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elyadlezmi / RNA2CM

Pipeline for the identification of cancer-related mutations from RNA-seq data
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install problem #6

Open licongge opened 5 months ago

licongge commented 5 months ago

N E X T F L O W ~ version 22.10.4 Launching setup.nf [agitated_newton] DSL1 - revision: 91398e75a8 executor > local (10) [7f/880725] process > downloadHumanGTF [ 50%] 1 of 2, failed: 1, retries: 1 [41/a2c7e3] process > downloadHumanFasta [ 50%] 1 of 2, failed: 1, retries: 1 executor > local (10) [7f/880725] process > downloadHumanGTF [100%] 1 of 1, failed: 1, retries: 1 [41/a2c7e3] process > downloadHumanFasta [100%] 2 of 2, failed: 2, retries: 1 ✘ [59/71dde3] process > downloadMouseGenome [100%] 1 of 1, failed: 1, retries: 1 [34/72fe9c] process > downloadDBSNP [100%] 1 of 1, failed: 1, retries: 1 [- ] process > generateStarIndex - [- ] process > generateStarIndexMouse - [- ] process > indexFasta - [- ] process > createDictionery - [- ] process > createIntervals - [- ] process > indexIntervals - [d8/8e1f4e] process > indexCosmic (1) [100%] 1 of 1, failed: 1, retries: 1 [- ] process > renameDBSNP - [- ] process > renameCosmic - [- ] process > indexRenamedVCFs - [75/844ee3] NOTE: Process downloadHumanFasta terminated with an error exit status (127) -- Execution is retried (1) [dd/a881b2] NOTE: Process downloadHumanGTF terminated with an error exit status (127) -- Execution is retried (1) [70/752401] NOTE: Process downloadMouseGenome terminated with an error exit status (127) -- Execution is retried (1) [55/75c7a1] NOTE: Process downloadDBSNP terminated with an error exit status (127) -- Execution is retried (1) [fb/7d5e7d] NOTE: Process indexCosmic (1) terminated with an error exit status (127) -- Execution is retried (1) Error executing process > 'downloadHumanFasta'

Caused by: Process downloadHumanFasta terminated with an error exit status (127)

Command executed:

wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz gunzip GRCh38.primary_assembly.genome.fa.gz

Command exit status: 127

Command output: (empty)

Command error: docker: Error response from daemon: OCI runtime create failed: container_linux.go:367: starting container process caused: process_linux.go:495: container init caused: process_linux.go:458: setting cgroup config for procHooks process caused: open /sys/fs/cgroup/system.slice/docker-f82df48f5d8fd82da90f54e98c20ea970fd169b3e55c37f414a3c5776c4cf3b7.scope/memory.swap.max: no such file or directory: unknown. time="2024-04-09T09:32:24Z" level=error msg="error waiting for container: context canceled"

Work dir: /data/DATAprocess/licg/software/RNA2CM/work/41/a2c7e3cb3596eda078174ba5bf04ba

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

What should I do to solve it?

licongge commented 4 months ago

Excuse me, have you solved the above problems? I encountered the same error.