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deng-lab / viroprofiler

A containerized bioinformatics pipeline for viral metagenomic data analysis
https://deng-lab.github.io/viroprofiler
MIT License
23 stars 12 forks source link

Error with samplesheet check #2

Closed dvmbtk closed 1 year ago

dvmbtk commented 1 year ago

Description of the bug

Hello,

We are trying out the pipeline, the setup went ok. One note: the parameters for the "mode" option were not in the tutorial, but we found it when we tried running it.

Currently we are getting the below error at the first step of checking the samplesheet.

The samplesheet is also attached and appears to be the right format but perhaps we missed something.

Any advice is appreciated. Thank you in advance.

Best, Taylan & Nori

Command used and terminal output

(viroprofiler) [user@login01 viroprofiler]$  nextflow run deng-lab/viroprofiler -r v0.1 --input samplesheet.csv --max_cpus 48 -params-file params.yml -profile singularity --mode all
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NOTE: Your local project version looks outdated - a different revision is available in the remote repository [a0bcfcb502]
Launching `https://github.com/deng-lab/viroprofiler` [furious_noyce] DSL2 - revision: 74786572f9 [v0.1]

WARN: Found unexpected parameters:
* --gene_cluster_min_coverage: 0.9
* --gene_cluster_min_similarity: 0.9
* --save_reads_assignment: false
* --save_output_fastqs: false
* --kraken2_clean: true
* --kraken2_db: viral
* --use_decontam: false
* --use_phamb: true
* --use_dram: true
* --use_abricate: true
* --use_eggnog: true
* --use_iphop: true
* --use_kraken2: false
* --input_contigs: false
* --reads_type: clean
- Ignore this warning: params.schema_ignore_params = "gene_cluster_min_coverage,gene_cluster_min_similarity,save_reads_assignment,save_output_fastqs,kraken2_clean,kraken2_db,use_decontam,use_phamb,use_dram,use_abricate,use_eggnog,use_iphop,use_kraken2,input_contigs,reads_type" 

----------------------------------------------------------------------------------------------------------------
                                               __                                                                
 oooooo     oooo  o8o                        88  88                        .o88o.  o8o  oooo                     
  `888.     .8'   `"'                       88 ss 88                       888 `"  `"'  `888                     
   `888.   .8'   oooo  oooo d8b  .ooooo.     88__88    oooo d8b  .ooooo.  o888oo  oooo   888   .ooooo.  oooo d8b 
    `888. .8'    `888  `888""8P d88' `88b      ||      `888""8P d88' `88b  888    `888   888  d88' `88b `888""8P 
     `888.8'      888   888     888   888     _||_      888     888   888  888     888   888  888ooo888  888     
      `888'       888   888     888   888   // || \\    888     888   888  888     888   888  888    .o  888     
       `8'       o888o d888b    `Y8bod8P'  //      \\  d888b    `Y8bod8P' o888o   o888o o888o `Y8bod8P' d888b    
  ViroProfiler v1.0dev
----------------------------------------------------------------------------------------------------------------
Core Nextflow options
  revision             : v0.1
  runName              : furious_noyce
  containerEngine      : singularity
  launchDir            : /home/user/viroprofiler
  workDir              : /home/user/viroprofiler/work
  projectDir           : /home/user/.nextflow/assets/deng-lab/viroprofiler
  userName             : user
  profile              : singularity
  configFiles          : /home/user/.nextflow/assets/deng-lab/viroprofiler/nextflow.config

Input/output options
  mode                 : all
  input                : samplesheet.csv
  db                   : /home/user/data2/db/vpftest
  outdir               : /home/user/viroprofiler/output

Contig library parameters
  assemblies           : scaffolds
  contig_minlen        : 5000

Binning parameters
  binning              : vrhyme
  binning_minlen_contig: 5000
  binning_minlen_bin   : 5000

Viral detection parameters
  virsorter2_groups    : dsDNAphage,NCLDV,RNA,ssDNA,lavidaviridae

Others
  replicyc             : bacphlip

Max job request options
  max_cpus             : 48
  max_memory           : 128.GB
  max_time             : 240.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/10.5281/zenodo.XXXXXXX

