[External] [Bug] Unable to run pipeline

[ammaraziz]

What is the Bug Related To? Please Provide a Description. 

Place an ❌ in a Box that Best Matches the Bug's Importance:

• 1 - Most severe (a full-break in core function)
• [] 2-4 - Moderate (break for a particular aspect/feature) (how integral is the broken feature?)
• [] 5 - Least severe (non-functional issue, such as inconsitency / error in documentation or administrative in nature) 

Please Complete the Following Information:

• OS: [e.g. iOS]: Ubuntu 22.04.5 LTS
• Run environment (container, cloud service, HPC, platform, etc.): Running on local server with both Docker (Docker version 27.1.2, build d01f264) and Conda/mamba (mamba 1.4.2 conda 23.3.1)

Please Outline Necessary Steps to Replicate Bug :

I am attempting to run Polkapox (great name btw) on TWIST sequenced MPXV viruses. The command I am running is:

nextflow run polkapox/main.nf --indir input/ --outdir output --project_name whoqap --workflow full --kraken_db /path/to/kraken/STANDARD/ -profile docker

Where input contains:

A_S9_L001_R1_001.fastq.gz*
A_S9_L001_R2_001.fastq.gz*
B_S2_L001_R1_001.fastq.gz*
B_S2_L001_R2_001.fastq.gz*

I've also tried with -profile conda. I get errors related to either not finding the program or permissions denied.

Any Additional Context or Information? Has There Been Any Progress Made So Far Towards this Request? Any Concrete Instructions to Resolve the Bug or Helpful Resources to Reference? Screenshots or Logs?

I've attached .nextflow.log. Terminal output:

executor >  local (7)
[d1/164793] process > POLKAPOX_ASSEMBLY:POLKAPOX:CREATE_SAMPLESHEET                                     [100%] 1 of 1 ✔
[af/908c94] process > POLKAPOX_ASSEMBLY:POLKAPOX:INPUT_CHECK:SAMPLESHEET_CHECK (whoqap_samplesheet.csv) [100%] 1 of 1, failed: 1 ✔
[ed/d23dbc] process > POLKAPOX_ASSEMBLY:POLKAPOX:PREPARE_GENOME:BWA_INDEX (MPXV-UK_P2.noN.fasta)        [100%] 1 of 1, failed: 1 ✔
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:READ_FILTER:KRAKEN2                                    -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:READ_FILTER:SEQTK_SUBSEQ                               -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:READ_FILTER:FASTP                                      -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:BWA_MEM                                       -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:SAMTOOLS_FLAGSTAT                             -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:SAMTOOLS_DEPTH                                -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:IVAR_CONSENSUS_BWA                            -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:IVAR_VARIANTS                                 -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:VARIANT_CONVERT                               -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:SUMMARIZE_TSV                                 -
[28/c6b8a3] process > POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:AGGREGATE_TSVS (1)                            [100%] 1 of 1, failed: 1 ✔
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:UNICYCLER                                       -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:GRAPH_RECON                                     -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:BWA_MEM_DENOVO                                  -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:SAMTOOLS_FLAGSTAT_DENOVO                        -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:IVAR_CONSENSUS_POLISH                           -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:PUBLISH_CONTIGS                                 -
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:MUMMER                                          -
[25/3279bf] process > POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:QUAST                                           [100%] 1 of 1, failed: 1 ✔
[ec/98cec7] process > POLKAPOX_ASSEMBLY:POLKAPOX:CUSTOM_DUMPSOFTWAREVERSIONS (1)                        [100%] 1 of 1, failed: 1 ✔
[28/5e3bfd] process > POLKAPOX_ASSEMBLY:POLKAPOX:MULTIQC                                                [100%] 1 of 1, failed: 1 ✔
[-        ] process > POLKAPOX_ASSEMBLY:POLKAPOX:SUMMARIZE_QC                                           -
-[polkapox] Pipeline completed successfully, but with errored process(es) -
[ed/d23dbc] NOTE: Process `POLKAPOX_ASSEMBLY:POLKAPOX:PREPARE_GENOME:BWA_INDEX (MPXV-UK_P2.noN.fasta)` terminated with an error exit status (127) -- Error is ignored
[28/c6b8a3] NOTE: Process `POLKAPOX_ASSEMBLY:POLKAPOX:REFBASED:AGGREGATE_TSVS (1)` terminated with an error exit status (127) -- Error is ignored
[af/908c94] NOTE: Process `POLKAPOX_ASSEMBLY:POLKAPOX:INPUT_CHECK:SAMPLESHEET_CHECK (whoqap_samplesheet.csv)` terminated with an error exit status (127) -- Error is ignored
[25/3279bf] NOTE: Process `POLKAPOX_ASSEMBLY:POLKAPOX:DENOVO:QUAST` terminated with an error exit status (127) -- Error is ignored
[ec/98cec7] NOTE: Process `POLKAPOX_ASSEMBLY:POLKAPOX:CUSTOM_DUMPSOFTWAREVERSIONS (1)` terminated with an error exit status (127) -- Error is ignored
[28/5e3bfd] NOTE: Process `POLKAPOX_ASSEMBLY:POLKAPOX:MULTIQC` terminated with an error exit status (127) -- Error is ignored

Looking at the .command.log for one bwa process:

/raid/VIDRL-USERS/HOME/aaziz/projects/mpox/whoqap_2024/work/ed/d23dbcc0db7724d2452a50d3468ce0/.command.sh: line 4: bwa: command not found

I think I am missing something fairly basic. Any help would be appreciated.

Thanks,

Ammar

[ammaraziz]

One weird issue is that I keep getting access denied on the samplesheet:

java.nio.file.AccessDeniedException: /raid/VIDRL-USERS/HOME/aaziz/projects/mpox/whoqap_2024/work/73/6a6f29385a1e0e81a5cb28a26ddb1a/samplesheet.valid.csv
java.nio.file.AccessDeniedException: /raid/VIDRL-USERS/HOME/aaziz/projects/mpox/whoqap_2024/work/3b/57e2b3069bdecdd6dcb9222578bf50/versions.yml

[kyleoconnell-NIH]

Hi Ammar,

Can you try running the test profile with docker and see what happens? I am wondering if you need chmod on your samplesheet? Also conda isn't working right now, so would recommend Docker.