Closed XC-Zhai closed 1 year ago
Hi @XC-Zhai. Thanks for reporting this. I created a new release v0.2.2 that should have fixed the bug. Please update the pipeline using the following command,
nextflow pull deng-lab/viroprofiler
and then run the pipeline with -r main
parameter.
Thanks a lot. Now I had another issue. Error executing process > 'VIROPROFILER:VIRALHOST_IPHOP'
Caused by:
Process VIROPROFILER:VIRALHOST_IPHOP
terminated with an error exit status (255)
Command executed:
iphop predict --fa_file putative_vcontigs_pref1.fasta --out_dir out_iphop --db_dir /home/server/viroprofiler/iphop/Sept_2021_pub --num_threads 2
cat <<-END_VERSIONS > versions.yml "VIROPROFILER:VIRALHOST_IPHOP": iPHoP: $(iphop --version | head -n1 | sed 's/iPHoP v//;s/: .*//') seqkit: $( seqkit | sed '3!d; s/Version: //' ) END_VERSIONS
Command exit status: 255
Command output: (empty)
Command error: FATAL: while executing starter: while initializing starter command: /usr/local/libexec/singularity/bin/starter-suid not found, please check your installation
Work dir: /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/work/4c/e08f23797fbe0041aed55fc9331ad6
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
I am using singularity-ce version 3.11.1. Do you have any suggestions for trying it out? Best, Xichuan
This problem seems related to the container image. I made a fix to roll back the host prediction module to v0.1. Could you please try with -r fix_iphop
parameter and let me know the output?
-r fix_iphop
Hi Rujin, I tried with command: nextflow run deng-lab/viroprofiler -r fix_iphop -profile singularity,test -resume
[N E X T F L O W ~ version 22.10.6
Launching https://github.com/deng-lab/viroprofiler
[grave_montalcini] DSL2 - revision: 4820e9f13f [fix_iphop]]
And got another one with vs2: Error executing process > 'VIROPROFILER:VIRSORTER2'
Caused by: Failed to pull singularity image command: singularity pull --name denglab-viroprofiler-base-v0.2.2.img.pulling.1682416505908 docker://denglab/viroprofiler-base:v0.2.2 > /dev/null status : 255 message: FATAL: While making image from oci registry: error fetching image to cache: failed to get checksum for docker://denglab/viroprofiler-base:v0.2.2: reading manifest v0.2.2 in docker.io/denglab/viroprofiler-base: manifest unknown
Any suggestions to this?
Best, Xichuan
Sorry, there is a typo in previous revision. Please update the pipeline and run again with the -r fix_iphop
parameter. It should show DSL2 - revision: 7e29324 [fix_iphop]
now.
Sorry, there is a typo in previous revision. Please update the pipeline and run again with the
-r fix_iphop
parameter. It should showDSL2 - revision: 7e29324 [fix_iphop]
now.
Yes, it worked with -r fix_iphop, and it also needs to be setup with this parameter. But I had another following-up issue:
[f8/2313a8] process > VIROPROFILER:VIRALHOST_IPHOP [100%] 1 of 1, failed: 1 ✘ [60/121a7b] process > VIROPROFILER:BACPHLIP [100%] 1 of 1 ✔ [- ] process > VIROPROFILER:RESULTS_TSE - [- ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > VIROPROFILER:MULTIQC - Error executing process > 'VIROPROFILER:VIRALHOST_IPHOP'
Caused by:
Process VIROPROFILER:VIRALHOST_IPHOP
terminated with an error exit status (1)
Command executed:
iphop predict --fa_file putative_vcontigs_pref1.fasta --out_dir out_iphop --db_dir /home/server/viroprofiler/iphop/Sept_2021_pub --num_threads 12
cat <<-END_VERSIONS > versions.yml "VIROPROFILER:VIRALHOST_IPHOP": iPHoP: $(iphop --version | head -n1 | sed 's/iPHoP v//;s/: .*//') seqkit: $( seqkit | sed '3!d; s/Version: //' ) END_VERSIONS
Command exit status: 1
Command output:
Command error: Looks like everything is now set up, we will first clean up the input file, and then we will start the host prediction steps themselves [1/1/Run] Running blastn against genomes... [1/3/Run] Get relevant blast matches... The blastn output file was empty, this may be ok, but is still unusual, so you may want to check the blastn log (Wdir/blastgenomes.tsv.log) [2/1/Run] Running blastn against CRISPR... [2/2/Run] Get relevant crispr matches... The blastn output file for the CRISPR spacers was empty, this may be ok, but is still unusual, so you may want to check the blastn log (Wdir/blastcrispr.tsv.log) [3/1/Run] Running WIsH... [3/2/Run] Get relevant WIsH hits...
