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stjude / CICERO

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
https://stjude.github.io/CICERO
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Failure to run CICERO #119

Closed maximus3219 closed 11 months ago

maximus3219 commented 12 months ago

I try running Cicero either locally or using Docker, and it just stuck at "Step 01 - 2023.12.02 17:53:45 - ExtractSClips", without any progression. The bam file is just from a targeted RNA-seq, and running STAR-fusion and Arriba just takes less than 10 minutes. What has gone wrong? Is that it depends on the blat server? Anyway to correct this?

The code: Cicero.sh -b /media/Data/RNA-seq/Bam/08AH9897/Aligned.sortedByCoord.out.bam -r /media/Data/Reference/Cicero/reference -g GRCh38_no_alt -j /media/Data/RNA-seq/Bam/08AH9897/Aligned.sortedByCoord.out.bam.junctions.tab.shifted.tab -O /media/Data/RNA-seq/Bam/08AH9897 -p -n 8

docker: docker run -v $OUTDIR:/input -v $REFDIR:/reference ghcr.io/stjude/cicero:latest -n 8 -b /input/Aligned.sortedByCoord.out.bam -g GRCh38_no_alt -r /reference -j /input/Aligned.sortedByCoord.out.bam.junctions.tab.shifted.tab -o /input/Cicero -s 2 -no-optimize

Thanks.

adthrasher commented 12 months ago

Can you share the output? The Cicero.sh script attempts to start a BLAT server that the downstream steps will then query. Since you see logging output that Step 01 has started, the BLAT server should have already been successfully started. You can also check the running processes (using something like ps and if running with a container docker exec). How long has step 1 been running?