CTAT_LR Fusion Visualization

[Robert Forsyth]

Hi,

I've been using CTAT_LR fusion and when I get to the visualization step in IGV viewer, the file doesn't seem to make the HTML file correctly. The fusion predicition.tsv file seems to be generated correctly, but the HTML file is mostly blank. Is there anyone who can help me solve this issue to get a properly generated HTML file?

I ran the following command

singularity exec -e -B `pwd` -B /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir \
 ctat_lr_fusion.v0.13.0.simg \
 ctat-LR-fusion \
 -T /lustre1/project/stg_00096/home/rforsyth/stereo_seq/long_reads/UMI-tools/final/LR_white_combined.fastq.gz \
 --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ \
 --vis \
 --CPU 4 \

I have the following errors below from the output of the scripts 

CMD: samtools faidx /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa
* Running CMD: /usr/local/bin/ctat-minimap2/ctat-minimap2 -d /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa.mm2 /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa
[M::mm_idx_gen::4.804*1.40] collected minimizers
[M::mm_idx_gen::6.387*1.79] sorted minimizers
[M::main::7.687*1.65] loaded/built the index for 9801 target sequence(s)
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 9801
[M::mm_idx_stat::7.919*1.63] distinct minimizers: 12968701 (46.89% are singletons); average occurrences: 3.380; average spacing: 5.606; total length: 245729700
[M::main] Version: 2.26-r1175
[M::main] CMD: /usr/local/bin/ctat-minimap2/ctat-minimap2 -d /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa.mm2 /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa
[M::main] Real time: 7.933 sec; CPU: 12.960 sec; Peak RSS: 1.550 GB
* Running CMD: /usr/local/bin/ctat-minimap2/misc/paftools.ctat.js gff2bed /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf.mm2.splice.bed
* Running CMD: bash -c "set -eou pipefail && /usr/local/bin/ctat-minimap2/ctat-minimap2 --sam-hit-only  -ax splice -u b --junc-bed /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf.mm2.splice.bed -t 4 /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa.mm2 /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/chimeric_read_candidates.transcripts.fa | samtools view -Sb -o /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.bam"
[WARNING] [1;31m Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index. [0m
[M::main::0.985*1.00] loaded/built the index for 9801 target sequence(s)
[M::mm_mapopt_update::1.330*1.00] mid_occ = 286
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 9801
[M::mm_idx_stat::1.561*1.00] distinct minimizers: 12968701 (46.89% are singletons); average occurrences: 3.380; average spacing: 5.606; total length: 245729700
[M::worker_pipeline::864.250*3.94] mapped 60773 sequences
[M::main] Version: 2.26-r1175
[M::main] CMD: /usr/local/bin/ctat-minimap2/ctat-minimap2 --sam-hit-only -ax splice -u b --junc-bed /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf.mm2.splice.bed -t 4 /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa.mm2 /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/chimeric_read_candidates.transcripts.fa
[M::main] Real time: 864.281 sec; CPU: 3402.544 sec; Peak RSS: 3.208 GB
* Running CMD: /usr/local/bin/util/SAM_to_gxf.pl --sam /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.bam --format gff3 --allow_non_primary > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.gff3
* Running CMD: /usr/local/bin/util/LR-FI_fusion_align_extractor.pl  --FI_gtf /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf  --LR_gff3 /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.gff3  --output_prefix /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts  --snap_dist 3  >  /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts
* Running CMD: /usr/local/bin/util/incorporate_LR_FFPM.pl --fusions /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv --num_LR_total 3659022 --output_file /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM
* Running CMD: /usr/local/bin/FusionAnnotator/FusionAnnotator --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ --annotate /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot
* Running CMD: cp /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/ctat-LR-fusion.fusion_predictions.preliminary.tsv
* Running CMD: /usr/local/bin/FusionInspector/util/column_exclusions.pl ctat-LR-fusion.fusion_predictions.preliminary.tsv  LR_accessions,JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/ctat-LR-fusion.fusion_predictions.preliminary.abridged.tsv
* Running CMD: /usr/local/bin/FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot --out_prefix /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/
CMD: /usr/local/bin/FusionFilter/util/blast_filter.pl --fusion_preds /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/
CMD: /usr/local/bin/FusionFilter/util/promiscuity_filter.pl --fusion_preds /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_filter  --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/  --max_promiscuity 10  --min_pct_dom_promiscuity 20
CMD: cp /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_filter.post_promisc_filter /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter
* Running CMD: /usr/local/bin/FusionFilter/util/filter_by_annotation_rules.pl --fusions  /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/
-done, see /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter.annot_filter.pass
* Running CMD: /usr/local/bin/util/filter_LR_fusions_by_evidence_abundance.py  --min_num_LR 1  --min_FFPM 0.1  --min_LR_novel_junction_support 2  --min_J 1  --min_sumJS 1  --min_novel_junction_support 1  --fusions_input /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter.annot_filter.pass  --filtered_fusions_output /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter.annot_filter.pass.filt_by_min_reads
* Running CMD: /usr/local/bin/util/filter_low_pct_dom_iso.py  --min_frac_dom_iso 0.05  --fusions_input /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter.annot_filter.pass.filt_by_min_reads  --filtered_fusions_output /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter.annot_filter.pass.filt_by_min_reads.filt_by_min_dom_iso_frac
14:34:12 : INFO : -filter_low_pct_dom_iso.py removed low dom iso frac fusions: 61
14:34:12 : INFO : -filter_low_pct_dom_iso.py RETAINED above min dom iso frac fusions: 3421
