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Oshlack / JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
https://github.com/Oshlack/JAFFA/wiki
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Crash when no fusions are present #84

Open nrhorner opened 2 years ago

nrhorner commented 2 years ago

Hi,

Using JAFFA v2.2.

I run JAFFAL and get a several fusion transcripts reported as expected. In order to test what happens if no fusion transcripts are identified, I removed the previously found reads and rerun with the following command.

`bpipe run -n 4 -p jaffa_output="$JAFFAOUT/" -p refBase=chr20 -p genome=hg38_chr20 -p annotation=genCode22 -p fastqInputFormat="*.fastq" JAFFAL.groovy nofusion_genes_full_length_reads.fastq

`╒══════════════════════════════════════════════════════════════════════════════════════════════════╕ | Starting Pipeline at 2022-07-26 12:04 | ╘══════════════════════════════════════════════════════════════════════════════════════════════════╛

========================================= Stage run_check ==========================================

====================================== Stage get_fasta (all) =======================================

================================ Stage minimap2_transcriptome (all) ================================

================================== Stage filter_transcripts (all) ==================================

=============================== Stage extract_fusion_sequences (all) ===============================

=================================== Stage minimap2_genome (all) ====================================

================================ Stage make_fasta_reads_table (all) ================================

==================================== Stage get_final_list (all) ====================================

================================ Stage report_3_gene_fusions (all) =================================

==================================== Stage compile_all_results =====================================

options(echo=F) [1] "No fusions were found for the following samples:" [1] "all" Compiling the results from: all Error in file(file, "rt") : cannot open the connection Calls: read.delim -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted ERROR: stage compile_all_results failed: Command in stage compile_all_results failed with exit status = 1 :

Is there a way to prevent this happening? Thanks, Neil