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cpouchon / ORTHOSKIM

ORTHOSKIM allows in silico capture of targeted sequences in genomic or transcriptomic libraries.
GNU General Public License v3.0
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Exonerate executable not found #16

Open o-william-white opened 2 months ago

o-william-white commented 2 months ago

Hello,

I am trying to run the tutorial example provided, and I am hitting an error on the following command: 

/home/oww/software/ORTHOSKIM-v.1.6/orthoskim -m database -t chloroplast -c config_orthoskim.txt

The first error in the log file looks like this: 

Processing ORTHOSKIM

O       o O       o O       o
| O   o | | O   o | | O   o |
| | O R T H O S K I M | O | |
| o   O | | o   O | | o   O |
o       O o       O o       O

INFO: Creation of chloroplast database from annotations for CDS, tRNA and rRNA features
*** extraction of all genes from annotations ***
CMD: /home/oww/software/ORTHOSKIM-v.1.6/src/AnoRef_extraction.py --single -in /home/oww/software/ORTHOSKIM-v.1.6/data/chloroplast_viridiplantae.gb -o /home/oww/test/orthoskim/run_orthoskim/references/unclean -m chloroplast -fmt genbank --codon /home/oww/software/ORTHOSKIM-v.1.6/resources/tRNA_codons.tab
path '/home/oww/test/orthoskim/run_orthoskim/references/unclean' already exists
         Extraction of sequences [.......................                                     ]  39 % *** alignment of CDS into seeds, and extraction of final CDS of reference ***
CMD: /usr/local/bin/exonerate -s 50 -q /home/oww/software/ORTHOSKIM-v.1.6/resources/chloroCDS.seeds -t /home/oww/test/orthoskim/run_orthoskim/references/unclean/chloroplast_CDS/51328_Floydiella_terrestris.fa --showquerygff yes --showtargetgff yes --showvulgar no --showcigar no --showalignment no | awk '!/^Hostname:|^Command line:|^-- completed exonerate analysis|#/ {print $0}' | awk '/Target/ { if (ok) print entry; ok=1;entry=$0;next;}{entry = entry "\n" $0;}/intron\t-/{ok=0;}END{if (ok) print entry;}' > /home/oww/test/orthoskim/run_orthoskim/references/tmp.exonerate
/home/oww/software/ORTHOSKIM-v.1.6/orthoskim: line 612: /usr/local/bin/exonerate: No such file or directory

Based on the error message I am guessing that orthoskim assumes exonerate is located here /usr/local/bin/exonerate, however, the tools.sh file reads as follows: 

#!/bin/bash

SPADES=/home/oww/software/miniconda3/envs/orthoskim_env/bin/spades.py
EXONERATE=/home/oww/software/miniconda3/envs/orthoskim_env/bin/exonerate
BLASTDB=/home/oww/software/miniconda3/envs/orthoskim_env/bin/makeblastdb
BLASTN=/home/oww/software/miniconda3/envs/orthoskim_env/bin/blastn
MAFFT=/home/oww/software/miniconda3/envs/orthoskim_env/bin/mafft
TRIMAL=/home/oww/software/miniconda3/envs/orthoskim_env/bin/trimal
TBLASTN=/home/oww/software/miniconda3/envs/orthoskim_env/bin/tblastn

I have given the path to the tools.sh file in the config as follows: 

# ORTHOSKIM (v.1.6) config file
# Global parameters ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
TOOLS=/home/oww/test/orthoskim/tools.sh                                                                     ## [1] file with dependencies aliases
RES=/home/oww/test/orthoskim/run_orthoskim                                                                  ## [2] working directory for all ORTHOSKIM outputs

Can you spot an obvious mistake I could have made with the analysis, or a possible resolution to the error?

Cheers Ollie