Missing assets

[gui11aume]

Hi @alesssia,

I am trying to run the pipeline on a fresh install but there seems to be some issues with the repository as is (YAMP commit eae0e05). After fixing a typo in nextflow.conf (see this issue), the basic command seems to run, but it crashes because of some missing asset.

$ nextflow run YAMP.nf --reads1 SRR12328886_1.fastq.gz --reads2 SRR12328886_2.fastq.gz --prefix my_sample --outdir output_folder --mode complete --profile base,docker
N E X T F L O W  ~  version 20.10.0
Launching `YAMP.nf` [happy_poincare] - revision: 521633a8a3
---------------------------------------------
YET ANOTHER METAGENOMIC PIPELINE (YAMP) 
---------------------------------------------

Analysis introspection:
Starting time              : Mon Apr 12 12:49:07 EDT 2021
Environment                : 
Pipeline Name              : YAMP
Pipeline Version           : 0.9.5.0
Config Profile             : standard
Resumed                    : false
Nextflow version           : 20.10.0 build 5430 (01-11-2020 15:14 UTC)
Java version               : 11.0.10
Java Virtual Machine       : OpenJDK 64-Bit Server VM(11.0.10+9-Ubuntu-0ubuntu1.20.04)
Operating system           : Linux amd64 v5.8.0-38-generic
User name                  : gfilion
Container Engine           : null
BBmap                      : No container information
FastQC                     : No container information
biobakery                  : No container information
qiime                      : No container information
MultiQC                    : No container information
Running parameters         : 
Reads                      : [SRR12328886_1.fastq.gz, SRR12328886_2.fastq.gz]
Prefix                     : my_sample
Running mode               : complete
Layout                     : Paired-End
Performing de-duplication  : false
Synthetic contaminants     : 
Artefacts                  : /home/gfilion/src/YAMP/assets/data/sequencing_artifacts.fa.gz
Phix174ill                 : /home/gfilion/src/YAMP/assets/data/phix174_ill.ref.fa.gz
Adapters                   : /home/gfilion/src/YAMP/assets/data/adapters.fa
Trimming parameters        : 
Input quality offset       : ASCII+33
Min phred score            : 10
Min length                 : 60
kmer lenght                : 23
Shorter kmer               : 11
Max Hamming distance       : 1
Decontamination parameters : 
Contaminant (pan)genome    : /home/gfilion/src/YAMP/assets/data/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz
Min alignment identity     : 0.95
Max indel length           : 3
Max alignment band         : 0.16
MetaPhlAn parameters       : 
MetaPhlAn database         : /home/gfilion/src/YAMP/assets/data/metaphlan_databases/
Bowtie2 options            : very-sensitive
HUMAnN parameters          : 
Chocophlan database        : /home/gfilion/src/YAMP/assets/data/chocophlan
Uniref database            : /home/gfilion/src/YAMP/assets/data/uniref
Folders                    : 
Output dir                 : output_folder
Working dir                : /home/gfilion/src/YAMP/work
Script dir                 : /home/gfilion/src/YAMP
Lunching dir               : /home/gfilion/src/YAMP

[-        ] process > get_software_versions         -
[-        ] process > dedup                         -
[-        ] process > remove_synthetic_contaminants -
[-        ] process > get_software_versions         [  0%] 0 of 1
[-        ] process > dedup                         -
[-        ] process > remove_synthetic_contaminants [  0%] 0 of 1
[-        ] process > trim                          -
[-        ] process > index_foreign_genome          -
[-        ] process > decontaminate                 -
[-        ] process > quality_assessment            [  0%] 0 of 1
[-        ] process > merge_paired_end_cleaned      -
[-        ] process > profile_taxa                  -
[-        ] process > profile_function              -
[-        ] process > alpha_diversity               -
[-        ] process > log                           -
No such file: /home/gfilion/src/YAMP/assets/data/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz

The file hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz seems to be required and not downloaded.

[gui11aume]

Following up on this issue, I could download the file hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz from the Internet. This time the pipeline crashes with the error message below.

No such file: /home/gfilion/src/YAMP/assets/data/metaphlan_databases

[alesssia]

Hi @gui11aume! Have you downloaded the MetaPhlAn databases? You can find more information on how to download them here: https://github.com/alesssia/YAMP/wiki/Getting-started (Section: External databases and subsection Notes on the MetaPhlAn databases). Let me know if it works!

[gui11aume]

Thanks @alesssia! My bad, I read this part too fast because it was not int he Dependencies section. The instructions for download were clear and that worked without problem. Closing this issue.