Create Database cdhit_cluster.sh

[Nilad]

In your script, you used an outdated version of cdhit (v4.6.6 of 2016). If you have no reason to conserve it please update cdhit_cluster.sh script with the newest version of cdhir and uncomment this line #cluster_cutoff=${cluster_cutoff%.*} #Remove float value to have a valid cutoff ('1.' to '1') and change '-core $threads' in the cdhit call by '-para $threads' (i also specify -blp 4 (for 8 threads) ).

Now i am loking for a dbblast problem...

#Executing cdhit_cluster.sh 

DEPENDENCY                STATUS
----------                ------
cd-hit-est                   INSTALLED 
Default output directory is /MYPATH/plasmidID
filename is plasmids_term.fasta
lundi 22 octobre 2018, 16:20:27 (UTC+0200)
Clustering sequences with identity 100% or higher
Using psi-cd-hit.pl with file /MYPATH/plasmidID/plasmids_term.fasta

DEPENDENCY                STATUS
----------                ------
psi-cd-hit.pl                INSTALLED 
psi-cd-hit.pl -i plasmids_term.fasta -o plasmids_term.fasta_100 -c 1 -G 1 -g 1 -prog blastn -circle 1 -para 8 -blp 4
Name "main::bl_dir" used only once: possible typo at /usr/local/cd-hit-v4.6.7/psi-cd-hit/psi-cd-hit.pl line 103.
BLAST options error: max_file_sz must be < 2 GiB
Can not formatdb at /usr/local/cd-hit-v4.6.7/psi-cd-hit//psi-cd-hit-local.pl line 999.

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ERROR in Script cdhit_cluster.sh on or near line 275; exiting with status 1
MESSAGE:

PSI-CD-HIT command failed. See /MYPATH/plasmidID/logs for more information.

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[saramonzon]

Now