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 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
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: ProcessdownloadHumanFasta
terminated with an error exit status (127) -- Execution is retried (1) [dd/a881b2] NOTE: ProcessdownloadHumanGTF
terminated with an error exit status (127) -- Execution is retried (1) [70/752401] NOTE: ProcessdownloadMouseGenome
terminated with an error exit status (127) -- Execution is retried (1) [55/75c7a1] NOTE: ProcessdownloadDBSNP
terminated with an error exit status (127) -- Execution is retried (1) [fb/7d5e7d] NOTE: ProcessindexCosmic (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 lineWhat should I do to solve it?