STAR-FUSION error

Question

[mc123]

When I run the CTAT genome preparation lib.

${PATH_STAR_FUSION}/ctat-genome-lib-builder/prep_genome_lib.pl \
        --genome_fa $FASTA \
        --gtf $GTF \
    --dfam_db human \
        --fusion_annot_lib $CTAT_OUT/GRCh38_gencode_v37_CTAT_lib_Mar012021.source.tar.gz

I get the following error:

Error, no seek pos for acc: chr10_GL383545v1_alt at /home///STAR-Fusion/ctat-genome-lib-builder/util/../lib/Fasta_retriever.pm line 71, <$fh> line 49752807.
    Fasta_retriever::get_seq(Fasta_retriever=HASH(0x563a8083f608), "chr10_GL383545v1_alt") called at /home///STAR-Fusion/ctat-genome-lib-builder/util/gtf_file_to_feature_seqs.pl line 97
Error, cmd: /home///STAR-Fusion/ctat-genome-lib-builder/util/gtf_file_to_feature_seqs.pl --gtf_file /home/ref_annot.gtf --genome_fa /home//ref_genome.fa --seqType CDSplus > ref_annot.cdsplus.fa died with ret 65280 No such file or directory at /home///STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm line 186.
    Pipeliner::run(Pipeliner=HASH(0x555787d7c090)) called at /home///STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl line 460

I checked if chr10_GL383545v1_alt was in gtf and fasta file. I removed the entry in the gtf file and I rerun it but I have still the same error. Do you how to solve it?

Thank you in advance

Answer 1

[Yogi]

Couple of things.

• In the future, when posting questions, you may want to include some reference to what the actual tool is. I happen to know STAR-Fusion so I got lucky there.
  • I avoided doing this step and the tool recommends you do the same by downloading the "plug-n-play" archive. Details here: https://groups.google.com/g/star-fusion?pli=1
  • All errors and questions about STAR-Fusion are handled by the author, Brian Haas, through this Google group here. https://groups.google.com/g/star-fusion?pli=1

Definitely post in there since Brian is SUPER FAST at replying!

Hope this helps.

[Yogi]

Just wanted to follow up and see if this helped.