", "grey")
}
if ( set[1] == 'Low confidence' && set[2] == 'No hit') {
categories <- c("orange", "grey")
}
}
if ( length(set) == 1 ) {
if ( set[1] == 'High confidence') {
categories <- c("limegreen")
}
if ( set[1] == 'Low confidence') {
categories <- c("orange")
}
if ( set[1] == 'No hit') {
categories <- c("grey")
}
}
p <- chromoMap(c, a,
data_based_color_map = T,
data_type = "categorical",
data_colors = list(categories),
legend = T, lg_y = 400, lg_x = 100, segment_annotation = T,
left_margin = 100, canvas_width = 1000, chr_length = 8, ch_gap = 6)
htmlwidgets::saveWidget(as_widget(p), paste("Flavivirus.chromomap-", k, ".html", sep=''))
}
Command exit status:
1
Command output:
(empty)
Command error:
Attaching package: ‘plotly’
The following object is masked from ‘package:ggplot2’:
last_plot
The following object is masked from ‘package:stats’:
filter
The following object is masked from ‘package:graphics’:
layout
Error in chromoMap(c, a, data_based_color_map = T, data_type = "categorical", :
unused arguments (data_based_color_map = T, data_type = "categorical", data_colors = list(categories), legend = T, lg_y = 400, lg_x = 100, segment_annotation = T, left_margin = 100, canvas_width = 1000, chr_length = 8, ch_gap = 6)
Execution halted
Work dir:
/home/stone/20T/DataBase/SoftwaresEnsembel/MAG/test_2021_12_27/work/70/44b6c3ddeddc8aaa8f5dc533752571
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line
Second, I determined that all the sequences belonged to flaviviruses
I download these sequences through the following links:
https://www.ncbi.nlm.nih.gov/nuccore?term=%28%22Flavivirus%22%5BOrganism%5D%20OR%20Flavivirus%5BAll%20Fields%5D%29%20AND%20%28viruses%5Bfilter%5D%20AND%20refseq%5Bfilter%5D%29&cmd=DetailsSearch
("Flavivirus"[Organism] OR ("Flavivirus"[Organism] OR Flavivirus[All Fields])) AND (viruses[filter] AND refseq[filter])
There is only one ORF (code polyproteins) in flaviviruses. So, it may be hard to categorize.
Thrid, I test 67 coronavirus, which have many orfs. It can work well with 66 sequencens.
("Alphacoronavirus"[Organism] OR "Betacoronavirus"[Organism] OR "Gammacoronavirus"[Organism] OR coronavirus[All Fields]) AND (viruses[filter] AND biomol_genomic[PROP] AND refseq[filter])
from emg-viral-pipeline.
Hi @NailouZhang , also a happy and healthy '22 to you!
Thanks for the detailed reporting.
-
So
chromomap
still fails? Or do you were able to solve this by modifying the Docker container? -
Flavivirus detection
There is only one ORF (code polyproteins) in flaviviruses. So, it may be hard to categorize.
Yes, this is unfortunately a current limitation of VIRify. It might be possible to tune some parameters to get these recognized, but while also increasing the false-positive detection rate. I think this might be doable via this parameter:
help="Minimum number of proteins with ViPhOG annotations at each taxonomic level, required for taxonomic assignment (default: 2)",
For your use-case, it might be reasonable to allow the user to easily adjust this parameter. I will open a separate issue about this topic because currently the pipeline does not provide a parameter to easily change this.
- Coronavirus test
Great, nice to hear. We also had good experiences w/ contigs derived from Coronavirus reads.
from emg-viral-pipeline.
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from emg-viral-pipeline.