Erreur Snippy problème chargement version samtools?

IFB Core Cluster
1

Bonjour @team.software,
j'essaye de faire tourner snippy sur des fichiers multiples afin de créer un fichier core génome mais il semble que la version à laquelle snippy se refère fait beuger la ligne de commande.
j'ai beau charger la version 1.9, il ne l'utilise pas .. et ne fait donc pas d'alignement ni d'appel de variant ni d'alignement core ...
Pourriez vous m'aider s'il vous plait ?
voici la sortie pour cette ligne : srun runme.sh
head fichier runme:
#! /bin/bash
#! /bin/zsh
#SBATCH --mem=64G
#SBATCH --cpus-per-task=20

module load samtools/1.9
module load snippy/4.3.3

snippy --outdir 'Mmc10354' --ctgs '/shared/ifbstor1/projects/mbovis_diversity/ADAPT-MYCO/Mmc/Mmc_fa/Mmc_10354.fa' --ref ../../../data/reference/Mmc-13035.fasta --cpus 20

[11:02:34] This is snippy 4.3.3
[11:02:34] Written by Torsten Seemann
[11:02:34] Obtained from GitHub - tseemann/snippy: Rapid haploid variant calling and core genome alignment
[11:02:34] Detected operating system: linux
[11:02:34] Enabling bundled linux tools.
[11:02:34] Found bwa - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bwa
[11:02:34] Found bcftools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bcftools
[11:02:34] Found samtools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/samtools
[11:02:34] Found java - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/java
[11:02:34] Found snpEff - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snpEff
[11:02:34] Found samclip - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/samclip
[11:02:34] Found seqtk - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/seqtk
[11:02:34] Found parallel - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/parallel
[11:02:34] Found freebayes - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/freebayes
[11:02:34] Found freebayes-parallel - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/freebayes-parallel
[11:02:34] Found fasta_generate_regions.py - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/fasta_generate_regions.py
[11:02:34] Found vcfstreamsort - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcfstreamsort
[11:02:34] Found vcfuniq - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcfuniq
[11:02:34] Found vcffirstheader - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcffirstheader
[11:02:34] Found gzip - /usr/bin/gzip
[11:02:35] Found vt - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vt
[11:02:35] Found bedtools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bedtools
[11:02:35] Found snippy-vcf_to_tab - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snippy-vcf_to_tab
[11:02:35] Found snippy-vcf_report - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snippy-vcf_report
[11:02:35] Need samtools --version >= 1.7 but you have 1.11 - please upgrade it.

2

Bonjour Chloe,

L'ordre de chargement des modules a une importance.
En effet, snippy mets à disposition une version de samtools (1.11).

Pouvez-vous essayer avec:

module load snippy/4.3.3
module load samtools/1.9

samtools étant chargé en dernier, les binaires "samtools" (v1.9) seront prioritaires.

3

j'ai essayé dans le script et en ligne de commande sur une seule souche avec les deux modules chargés et j'ai toujours la même erreur... désolée
This is snippy 4.3.3
[11:33:21] Written by Torsten Seemann
[11:33:21] Obtained from GitHub - tseemann/snippy: Rapid haploid variant calling and core genome alignment
[11:33:21] Detected operating system: linux
[11:33:21] Enabling bundled linux tools.
[11:33:21] Found bwa - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bwa
[11:33:21] Found bcftools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bcftools
[11:33:21] Found samtools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/samtools
[11:33:21] Found java - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/java
[11:33:21] Found snpEff - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snpEff
[11:33:21] Found samclip - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/samclip
[11:33:21] Found seqtk - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/seqtk
[11:33:21] Found parallel - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/parallel
[11:33:21] Found freebayes - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/freebayes
[11:33:21] Found freebayes-parallel - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/freebayes-parallel
[11:33:21] Found fasta_generate_regions.py - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/fasta_generate_regions.py
[11:33:21] Found vcfstreamsort - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcfstreamsort
[11:33:21] Found vcfuniq - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcfuniq
[11:33:21] Found vcffirstheader - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcffirstheader
[11:33:21] Found gzip - /usr/bin/gzip
[11:33:21] Found vt - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vt
[11:33:21] Found bedtools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bedtools
[11:33:21] Found snippy-vcf_to_tab - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snippy-vcf_to_tab
[11:33:21] Found snippy-vcf_report - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snippy-vcf_report
[11:33:21] Need samtools --version >= 1.7 but you have 1.11 - please upgrade it.
srun: error: cpu-node-16: task 0: Exited with exit code 2

4

Avez vous déchargé tous les modules (module purge ou déconnexion/reconnexion) avant de les recharger ?

