Entering edit mode
                    6.0 years ago
        MatthewP
        
    
        ★
    
    1.4k
    My data is WGS not RNA-seq. 
My STAR-Fusion command  
./STAR-Fusion --CPU 10 --genome_lib_dir /hg19/GRCh37_gencode_v19_CTAT_lib_Oct012019.plug-n-play/ctat_genome_lib_build_dir --left_fq /rawdata/1.clean.fq.gz --right_fq /rawdata/2.clean.fq.gz --output_dir /output
--genome_lib_dir file download from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/ 
Rsult files  
$ls
Aligned.out.bam        Log.out              ReadsPerGene.out.tab  star-fusion.fusion_predictions.abridged.tsv  _STARgenome
Chimeric.out.junction  Log.progress.out     SJ.out.tab            star-fusion.fusion_predictions.tsv           _STARpass1
Log.final.out          pipeliner.6993.cmds  _starF_checkpoints    star-fusion.preliminary
*predictions.tsv/*predictions.abridged.tsv is empty, Chimeric.out.junction seems normal(size 2.2G), I will show 3 lines  
1 chr_donorA      brkpt_donorA    strand_donorA   chr_acceptorB   brkpt_acceptorB strand_acceptorB        junction_type   repeat_left_lenA        rep      
1 eat_right_lenB       read_name       start_alnA      cigar_alnA      start_alnB      cigar_alnB      num_chim_aln    max_poss_aln_score      non_ch      
1 im_aln_score      this_chim_aln_score     bestall_chim_aln_score  PEmerged_bool   readgrp
2 chr4    99453489        -       chr10   9844169 +       -1      0       0       CL100124340L1C001R008_555048    99453490        150M    9844170 150      
2 M    3       300     156     294     294     0       GRPundef
3 chr4    128129935       -       chr10   9844169 +       -1      0       0       CL100124340L1C001R008_555048    128129936       58M18357N92M    984      
3 4170 150M    3       300     156     294     294     0       GRPundef
All logs and screen output is normal, no error. Maybe the reason is no result passed filtering
* Running CMD: /App/STAR-Fusion-v1.8.0_FULL/util/filter_likely_RT_artifacts.pl /output/sta
r-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass-filter_likely_RT_artifacts: (pass: 0, filtered: 6)
* Running CMD: /App/STAR-Fusion-v1.8.0_FULL/util/remove_lesser_candidates_at_breakpoint.pl /output/star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass-filter_lesser_candidates_at_breakpoint: (pass: 0, filtered: 0)