Just wanted to follow up and see if this helped.
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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
Couple of things.
Definitely post in there since Brian is SUPER FAST at replying!
Hope this helps.
Just wanted to follow up and see if this helped.
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