* Running CMD: cp /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter.annot_filter.pass.filt_by_min_reads.filt_by_min_dom_iso_frac /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/ctat-LR-fusion.fusion_predictions.tsv
* Running CMD: /usr/local/bin/FusionInspector/util/column_exclusions.pl /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/ctat-LR-fusion.fusion_predictions.tsv  LR_accessions,JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/ctat-LR-fusion.fusion_predictions.abridged.tsv
* Running CMD: ln -sf /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.genome.fa
* Running CMD: ln -sf /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.fa.fai /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.genome.fa.fai
* Running CMD: ln -sf /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.annot.gtf
* Running CMD: /usr/local/bin/FusionInspector/util/gtf_gene_to_bed.pl /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.annot.gtf > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.annot.bed
-parsing GTF file: /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.annot.gtf
* Running CMD: /usr/local/bin/util/LR_sam_fusion_read_extractor.pl --FI_LR_sam  /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.bam  --LR_fusion_report /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.fusion_transcripts.breakpoint_info.tsv.w_LR_FFPM.wAnnot.post_blast_and_promiscuity_filter.annot_filter.pass.filt_by_min_reads.filt_by_min_dom_iso_frac --max_alignments_per_fusion 100 > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.max_per_fusion-100.sam
* Running CMD: samtools view -Sb /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI.mm2.max_per_fusion-100.sam -o /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.LR.bam && samtools sort /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.LR.bam -o /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.LR.sorted.bam && samtools index /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.LR.sorted.bam
* Running CMD: /usr/local/bin/FusionInspector/util/get_pfam_domain_info.pl  --finspector_gtf /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf  --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/  > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.pfam.gff3
* Running CMD: /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.pfam.gff3 > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.pfam.bed
* Running CMD: /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl  --finspector_gtf /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/LR-FI_targets.gtf  --genome_lib_dir /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/  > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.seqsimilar.gff3
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_lend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
Use of uninitialized value $match_rend in join or string at /usr/local/bin/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl line 118.
* Running CMD: /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.seqsimilar.gff3 > /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.seqsimilar.bed
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 247.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 247.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 945.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 945.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 1139.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 1139.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 3691.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 3691.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 3874.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 3874.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 4012.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 4012.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 4225.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 4225.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 5875.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 5875.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 5989.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 5989.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 8525.
Argument "" isn't numeric in subtraction (-) at /usr/local/bin/FusionInspector/util/transcript_gff3_to_bed.pl line 77, <$fh> line 8525.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 856, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in numeric lt (<) at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 862, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1057, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1058, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1070, <$fh> line 8913.
Argument "" isn't numeric in sort at /usr/local/bin/FusionInspector/util/../PerlLib/Gene_obj.pm line 1071, <$fh> line 8913.
* Running CMD: /usr/local/bin/util/create_ctat-LR-fusion_inspector_igvjs.py --fusion_inspector_directory /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir  --json_outfile /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.fusion_inspector_web.json --roi_outfile /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.LR.breakoint.roi.bed --file_prefix ctat-LR-fusion
/usr/local/bin/util/create_ctat-LR-fusion_inspector_igvjs.py:93: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
  logger.warn(f"Missing text conversion for header field: {column_header}")
WARNING:__main__:Missing text conversion for header field: LeftLocalBreakpoint
WARNING:__main__:Missing text conversion for header field: RightLocalBreakpoint
WARNING:__main__:Missing text conversion for header field: LR_FFPM
WARNING:__main__:Missing text conversion for header field: max_LR_FFPM
WARNING:__main__:Missing text conversion for header field: frac_dom_iso
WARNING:__main__:Missing text conversion for header field: above_frac_dom_iso
* Running CMD: cp /usr/local/bin/util/fusion_report_html_template/tracks.json /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/tracks.json
* Running CMD: cd /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep &&  create_report  /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/igv.fusion_inspector_web.json  igv.genome.fa  --type fusion  --track-config /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/tracks.json  --output /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/ctat-LR-fusion.fusion_inspector_web.html