Traceback (most recent call last):
File "/opt/conda/bin/iphop", line 10, in
Work dir: /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/work/f8/2313a8ee29316f73333d652253d0fe
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
I checked the wish.log: ERROR:Cannot open model directory /home/server/viroprofiler/iphop/Sept_2021_pub/db/wish_models.
So there is something missing during the setup.
Any further step that I can manually put this module under the db of iphop?
Best, Xichuan
It seems the iphop database is not setup successfully. In the future version, we will add a step to check the completeness of the database. Currently you can manually download the database using the following command,
wget -c wget https://portal.nersc.gov/cfs/m342/iphop/db/iPHoP_db_Sept21.tar.gz
and then uncompress and put the content to viroprofiler folder. Please let me know if this helps.
It seems the iphop database is not setup successfully. In the future version, we will add a step to check the completeness of the database. Currently you can manually download the database using the following command,
wget -c wget https://portal.nersc.gov/cfs/m342/iphop/db/iPHoP_db_Sept21.tar.gz
and then uncompress and put the content to viroprofiler folder. Please let me know if this helps.
I am having the one issue with all the database, previous I used the default setup that database will be downloaded to the $HOME/viroprofiler directory, but now I moved all the database to my work directory due to the huge size of iphop. When I rerun the test pipeline, I got error from the assembling step, and I tried to use: nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup" --db /media/server/95d691e7-0d78-417e-b796-a49c36203e5e, but I got error: Command error: mkdir: cannot create directory ‘/media/server/95d691e7-0d78-417e-b796-a49c36203e5e/vibrant’: Read-only file system .
Do you have any suggestion for the configuration.
Are /media/server/95d691e7-0d78-417e-b796-a49c36203e5e
and your HOME directory in the same hard disk or partition? If not, you need to bind this directory to singularity. see an example in the custom.config file, https://github.com/deng-lab/viroprofiler/blob/222364d5b7416c5aab37045de8bcb97dbded282d/custom.config#L5
It was not successful for me by adjusting the bind directory for singularity. Can you possibly elaborate more if you have a different directory on another partition?
Description of the bug
Thanks for this one-pool pipeline for virome analysis. I had the issue when I run the test.
################################################################# nextflow run deng-lab/viroprofiler -r main -profile singularity,test
N E X T F L O W ~ version 22.10.6 NOTE: Your local project version looks outdated - a different revision is available in the remote repository [49aeaa6056] Launching
https://github.com/deng-lab/viroprofiler
[agitated_descartes] DSL2 - revision: 471c32e0ba [v0.2]oooooo oooo o8o 88 88 .o88o. o8o oooo
888. .8'
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8' o888o d888bY8bod8P' // \\ d888b
Y8bod8P' o888o o888o o888o `Y8bod8P' d888b ViroProfiler v0.2Core Nextflow options revision : v0.2 runName : agitated_descartes containerEngine : singularity launchDir : /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/JOSUE/Xichuan28122022 workDir : /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/JOSUE/Xichuan28122022/work projectDir : /home/server/.nextflow/assets/deng-lab/viroprofiler userName : server profile : singularity,test configFiles : /home/server/.nextflow/assets/deng-lab/viroprofiler/nextflow.config
Input/output options mode : all input : https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv db : /home/server/viroprofiler outdir : output
QC contamref_idx : /home/server/viroprofiler/contamination_refs/hg19/ref
Contig library parameters assemblies : scaffolds
Others replicyc : bacphlip use_iphop : true use_dram : true
Institutional config options config_profile_name : Test profile config_profile_description: Minimal test dataset to check pipeline function
Max job request options max_cpus : 2 max_memory : 6.GB max_time : 24.h
!! Only displaying parameters that differ from the pipeline defaults !!