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/deng-lab/ViroProfiler/blob/master/CITATIONS.md
----------------------------------------------------------------------------------------------------------------
executor >  local (1)
[53/fb8743] process > VIROPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [  0%] 0 of 1
[-        ] process > VIROPROFILER:FASTQC                                                  -
[-        ] process > VIROPROFILER:FASTP                                                   -
[-        ] process > VIROPROFILER:SPADES                                                  -
[-        ] process > VIROPROFILER:CONTIGLIB                                               -
[-        ] process > VIROPROFILER:CHECKV                                                  -
[-        ] process > VIROPROFILER:CONTIGLIB_CLUSTER                                       -
[-        ] process > VIROPROFILER:GENEPRED4CTG                                            -
[-        ] process > VIROPROFILER:NRPROT                                                  -
[-        ] process > VIROPROFILER:NRGENE                                                  -
executor >  local (1)
[53/fb8743] process > VIROPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:FASTQC                                                  -
[-        ] process > VIROPROFILER:FASTP                                                   -
[-        ] process > VIROPROFILER:SPADES                                                  -
[-        ] process > VIROPROFILER:CONTIGLIB                                               -
[-        ] process > VIROPROFILER:CHECKV                                                  -
[-        ] process > VIROPROFILER:CONTIGLIB_CLUSTER                                       -
[-        ] process > VIROPROFILER:GENEPRED4CTG                                            -
[-        ] process > VIROPROFILER:NRPROT                                                  -
[-        ] process > VIROPROFILER:NRGENE                                                  -
[-        ] process > VIROPROFILER:EMAPPER                                                 -
[-        ] process > VIROPROFILER:MAPPING2CONTIGS                                         -
executor >  local (1)
[53/fb8743] process > VIROPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1, failed: 1 ✘
[-        ] process > VIROPROFILER:FASTQC                                                  -
[-        ] process > VIROPROFILER:FASTP                                                   -
[-        ] process > VIROPROFILER:SPADES                                                  -
[-        ] process > VIROPROFILER:CONTIGLIB                                               -
[-        ] process > VIROPROFILER:CHECKV                                                  -
[-        ] process > VIROPROFILER:CONTIGLIB_CLUSTER                                       -
[-        ] process > VIROPROFILER:GENEPRED4CTG                                            -
[-        ] process > VIROPROFILER:NRPROT                                                  -
[-        ] process > VIROPROFILER:NRGENE                                                  -
[-        ] process > VIROPROFILER:EMAPPER                                                 -
[-        ] process > VIROPROFILER:MAPPING2CONTIGS                                         -
[-        ] process > VIROPROFILER:ABUNDANCE                                               -
[-        ] process > VIROPROFILER:DVF                                                     -
[-        ] process > VIROPROFILER:VIRCONTIGS_PREF1                                        -
[-        ] process > VIROPROFILER:vMAG_VRHYME:VRHYME                                      -
[-        ] process > VIROPROFILER:vMAG_VRHYME:CHECKV4VRHYME                               -
[-        ] process > VIROPROFILER:VIRSORTER2                                              -
[-        ] process > VIROPROFILER:DRAMV                                                   -
[-        ] process > VIROPROFILER:TAXONOMY_VCONTACT                                       -
[-        ] process > VIROPROFILER:TAXONOMY_MMSEQS                                         -
[-        ] process > VIROPROFILER:TAXONOMY_MERGE                                          -
[-        ] process > VIROPROFILER:VIRALHOST_IPHOP                                         -
[-        ] process > VIROPROFILER:BACPHLIP                                                -
[-        ] process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS                             -
[-        ] process > VIROPROFILER:MULTIQC                                                 [  0%] 0 of 1
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
WARN: Access to undefined parameter `decontam` -- Initialise it to a default value eg. `params.decontam = some_value`
Error executing process > 'VIROPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)'

Caused by:
  Process `VIROPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py \
      samplesheet.csv \
      samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "VIROPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  WARNING: Skipping mount /home/user/miniconda3/envs/viroprofiler/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  [CRITICAL] The given sample sheet does not appear to contain a header.
  INFO:    Cleaning up image...

Work dir:
  /home/user/viroprofiler/work/53/fb8743d6315da0b7d868dd3ef9346f

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Relevant files

sample,fastq_1,fastq_2 no131-0_2017,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no131-0_2017_R1_trimmed.fastq.gz,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no131-0_2017_R2_trimmed.fastq.gz no132-0_2017,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no132-0_2017_R1_trimmed.fastq.gz,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no132-0_2017_R2_trimmed.fastq.gz no133-1_2017,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no133-1_2017_R1_trimmed.fastq.gz,/home/user/trimming/fastp/fastp_results/trimmed_seq_files/no133-1_2017_R2_trimmed.fastq.gz

System information

Nextflow version: 22.10.6.5843
Hardware: HPC
Executor: none 
Container engine: singularity
OS: CentOS Linux
Version of nf-core/viroprofiler: v0.1
rujinlong commented 1 year ago

Hi Taylan,

Thanks for the bug report. I will update the tutorial in the next release.

The samplesheet file looks good. Could you run the following command and paste the output here,

cat /home/user/viroprofiler/work/53/fb8743d6315da0b7d868dd3ef9346f/.command.log
dvmbtk commented 1 year ago

Hello,

Here is the output of the above command:

INFO: Converting SIF file to temporary sandbox... WARNING: Skipping mount /home/user/miniconda3/envs/viroprofiler/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [CRITICAL] The given sample sheet does not appear to contain a header. INFO: Cleaning up image...

Best, Taylan

B. Taylan KOÇ, DVM, MSc, PhD Adnan Menderes University Faculty of Veterinary Medicine Department of Virology 09016 Isikli-Aydin/TURKEY Tel. +90 256 247 07 00 / 6204 Mail: @. @.>, @.***

On Wed, Apr 12, 2023 at 7:45 PM Jinlong Ru @.***> wrote:

Hi Taylan,

Thanks for the bug report. I will update the tutorial in the next release.

