Fusion detection tool error (STAR-fusion, STAR-SEQR,arriba)
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Entering edit mode
2.6 years ago

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!

RNA-Seq fusion detection STAR arriba ctat • 2.1k views
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2.5 years ago
Baoxu • 0

For the Star-fusion, have you downloaded the dfamscan.pl? Make sure the path of dfamscan.pl is in the ENV PATH and have the Executable modeļ¼ˆchmod +X)

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19 months ago
kkatoibaraki ▴ 10

I had the same problem building a reference library for Homo sapiens executed on STAR-fusion version 1.9.1. I downloaded the dfamscan.pl (perl module available in website), saved the dfamscan.pl in / home / usr / miniconda3 / envs / STAR-fusion / bin / and installed blast, dfam and hmmer in the same environment via bioconda. All issues have been resolved.

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