Permission denied error in "Stage filter_transcripts"

[yjx1217]

Hello,

I was running JAFFAL with the provided testing data ONT_fus_sim_85err.fastq but got the permission deny error at the filter_transcript step. Please note that when I direct run the command process_transcriptome_align_table /<working_dir_path>/ONT_fus_sim_85err.fastq/ONT_fus_sim_85err.fastq.paf 1000 /<genome_dir_path>/genome_annotation.tab > /<working_dir_path>/ONT_fus_sim_85err.fastq/ONT_fus_sim_85err.fastq.txt , it works. So I don't understand how has the error occurred.

========================= Stage minimap2_transcriptome (ONT_fus_sim_85err) ========================= [M::mm_idx_gen::12.5651.50] collected minimizers [M::mm_idx_gen::13.4142.08] sorted minimizers [M::main::13.4142.08] loaded/built the index for 251121 target sequence(s) [M::mm_mapopt_update::14.0642.03] mid_occ = 124 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 251121 [M::mm_idx_stat::14.4272.00] distinct minimizers: 20783992 (42.25% are singletons); average occurrences: 3.842; average spacing: 5.398; total length: 431011438 [M::worker_pipeline::22.0716.27] mapped 17531 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: //minimap2 -t 16 -x map-ont -c //genome_annotation.fa //ONT_fus_sim_85err.fastq/ONT_fus_sim_85err.fastq.fasta [M::main] Real time: 22.361 sec; CPU: 138.613 sec; Peak RSS: 3.522 GB

=========================== Stage filter_transcripts (ONT_fus_sim_85err) =========================== bash: line 1: //ONT_fus_sim_85err.fastq/ONT_fus_sim_85err.fastq.paf: Permission denied ERROR: Command failed with exit status = 1 :

$process_transcriptome_align_table //ONT_fus_sim_85err.fastq/ONT_fus_sim_85err.fastq.paf 1000 //genome_annotation.tab > //ONT_fus_sim_85err.fastq/ONT_fus_sim_85err.fastq.txt

Thanks in advance!

Best, Jia-Xing

[yjx1217]

Figured out the reason > forgot to put the path to process_transcriptome_align_table inside thetools.groovy file ...

Problem solved. Close the ticket.