Error: reference file is not indexed

[fabfabBesnard]

Hi, I'm trying ti use MetaSV for the first time. I installed version 0.5.2. I checked that reference.fa and reference.fa.fai are in the same folder with excatly the same name.

I'm trying the following command: run_metasv.py --reference ~/Documents/Post-Doc/Results/SequencingData/Reference_genomes/Celegans/c_elegans.PRJNA13758.WS243.genomic.fa --boost_sc --breakdancer_native breakdancer.out --breakseq_native breakseq.gff --cnvnator_native cnvnator.call --pindel_native pindel_D pindel_LI pindel_SI pindel_TD pindel_INV --sample 516 --bam ~/Bureau/temp_PSMN/Post-doc/N2vs516/NON-MASKED/BAM-516_20X-unM_RG-sorted-dedup-realign_BQSR1.bam --spades ~/softwares/SPAdes-3.13.0-Linux/bin/spades.py --age ~/softwares/AGE-master/age_align --num_threads 1 --workdir ~/Bureau/temp_PSMN/Post-doc/MetaSV/MetaSV_516/work --outdir ~/Bureau/temp_PSMN/Post-doc/MetaSV/MetaSV_516/out --isize_mean 470 --isize_sd 35

In the folder containing my ref file, I do have .fa and .fai (I re-generate it with samtools faidx to be sure) ls -l | grep "c_elegans.PRJNA13758.WS243.genomic.fa" -rwxrwxrwx 1 fabfab fabfab 102292161 mai 19 2014 c_elegans.PRJNA13758.WS243.genomic.fa -rwxrwxrwx 1 fabfab fabfab 14 avril 22 2015 c_elegans.PRJNA13758.WS243.genomic.fa.amb -rwxrwxrwx 1 fabfab fabfab 231 avril 22 2015 c_elegans.PRJNA13758.WS243.genomic.fa.ann -rwxrwxrwx 1 fabfab fabfab 100286508 avril 22 2015 c_elegans.PRJNA13758.WS243.genomic.fa.bwt -rwxrwxrwx 1 fabfab fabfab 181 oct. 18 11:28 c_elegans.PRJNA13758.WS243.genomic.fa.fai -rwxrwxrwx 1 fabfab fabfab 25071602 avril 22 2015 c_elegans.PRJNA13758.WS243.genomic.fa.pac -rwxrwxrwx 1 fabfab fabfab 50143256 avril 22 2015 c_elegans.PRJNA13758.WS243.genomic.fa.sa

Any idea of what I'm doing wrong ?

thanks, Fabrice