Error in chr discrepancy when running FusionInspector

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Jomar S

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May 2, 2023, 5:48:54 PM5/2/23
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Hello!

I'm running a pipeline to detect RNA fusions, and one of the tools is STAR Fusion. When running FusionInspector, there seems to be an error relating to chr discrepancies on gtf and/or no gtf annotations found for some genes.

I'm not sure how to solve this issue right now. Could you please enlighten? Thank you!

Using the command:
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/ctat_genome_lib_build_dir/ref_genome.fa --patch /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.fa --max_mate_dist 100000 -G /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.gtf --CPU 12 --out_prefix sample103.star --out_dir /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir --reads "/mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R1.fastq.gz /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R2.fastq.gz" --STAR_xtra_params "--limitSjdbInsertNsj 50000000" Apr 20 08:17:05 ..... started STAR run Apr 20 08:17:06 ..... loading genome Error: Command '/usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/ctat_genome_lib_build_dir/ref_genome.fa --patch /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.fa --max_mate_dist 100000 -G /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.gtf --CPU 12 --out_prefix sample103.star --out_dir /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir --reads "/mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R1.fastq.gz /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R2.fastq.gz" --STAR_xtra_params "--limitSjdbInsertNsj 50000000" ' returned non-zero exit status 2., exit val: 2 Error, command: [ /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/ctat_genome_lib_build_dir/ref_genome.fa --patch /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.fa --max_mate_dist 100000 -G /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.gtf --CPU 12 --out_prefix sample103.star --out_dir /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir --reads "/mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R1.fastq.gz /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R2.fastq.gz" --STAR_xtra_params "--limitSjdbInsertNsj 50000000" ] failed, stack trace: [ st: file:/usr/local/src/STAR-Fusion/FusionInspector/PyLib/Pipeliner.py, lineno:86 st: file:/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector, lineno:788 st: file:/usr/local/src/STAR-Fusion/FusionInspector/FusionInspector, lineno:1942 ]

Output:
Error, chr discrepancy in gtf info for 20 ensembl exon 29297095 29297246 . - . gene_id "5_8S_rRNA^ENSG00000283568"; gene_version "1"; transcript_id "ENST00000637374"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.9-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003799614"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000283568"; orig_coord_info "20,29297095,29297246,-"; Error, chr discrepancy in gtf info for 20 ensembl exon 29741510 29741661 . - . gene_id "5_8S_rRNA^ENSG00000283291"; gene_version "1"; transcript_id "ENST00000638132"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.8-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003794628"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000283291"; orig_coord_info "20,29741510,29741661,-"; Error, chr discrepancy in gtf info for 20 ensembl exon 30484925 30485076 . - . gene_id "5_8S_rRNA^ENSG00000275877"; gene_version "1"; transcript_id "ENST00000614365"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.3-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003742842"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000275877"; orig_coord_info "20,30484925,30485076,-"; Error, chr discrepancy in gtf info for 22 ensembl exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871"; gene_version "1"; transcript_id "ENST00000612732"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.4-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003735240"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000276871"; orig_coord_info "22,11249809,11249959,-"; Error, chr discrepancy in gtf info for 21 ensembl exon 8256781 8256933 . + . gene_id "5_8S_rRNA^ENSG00000277739"; gene_version "1"; transcript_id "ENST00000610460"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.5-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003746458"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000277739"; orig_coord_info "21,8256781,8256933,+"; WARNING, no gtf annotations found for [AC145212.1] WARNING, no gtf annotations found for [AC145212.1] WARNING, no gtf annotations found for [C6ORF47] WARNING, no gtf annotations found for [C3ORF35] WARNING, no gtf annotations found for [MAFIP] WARNING, no gtf annotations found for [MAFIP] WARNING, no gtf annotations found for [MAFIP] WARNING, no gtf annotations found for [TRB@] Error, chr discrepancy in gtf info for 20 ensembl exon 29297095 29297246 . - . gene_id "5_8S_rRNA^ENSG00000283568"; gene_version "1"; transcript_id "ENST00000637374"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.9-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003799614"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000283568"; orig_coord_info "20,29297095,29297246,-"; Error, chr discrepancy in gtf info for 20 ensembl exon 29741510 29741661 . - . gene_id "5_8S_rRNA^ENSG00000283291"; gene_version "1"; transcript_id "ENST00000638132"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.8-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003794628"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000283291"; orig_coord_info "20,29741510,29741661,-"; Error, chr discrepancy in gtf info for 20 ensembl exon 30484925 30485076 . - . gene_id "5_8S_rRNA^ENSG00000275877"; gene_version "1"; transcript_id "ENST00000614365"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.3-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003742842"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000275877"; orig_coord_info "20,30484925,30485076,-"; Error, chr discrepancy in gtf info for 22 ensembl exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871"; gene_version "1"; transcript_id "ENST00000612732"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.4-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003735240"; exon_version "1"; tag "basic";30485076,-"; Error, chr discrepancy in gtf info for 22 ensembl exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871"; gene_version "1"; transcript_id "ENST00000612732"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.4-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003735240"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000276871"; orig_coord_info "22,11249809,11249959,-"; Error, chr discrepancy in gtf info for 21 ensembl exon 8256781 8256933 . + . gene_id "5_8S_rRNA^ENSG00000277739"; gene_version "1"; transcript_id "ENST00000610460"; transcript_version "1"; exon_number "1"; gene_name "5_8S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name "5_8S_rRNA.5-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id "ENSE00003746458"; exon_version "1"; tag "basic"; transcript_support_level "NA"; FI_gene_label "5_8S_rRNA^ENSG00000277739"; orig_coord_info "21,8256781,8256933,+"; WARNING, no gtf annotations found for [AC240274.1] WARNING, no gtf annotations found for [TRB@] Done. -parsing GTF file: /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.gtf * Running CMD: /usr/local/bin/STAR --runThreadN 12 --genomeDir /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47096389155 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R1.fastq.gz /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/sample103.R2.fastq.gz --genomeFastaFiles /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /mnt/beegfs/scratch/tmp_dir/nxf.ZLukqUeVDE/fi_workdir/sample103.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' --limitSjdbInsertNsj 50000000 EXITING because of FATAL ERROR: cannot insert sequence on the fly because of strand GstrandBit problem SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star

Alexander Dobin

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May 2, 2023, 5:53:12 PM5/2/23
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Please post FusionInspector questions on the GitHub:
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