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suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data
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PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions #172

Closed deb0612 closed 1 year ago

deb0612 commented 1 year ago

Dear sir, I use command : bash "/biotools/arriba_v2.3.0/run_arriba.sh" "/biotools/arriba_v2.3.0/STAR_index_GRCh38_GENCODE38/" "/biotools/arriba_v2.3.0/GENCODE38.gtf" "/biotools/arriba_v2.3.0/GRCh38.fa" "/biotools/arriba_v2.3.0/database/blacklist_hg38_GRCh38_v2.3.0.tsv.gz" "/biotools/arriba_v2.3.0/database/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz" "/biotools/arriba_v2.3.0/database/protein_domains_hg38_GRCh38_v2.3.0.gff3" 8 rePB223_S101_L002_R1_001.fastq.gz rePB223_S101_L002_R2_001.fastq.gz and show the error message

EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions SOLUTION: re-run with --chimOutType Junctions

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suhrig commented 1 year ago

You need to install a more recent version of STAR. I recommend the most recent version.

deb0612 commented 1 year ago

Thanks, I tried to update my star to the latest version 2.7.10b, and other error occurred! image

suhrig commented 1 year ago

Apparently, the NAS storage on which you are running the script does not support FIFO files. STAR needs to create these files in order to run. Can you launch the script on a file system which supports FIFOs? For example, /tmp usually works.

suhrig commented 1 year ago

Did it work with /tmp?