Running index_default_ssu_rrna_db.py before building should raise an error

When running index_default_ssu_rrna_db.py before building MATAM, SortMeRNA indexdb_rna executable is not found but indexing script terminates with no error...

$ ./index_default_ssu_rrna_db.py

2017-01-30 11:26:01,604 - INFO - -- Get compressed archive -- 2017-01-30 11:26:01,604 - DEBUG - PWD: /home/pericard/matam 2017-01-30 11:26:01,604 - DEBUG - CMD: mkdir /home/pericard/matam/db; wget http://bioinfo.lifl.fr/matam/SILVA_128_SSURef_NR95.tar.bz2 -O /home/pericard/matam/db/SILVA_128_SSURef_NR95.tar.bz2 mkdir: impossible de créer le répertoire «/home/pericard/matam/db»: Le fichier existe --2017-01-30 11:26:01-- http://bioinfo.lifl.fr/matam/SILVA_128_SSURef_NR95.tar.bz2 Résolution de bioinfo.lifl.fr (bioinfo.lifl.fr)… 193.48.186.71 Connexion à bioinfo.lifl.fr (bioinfo.lifl.fr)|193.48.186.71|:80… connecté. requête HTTP transmise, en attente de la réponse… 200 OK Taille : 140567671 (134M) [application/x-bzip2] Enregistre : «/home/pericard/matam/db/SILVA_128_SSURef_NR95.tar.bz2»

100%[====================================================================================================================================================================================================>] 140 567 671 10,6MB/s ds 12s

2017-01-30 11:26:14 (10,8 MB/s) - «/home/pericard/matam/db/SILVA_128_SSURef_NR95.tar.bz2» enregistré [140567671/140567671]

2017-01-30 11:26:14,032 - INFO - -- Extracting default ref db -- 2017-01-30 11:26:14,032 - DEBUG - PWD: /home/pericard/matam/db 2017-01-30 11:26:14,032 - DEBUG - CMD: tar jxvf SILVA_128_SSURef_NR95.tar.bz2 SILVA_128_SSURef_NR95.clustered.fasta SILVA_128_SSURef_NR95.complete.fasta SILVA_128_SSURef_NR95.complete.taxo.tab

2017-01-30 11:26:58,580 - INFO - -- Indexing default ref db -- 2017-01-30 11:26:58,580 - DEBUG - PWD: /home/pericard/matam/db 2017-01-30 11:26:58,580 - DEBUG - CMD: /home/pericard/matam/scripts/index_ref_db.py -v -i /home/pericard/matam/db/SILVA_128_SSURef_NR95 --max_memory 10000 INFO - Indexing complete ref db /bin/sh: 1: /home/pericard/matam/sortmerna/indexdb_rna: not found

INFO - Indexing clustered ref db /bin/sh: 1: /home/pericard/matam/sortmerna/indexdb_rna: not found

2017-01-30 11:26:58,617 - INFO - -- Completed default SSU rRNA DB indexing -- 2017-01-30 11:26:58,617 - DEBUG - Indexing completed in 57.01 seconds 2017-01-30 11:26:58,617 - INFO - Indexing went well. Default SSU rRNA DB and its indexes can be found in: /home/pericard/matam/db/SILVA_128_SSURef_NR95*

bonsai-team / matam

Running index_default_ssu_rrna_db.py before building should raise an error #14