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CGAT-Group / DICAST

Docker Integrated Comparison of Alternative Splicing (AS) Tools. Benchmarking AS tools and genomic alignment tools.
GNU Lesser General Public License v3.0
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Error when trying to run ASimulator in terminal with run_asimulator.sh #3

Closed NormanRog closed 2 years ago

NormanRog commented 2 years ago

Hi Quirin, I received the following error message when I tried to run ASimulatoR with the run_asimulator.sh script.

finished loading superset

assign variants to supersets... create splicing variants and annotation. This may take a while... finished creating splicing variants and annotation

exporting gtf for read simulation... Error in file(file, ifelse(append, "a", "w")) : cannot open the connection Calls: do.call ... -> export -> export -> .local -> cat -> file In addition: Warning messages: 1: In mclapply(X, FUN, ..., mc.cores = mc.cores, mc.preschedule = mc.preschedule, : scheduled cores 2, 3, 4, 10, 11, 18 did not deliver results, all values of the jobs will be affected 2: In file(file, ifelse(append, "a", "w")) : cannot open file '/output//splicing_variants.gtf': Permission denied Execution halted mv: cannot stat '/mnt/301e9812-51b9-4539-a38f-225aa84a1d0b/DICAST/DICAST/src/ASimulatoR/out/gtf': No such file or directory mv: cannot stat '/mnt/301e9812-51b9-4539-a38f-225aa84a1d0b/DICAST/DICAST/src/ASimulatoR/out/gff3': No such file or directory ls: cannot access '/mnt/301e9812-51b9-4539-a38f-225aa84a1d0b/DICAST/DICAST/src/ASimulatoR/out/*fastq': No such file or directory

quirinmanz commented 2 years ago

Please check this answer in issue #2

amitfenn commented 2 years ago

Thanks Quirin, This works. :)