Question: Fusion detection tool error (STAR-fusion, STAR-SEQR,arriba)
3
gravatar for lucas.caue.jacintho
14 months ago by
lucas.caue.jacintho30 wrote:

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!

ADD COMMENTlink modified 3 months ago by kkatoibaraki10 • written 14 months ago by lucas.caue.jacintho30
0
gravatar for Baoxu
13 months ago by
Baoxu0
China/Changchun/Northeast Nomal University
Baoxu0 wrote:

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 mode(chmod +X)

ADD COMMENTlink modified 13 months ago • written 13 months ago by Baoxu0
0
gravatar for kkatoibaraki
3 months ago by
kkatoibaraki10
kkatoibaraki10 wrote:

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.

ADD COMMENTlink written 3 months ago by kkatoibaraki10
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