Done. See fusion predictions at: /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/ctat-LR-fusion.fusion_predictions.tsv

[Brian Haas]

Hi Robert,

I wonder if it's an issue with the v44 annotations here.  I'll look into it.  In the meantime, if you try with the v22 annotation lib, does that work ok for you?

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--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Brian Haas]

Hi Robert,

Sorry to hear it's still not working.   I have a test for this that comes with the software. Can you try this?

cd CTAT-LR-fusion/testing

singularity exec -e -B `pwd`:/data -B ${CTAT_GENOME_LIB}:/ctat_genome_lib ctat_lr_fusion.simg ctat-LR-fusion -T /data/transcripts.fa --genome_lib_dir /ctat_genome_lib --min_J 1  --min_sumJS 1 --left_fq reads_1.fq.gz --right_fq reads_2.fq.gz -o ctat_LR_fusion_outdir.singularity --vis

and use the v22 ctat genome library?

best,

Brian

[Robert Forsyth]

Hi,

The output for the testing data seems to generate the HTML file fine. I'm a little confused on what's causing my data to not be properly visualized by CTAT-LR, because the prediction.tsv file is being generated properly. I compared it to the prediction file generated by the example data and it looks to contain the same fields.

best,

-Robert Forsyth

[Brian Haas]

Hi Robert,

Would you be able to tar up and privately share with me the directory: /lustre1/project/stg_00096/home/rforsyth/stereo_seq/CTAT_LR/ctat_LR_fusion_outdir/fusion_intermediates_dir/IGV_prep/
?

I'll aim to look into what the issue is with your data wrt the igv html.

best,

Brian. (bhaas at broadinstitute dot org)

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[Asher Preska Steinberg]

Hi there,

I'm experiencing the same issue. I'm wondering if this was resolved in the end?

Thanks for your time and help.

Best,

Asher

[Brian Haas]

Hi Asher,

This neighbor-overlap related issues should have been resolved in the current release.  Maybe it's a related issue you're experiencing. 

If you have shareable data, it'll make it easier for me to explore it with you. Let's follow it up on a different github issue or thread, though, to keep it manageable.

best,

Brian

To view this discussion visit https://groups.google.com/d/msgid/trinity_ctat_users/0b887dd3-ec95-452b-8589-6496179feb40n%40googlegroups.com.

[Asher Preska Steinberg]

Hi Brian,

Thanks for your help. Sounds good, let me follow-up with you on github now.

Best,

Asher