Hi,
After installation with conda install -c bioconda seroba the ariba database doesn't load with seroba createDBs my_database/ 71 because installed tbb=2021.2.0 is incompatible with bowtie2 (for ariba). After downgrading to tbb=2020.2 there is no bowtie2 issue anymore, but I'm getting another error while trying to load the database (see below and attached), namely the prepare_ref issue related to issue #37 despite PR #38, this also result in segmentation fault (core dumped) issue. Any help would be greatly appreciated.
See also attached log.
False no such file ariba prepareref -f /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/temp_aribaXjuhh_i6n/temp_fasta_ref.fasta -m /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/temp_aribaXjuhh_i6n/temp_meta_ref.tsv --max_noncoding_length 50000 --cdhit_clusters /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/temp_aribaXjuhh_i6n/cdhit_cluster_ref /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/ariba_db/01/ref False
wmiellet
commented
2 years ago
Hi, After installation with
conda install -c bioconda serobathe ariba database doesn't load withseroba createDBs my_database/ 71because installedtbb=2021.2.0is incompatible with bowtie2 (for ariba). After downgrading totbb=2020.2there is no bowtie2 issue anymore, but I'm getting another error while trying to load the database (see below and attached), namely the prepare_ref issue related to issue #37 despite PR #38, this also result in segmentation fault (core dumped) issue. Any help would be greatly appreciated. See also attached log.False no such file ariba prepareref -f /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/temp_aribaXjuhh_i6n/temp_fasta_ref.fasta -m /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/temp_aribaXjuhh_i6n/temp_meta_ref.tsv --max_noncoding_length 50000 --cdhit_clusters /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/temp_aribaXjuhh_i6n/cdhit_cluster_ref /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/ariba_db/01/ref False-ci1 -m1 -t1 -fm /home/wmiellet/anaconda3/envs/env-seroba/bin/kmc -k71 -ci1 -m1 -t1 -fm /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/kmer_db/01/01.fasta /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/kmer_db/01/01 /mnt/c/Users/wille/Documents/Pneumococcus/ngsserotyping/db/kmer_db/01 Segmentation fault (core dumped)seroba_log.txt