If you use ViroProfiler for your analysis please cite:
The ViroProfiler pipeline https://doi.org/10.1080/19490976.2023.2192522
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
executor > local (76) [dd/cbb924] process > VIROPROFILER:FASTQC (UC32) [100%] 15 of 15 ✔ [46/424649] process > VIROPROFILER:FASTP (UC32) [100%] 15 of 15 ✔ [77/987637] process > VIROPROFILER:SPADES (HT24) [100%] 15 of 15 ✔ [a5/9016af] process > VIROPROFILER:CONTIGLIB [100%] 1 of 1 ✔ [da/308559] process > VIROPROFILER:CHECKV [100%] 1 of 1 ✔ [6e/5495ab] process > VIROPROFILER:CONTIGLIB_CLUSTER [100%] 1 of 1 ✔ [ef/63545a] process > VIROPROFILER:GENEPRED4CTG [100%] 1 of 1 ✔ [b4/0066d8] process > VIROPROFILER:NRPROT [100%] 1 of 1 ✔ [eb/af559c] process > VIROPROFILER:NRGENE [100%] 1 of 1 ✔ [18/b67f48] process > VIROPROFILER:CONTIGINDEX [100%] 1 of 1 ✔ [53/590329] process > VIROPROFILER:MAPPING2CONTIGS2 (HT24) [100%] 15 of 15 ✔ [a4/c915e6] process > VIROPROFILER:ABUNDANCE [100%] 1 of 1 ✔ [fd/927382] process > VIROPROFILER:VIBRANT [100%] 1 of 1 ✔ [d8/46a01a] process > VIROPROFILER:DVF [100%] 1 of 1 ✔ [b1/61de86] process > VIROPROFILER:VIRCONTIGS_PRE [100%] 1 of 1 ✔ [2c/9e0adc] process > VIROPROFILER:VIRSORTER2 [100%] 1 of 1, failed: 1 ✘ [- ] process > VIROPROFILER:DRAMV - [8c/6f1c0b] process > VIROPROFILER:TAXONOMY_VCONTACT [ 0%] 0 of 1 [b6/1c9bb5] process > VIROPROFILER:TAXONOMY_MMSEQS [100%] 1 of 1, failed: 1 ✘ [- ] process > VIROPROFILER:TAXONOMY_MERGE - [5f/ed89c8] process > VIROPROFILER:VIRALHOST_IPHOP [100%] 1 of 1, failed: 1 ✘ [7d/2647ea] process > VIROPROFILER:BACPHLIP [100%] 1 of 1, failed: 1 ✘ [- ] process > VIROPROFILER:RESULTS_TSE - [- ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > VIROPROFILER:MULTIQC - Error executing process > 'VIROPROFILER:TAXONOMY_MMSEQS'
Caused by: Process
VIROPROFILER:TAXONOMY_MMSEQS
terminated with an error exit status (132)Command executed:
Run mmseqs taxonomy
mmseqs createdb putative_vcontigs_pref1.fasta qry mmseqs taxonomy qry /home/server/viroprofiler/taxonomy/mmseqs_vrefseq/refseq_viral mmseqsTaxaRst tmp --tax-lineage 1 --majority 0.4 --vote-mode 1 --lca-mode 3 --
report
mmseqs createtsv qry mmseqsTaxaRst mmseqsTaxaRst.tsv mmseqs taxonomyreport /home/server/viroprofiler/taxonomy/mmseqs_vrefseq/refseq_viral mmseqsTaxaRst mmseqsTaxaRst_report.txt --report-mode 0 mmseqs taxonomyreport /home/server/viroprofiler/taxonomy/mmseqs_vrefseq/refseq_viral mmseqsTaxaRst mmseqsTaxaRst_report.html --report-mode 1
cat <<-END_VERSIONS > versions.yml "VIROPROFILER:TAXONOMY_MMSEQS": MMseqs2: $(grep "MMseqs Version" .command.log | head -n1 | sed 's/.* //g') END_VERSIONS
Command exit status: 132
Command output: (empty)
Command error: .command.sh: line 3: 6861 Illegal instruction (core dumped) mmseqs createdb putative_vcontigs_pref1.fasta qry
Work dir: /media/server/95d691e7-0d78-417e-b796-a49c36203e5e/JOSUE/Xichuan28122022/work/b6/1c9bb5c790e6b80ec842d72276a8ac
Tip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line########################################
Command used and terminal output
Relevant files
No response
System information
Distributor ID: Ubuntu Description: Ubuntu 16.04.7 LTS Release: 16.04 Codename: xenial