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elyadlezmi / RNA2CM

Pipeline for the identification of cancer-related mutations from RNA-seq data
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error exit status (126) while running setup.nf #2

Closed Emberwhirl closed 2 years ago

Emberwhirl commented 2 years ago

Hi. I have encountered error exit status (126) when I run the command as the manual instructed nextflow run setup.nf

The error output is presented below. Any idea how to fix this? Thank you.

N E X T F L O W ~ version 21.04.3 Launching setup.nf [furious_gautier] - revision: d470aac456 executor > local (10) [aa/4fb403] process > downloadHumanGTF [ 50%] 1 of 2, failed: 1, retries: 1 [0f/c1a3db] process > downloadHumanFasta [ 50%] 1 of 2, failed: 1, retries: 1 [9f/8c56d4] process > downloadMouseGenome [ 50%] 1 of 2, failed: 1, retries: 1 [0f/3f1dea] process > downloadDBSNP [ 50%] 1 of 2, failed: 1, retries: 1 [- ] process > generateStarIndex - [- ] process > generateStarIndexMouse - [- ] process > indexFasta - [- ] process > createDictionery - [- ] process > createIntervals - [- ] process > indexIntervals - [f7/b3a6d1] process > indexCosmic (1) [ 50%] 1 of 2, failed: 1, retries: 1 [- ] process > renameDBSNP - [- ] process > renameCosmic - [- ] process > indexRenamedVCFs - [2f/8ead5a] NOTE: Process downloadHumanFasta terminated with an error exit status (126) -- Execution is retried (1) [bc/a59958] NOTE: Process downloadHumanGTF terminated with an error exit status (126) -- Execution is retried (1) [82/a03e7b] NOTE: Process downloadDBSNP terminated with an error exit status (126) -- Execution is retried (1) [be/cc82f8] NOTE: Process downloadMouseGenome terminated with an error exit status (126) -- Execution is retried (1) [c9/fa1456] NOTE: Process indexCosmic (1) terminated with an error exit status (126) -- Execution is retried (1) Error executing process > 'downloadHumanFasta'

executor > local (10) [aa/4fb403] process > downloadHumanGTF [100%] 2 of 2, failed: 2, retries: 1 ✘ [0f/c1a3db] process > downloadHumanFasta [100%] 2 of 2, failed: 2, retries: 1 ✘ [9f/8c56d4] process > downloadMouseGenome [100%] 2 of 2, failed: 2, retries: 1 ✘ [0f/3f1dea] process > downloadDBSNP [100%] 2 of 2, failed: 2, retries: 1 ✘ [- ] process > generateStarIndex - [- ] process > generateStarIndexMouse - [- ] process > indexFasta - [- ] process > createDictionery - [- ] process > createIntervals - [- ] process > indexIntervals - [f7/b3a6d1] process > indexCosmic (1) [100%] 2 of 2, failed: 2, retries: 1 ✘ [- ] process > renameDBSNP - [- ] process > renameCosmic - [- ] process > indexRenamedVCFs - [2f/8ead5a] NOTE: Process downloadHumanFasta terminated with an error exit status (126) -- Execution is retried (1)[bc/a59958] NOTE: Process downloadHumanGTF terminated with an error exit status (126) -- Execution is retried (1)[82/a03e7b] NOTE: Process downloadDBSNP terminated with an error exit status (126) -- Execution is retried (1) [be/cc82f8] NOTE: Process downloadMouseGenome terminated with an error exit status (126) -- Execution is retried (1) [c9/fa1456] NOTE: Process indexCosmic (1) terminated with an error exit status (126) -- Execution is retried (1) Error executing process > 'downloadHumanFasta'

Caused by: Process downloadHumanFasta terminated with an error exit status (126)

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: 126

Command output: (empty)

Command error: docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create?name=nxf-7XvifApzEZGSkkAMjnFOO0l8": dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'.

Work dir: /home/emberwhirl/Software/RNA2CM/work/0f/c1a3db3e43b5470bf028ef5057f8a3

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out