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Non-Fatal Error in log, should I worry? #346

Closed rLannes closed 1 year ago

rLannes commented 1 year ago

Hi,

I ran STAR FUSION after having to build a reference. I have some Error In log. I wonder if those Errors only affects a specific transcript or if it makes STAR-FUSION to stop and abort this part of the analyses. I am working on Drosophila Melanogaster. And there is "mod(mdg4)" a very unique transcript that use trans-splicing with RNA transcribed in the other strands (Dorn 2001). I am not really interested in it and don't mind it not being analyzed. But I want to be sure it does not break the analyses...

subset of the log:

[faidx] Failed to fetch sequence in chr4:-121-6039
Error, cmd: samtools faidx /lab/solexa_yamashita/people/Romain/Projets/Jackie/StarFusion/Reference/ctat_genome_lib_build_dir/ref_genome.fa chr4:-121-6039 died with ret 256 at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 453.

Error, strand conflict in gtf info for chr3R    FlyBase CDS 21366291    21366335    .   +   2   gene_id "FBgn0002781"; gene_symbol "mod(mdg4)"; transcript_id "FBtr0084084"; transcript_symbol "mod(mdg4)-RY"; # SO:0000459:gene_with_trans_spliced_transcript FI_gene_label "FBgn0002781"; orig_coord_info "chr3R,21366291,21366335,+";

any help appreciated

brianjohnhaas commented 1 year ago

Hi,

If you find genes that it complains about in the log, then these are genes that will probably just be blind to finding fusions but it shouldn't impact the rest of the analysis. If you find genes in there that you do care about and don't want to ignore, then patching the gtf file would be needed.

best,

~brian

On Thu, Dec 15, 2022 at 2:12 PM rLannes @.***> wrote:

Hi,

I ran STAR FUSION after having to build a reference. I have some Error In log. I wonder if those Errors only affects a specific transcript or if it makes STAR-FUSION to stop and abort this part of the analyses. I am working on Drosophila Melanogaster. And there is "mod(mdg4)" a very unique transcript that use trans-splicing with RNA transcribed in the other strands (Dorn 2001). I am not really interested in it and don't mind it not being analyzed. But I want to be sure it does not break the analyses...

subset of the log:

[faidx] Failed to fetch sequence in chr4:-121-6039 Error, cmd: samtools faidx /lab/solexa_yamashita/people/Romain/Projets/Jackie/StarFusion/Reference/ctat_genome_lib_build_dir/ref_genome.fa chr4:-121-6039 died with ret 256 at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 453.

Error, strand conflict in gtf info for chr3R FlyBase CDS 21366291 21366335 . + 2 gene_id "FBgn0002781"; gene_symbol "mod(mdg4)"; transcript_id "FBtr0084084"; transcript_symbol "mod(mdg4)-RY"; # SO:0000459:gene_with_trans_spliced_transcript FI_gene_label "FBgn0002781"; orig_coord_info "chr3R,21366291,21366335,+";

any help appreciated

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rLannes commented 1 year ago

Perfect, thank you so much!