The samplesheet file looks good. Could you run the following command and paste the output here,

cat /home/user/viroprofiler/work/53/fb8743d6315da0b7d868dd3ef9346f/.command.log

— Reply to this email directly, view it on GitHub https://github.com/deng-lab/viroprofiler/issues/2#issuecomment-1505687239, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5VR67WP7IZG5E3UZJ53C7TXA3S35ANCNFSM6AAAAAAW3W65NU . You are receiving this because you authored the thread.Message ID: @.***>

-- Aydın Adnan Menderes Üniversitesi GIZLILIK NOTU: Bu mesaj ve ekleri yalnizca gönderildigi kisi(lere) ozeldir ve gizlidir. Mesaj sizin adiniza degilse, içerigini ve varsa ekindeki dosyalari kimseye göndermeyiniz ya da kopyalamayiniz. Bu mesajin herhangi bir sekilde açiklanmasi, kullanilmasi, kopyalanmasi, yayilmasi veya mesaj içerigi ile ilgili olarak herhangi bir islem yapilmasi kesinlikle yasaktir. Böyle bir durumda lütfen göndereni uyarip, mesaji siliniz. Aydın Adnan Menderes Üniversitesi bu mesajin içerigi ve ekleri ile ilgili olarak hiçbir hukuksal sorumlulugu kabul etmez.

rujinlong commented 1 year ago

I guess the error is caused by singularity. Did you install singularity using root or conda? What is the version and path of installed singularity?

dvmbtk commented 1 year ago

Hello, I installed using conda. Version 3.8.6.

B. Taylan KOÇ, DVM, MSc, PhD Adnan Menderes University Faculty of Veterinary Medicine Department of Virology 09016 Isikli-Aydin/TURKEY Tel. +90 256 247 07 00 / 6204 Mail: @. @.>, @.***

On Fri, Apr 14, 2023 at 1:15 PM Jinlong Ru @.***> wrote:

I guess the error is caused by singularity. Did you install singularity using root or conda? What is the version and path of installed singularity?

— Reply to this email directly, view it on GitHub https://github.com/deng-lab/viroprofiler/issues/2#issuecomment-1508351591, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5VR67RTFBPECVAYUUBW443XBEWTPANCNFSM6AAAAAAW3W65NU . You are receiving this because you authored the thread.Message ID: @.***>

-- Aydın Adnan Menderes Üniversitesi GIZLILIK NOTU: Bu mesaj ve ekleri yalnizca gönderildigi kisi(lere) ozeldir ve gizlidir. Mesaj sizin adiniza degilse, içerigini ve varsa ekindeki dosyalari kimseye göndermeyiniz ya da kopyalamayiniz. Bu mesajin herhangi bir sekilde açiklanmasi, kullanilmasi, kopyalanmasi, yayilmasi veya mesaj içerigi ile ilgili olarak herhangi bir islem yapilmasi kesinlikle yasaktir. Böyle bir durumda lütfen göndereni uyarip, mesaji siliniz. Aydın Adnan Menderes Üniversitesi bu mesajin içerigi ve ekleri ile ilgili olarak hiçbir hukuksal sorumlulugu kabul etmez.

rujinlong commented 1 year ago

Do you have any other container platform installed on your HPC using root? For example, charliecloud. or ask your sys-admin to install singularity using root?

dvmbtk commented 1 year ago

As far as I know, no other container, including charliecloud, was installed but I am not sure. As you said, I will ask our admin. If problem persists, I will let you know

B. Taylan KOÇ, DVM, MSc, PhD Adnan Menderes University Faculty of Veterinary Medicine Department of Virology 09016 Isikli-Aydin/TURKEY Tel. +90 256 247 07 00 / 6204 Mail: @. @.>, @.***

On Fri, Apr 14, 2023 at 1:52 PM Jinlong Ru @.***> wrote:

Do you have any other container platform installed on your HPC using root? For example, charliecloud. or ask your sys-admin to install singularity using root?

— Reply to this email directly, view it on GitHub https://github.com/deng-lab/viroprofiler/issues/2#issuecomment-1508389109, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5VR67QKEPTBVLNYELVQALLXBE3BRANCNFSM6AAAAAAW3W65NU . You are receiving this because you authored the thread.Message ID: @.***>

-- Aydın Adnan Menderes Üniversitesi GIZLILIK NOTU: Bu mesaj ve ekleri yalnizca gönderildigi kisi(lere) ozeldir ve gizlidir. Mesaj sizin adiniza degilse, içerigini ve varsa ekindeki dosyalari kimseye göndermeyiniz ya da kopyalamayiniz. Bu mesajin herhangi bir sekilde açiklanmasi, kullanilmasi, kopyalanmasi, yayilmasi veya mesaj içerigi ile ilgili olarak herhangi bir islem yapilmasi kesinlikle yasaktir. Böyle bir durumda lütfen göndereni uyarip, mesaji siliniz. Aydın Adnan Menderes Üniversitesi bu mesajin içerigi ve ekleri ile ilgili olarak hiçbir hukuksal sorumlulugu kabul etmez.