Hi everybody, I am having some problems with fusion detection tools. Some of the most used ones, like STAR-Fusion STAR-SEQR required a CTAT-library, but I have a custom genome which I would like to use for my fusion detection, I follow the instructions found at CTAT repository https://github.com/NCIP/Trinity_CTAT/wiki to build a custom library but I am having some trouble. this is my error log:
> * Running CMD: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile /home/lcj12/ctat/Dfamm.hmm -dfam_outfile
> __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 10 Can't exec "dfamscan.pl": No such file or directory at
> /home/lcj12/ctat/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line
> 175. Error, cmd: dfamscan.pl -fastafile ref_annot.cdsplus.fa -hmmfile /home/lcj12/ctat/Dfamm.hmm -dfam_outfile
> __dfam_ref_annot.cdsplus.fa/dfam.out --masking_thresh --cpu 10 died with ret -1 No such file or directory at
> /home/lcj12/ctat/ctat-genome-lib-builder/util/../lib/Pipeliner.pm line
> 186.
> Pipeliner::run(Pipeliner=HASH(0x7fc2a7eaf920)) called at /home/lcj12/ctat/ctat-genome-lib-builder/util/dfam_repeat_masker.pl
> line 84 Error, cmd:
> /home/lcj12/ctat/ctat-genome-lib-builder/util/dfam_repeat_masker.pl
> --dfam_hmm /home/lcj12/ctat/Dfamm.hmm --target_fa ref_annot.cdsplus.fa --out_masked ref_annot.cdsplus.dfam_masked.fa --CPU 10 died with ret 512 No such file or directory at
> /home/lcj12/ctat/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
> Pipeliner::run(Pipeliner=HASH(0x7f448fbfc9c8)) called at ctat-genome-lib-builder/prep_genome_lib.pl line 451
That was my ctat command line: ctat-genome-lib-builder/prep_genome_lib.pl --genome_fa genome.fna --gtf genannotation.gtf --pfam_db current --dfam_db /home/lcj12/ctat/Dfamm.hmm --CPU 12
In addition to that, I am trying to use arriba, but wiith some errors too:
Loading assembly from 'genome.fna'
ERROR: could not find sequence of contig '10'
That was my Arriba command-line: arriba -c S9Chimeric.out.junction -x S9Aligned.sortedByCoord.out.bam -g genannotation.gtf -a genome.fna -f blacklist -o fusions.tsv -O fusions.discarded.tsv-d S9_sorted.vcf -s auto -V 0.1 -T -P -I
I was wondering if the problem would be with the chromosomes names into my files, or even to stating them with -i options of contig. I tried to change it but with no progress.
Any insight about these errors or another recommendation of detection tool that do not need that ctat lib are welcome!
