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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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ERROR: Required file detect is missing, exiting #94

Closed semiramisgh closed 2 years ago

semiramisgh commented 3 years ago

when I am going to run my bash script "circtools detect ", I get this error: Required file detect is missing, exiting. The following is my bash code which is the same as the manual. circtools detect @samplesheet -D -B @bam_file_list -R GRCm38_90_repeatmasker.gtf -an Mus_musculus.GRCm38.101.gtf -F -Nr 5 6 -M -fg -G -A Mus_musculus.GRCm38.dna.primary_assembly.fa

@samplesheet is a file name including all the paths for chimeric.out.junction files for multiple samples. @bam_file_list is a file name including all the paths .bam files I also tried without -B flag and some other options but still, I get the same error! I am wondering which file is missing, and why detect module is not working with adding paths directly without using @flag.

Thank you in advance!

tjakobi commented 3 years ago

Dear @semiramisgh,

for some reason circtools seems to try to load a file named detect.

Just to start with the basics, what does circtools detect --version return?