$ module load samtools/1.9
$ module load snippy/4.3.3
$ samtools --version
samtools 1.11
Using htslib 1.11
Copyright (C) 2020 Genome Research Ltd.

$ module purge
$ module load snippy/4.3.3
$ module load samtools/1.9
$ samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.
5

oui c'est toujours pareil. je suis désolée vraiment...
module load snippy/4.3.3
[cambroset@core-login2 Snippy_coreSNP]$ module load samtools/1.9
[cambroset@core-login2 Snippy_coreSNP]$ samtools --version
samtools 1.9
Using htslib 1.9
Copyright (C) 2018 Genome Research Ltd.
[cambroset@core-login2 Snippy_coreSNP]$ srun snippy --ctgs ../Mmc_fa/Mmc_10354.fa --ref ../../../data/reference/Mmc-13035.fasta --outdir 10354 --cpus 4
srun: job 31385679 queued and waiting for resources
srun: job 31385679 has been allocated resources
[12:55:48] This is snippy 4.3.3
[12:55:48] Written by Torsten Seemann
[12:55:48] Obtained from GitHub - tseemann/snippy: Rapid haploid variant calling and core genome alignment
[12:55:48] Detected operating system: linux
[12:55:48] Enabling bundled linux tools.
[12:55:48] Found bwa - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bwa
[12:55:48] Found bcftools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bcftools
[12:55:48] Found samtools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/samtools
[12:55:48] Found java - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/java
[12:55:48] Found snpEff - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snpEff
[12:55:48] Found samclip - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/samclip
[12:55:48] Found seqtk - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/seqtk
[12:55:48] Found parallel - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/parallel
[12:55:48] Found freebayes - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/freebayes
[12:55:48] Found freebayes-parallel - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/freebayes-parallel
[12:55:48] Found fasta_generate_regions.py - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/fasta_generate_regions.py
[12:55:48] Found vcfstreamsort - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcfstreamsort
[12:55:48] Found vcfuniq - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcfuniq
[12:55:48] Found vcffirstheader - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vcffirstheader
[12:55:48] Found gzip - /usr/bin/gzip
[12:55:48] Found vt - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/vt
[12:55:48] Found bedtools - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/bedtools
[12:55:48] Found snippy-vcf_to_tab - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snippy-vcf_to_tab
[12:55:48] Found snippy-vcf_report - /shared/ifbstor1/software/miniconda/envs/snippy-4.3.3/bin/snippy-vcf_report
[12:55:49] Need samtools --version >= 1.7 but you have 1.11 - please upgrade it.
srun: error: cpu-node-20: task 0: Exited with exit code 2

6

En effet, snippy ne prends pas en compte le PATH (alors qu'il devrait le faire). Je pense à un bug.
D'autant que l'erreur "samtools --version >= 1.7 but you have 1.11" n'est pas très logique (1.11 > 1.7).

Du coup, j'ai installé la version 4.6.0 (add snippy/4.6.0 (bioconda) (!989) · Merge requests · Institut Français de Bioinformatique / Cluster / tools · GitLab) pour tester.

module load snippy/4.6.0

Ca a l'air mieux:

$ snippy --check
[15:33:26] This is snippy 4.6.0
[...]
[15:33:28] Checking version: samtools --version is >= 1.7 - ok, have 1.16
[15:33:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.16
[15:33:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6
[15:33:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.1
[15:33:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17
[15:33:31] Dependences look good!

Est-ce que cela vous convient de basculer sur cette version ?

7

ah oui merci beaucoup !
pas de soucis avec cette version
je vais la tester et si pas de problème vous n'aurez pas de retour :wink:
Chloé