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junaruga/nextflow-run-nanoseq-test-docker-debug.log

Created August 31, 2020 10:25
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nextflow-run-nanoseq-test-docker-debug
Raw
nextflow-run-nanoseq-test-docker-debug.log
$ cat nextflow-run-nanoseq-test-docker-debug.log
N E X T F L O W ~ version 20.07.1
Launching `nf-core/nanoseq` [angry_yalow] - revision: b88e1c9a77 [master]
[- ] process > GetTestData [ 0%] 0 of 1
[- ] process > CheckSampleSheet -
[- ] process > Guppy -
[- ] process > PycoQC -
[- ] process > NanoPlotSummary -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : angry_yalow
Samplesheet : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/samplesheet_bc_dx.csv
Protocol : cDNA
Stranded : No
Skip Basecalling : No
Skip Demultiplexing: No
Run Dir : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/fast5/barcoded/
Flowcell ID : FLO-MIN106
Kit ID : SQK-DCS109
Barcode Kit ID : EXP-NBD103
Guppy Config File : Unspecified
Guppy Model File : Unspecified
Guppy GPU Mode : No
Guppy GPU Runners : 6
Guppy CPU Threads : 1
Guppy GPU Device : auto
Guppy GPU Options : Unspecified
Aligner : minimap2
Save Intermeds : No
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - nfcore/nanoseq:1.0.0
Output dir : ./results
Launch dir : /home/jaruga/git/nf-core/nanoseq
Working dir : /home/jaruga/git/nf-core/nanoseq/work
Script dir : /home/jaruga/.nextflow/assets/nf-core/nanoseq
User : jaruga
Config Profile : test,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (2)
[5e/b6a6a4] process > GetTestData [ 0%] 0 of 1
[00/4fd003] process > CheckSampleSheet (samplesheet_bc_dx.csv) [ 0%] 0 of 1
[- ] process > Guppy -
[- ] process > PycoQC -
[- ] process > NanoPlotSummary -
[- ] process > NanoPlotFastQ -
[- ] process > FastQC -
[- ] process > GetChromSizes -
[- ] process > GTFToBED -
[- ] process > MiniMap2Index -
[- ] process > MiniMap2Align -
[- ] process > SortBAM -
[- ] process > BAMToBedGraph -
[- ] process > BedGraphToBigWig -
[- ] process > BAMToBed12 -
[- ] process > Bed12ToBigBed -
[- ] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : angry_yalow
Samplesheet : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/samplesheet_bc_dx.csv
Protocol : cDNA
Stranded : No
Skip Basecalling : No
Skip Demultiplexing: No
Run Dir : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/fast5/barcoded/
Flowcell ID : FLO-MIN106
Kit ID : SQK-DCS109
Barcode Kit ID : EXP-NBD103
Guppy Config File : Unspecified
Guppy Model File : Unspecified
Guppy GPU Mode : No
Guppy GPU Runners : 6
Guppy CPU Threads : 1
Guppy GPU Device : auto
Guppy GPU Options : Unspecified
Aligner : minimap2
Save Intermeds : No
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - nfcore/nanoseq:1.0.0
Output dir : ./results
Launch dir : /home/jaruga/git/nf-core/nanoseq
Working dir : /home/jaruga/git/nf-core/nanoseq/work
Script dir : /home/jaruga/.nextflow/assets/nf-core/nanoseq
User : jaruga
Config Profile : test,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (3)
[5e/b6a6a4] process > GetTestData [ 0%] 0 of 1
[00/4fd003] process > CheckSampleSheet (samplesheet_bc_dx.csv) [ 0%] 0 of 1
[- ] process > Guppy -
[- ] process > PycoQC -
[- ] process > NanoPlotSummary -
[- ] process > NanoPlotFastQ -
[- ] process > FastQC -
[- ] process > GetChromSizes -
[- ] process > GTFToBED -
[- ] process > MiniMap2Index -
[- ] process > MiniMap2Align -
[- ] process > SortBAM -
[- ] process > BAMToBedGraph -
[- ] process > BedGraphToBigWig -
[- ] process > BAMToBed12 -
[- ] process > Bed12ToBigBed -
[79/18fb1a] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : angry_yalow
Samplesheet : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/samplesheet_bc_dx.csv
Protocol : cDNA
Stranded : No
Skip Basecalling : No
Skip Demultiplexing: No
Run Dir : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/fast5/barcoded/
Flowcell ID : FLO-MIN106
Kit ID : SQK-DCS109
Barcode Kit ID : EXP-NBD103
Guppy Config File : Unspecified
Guppy Model File : Unspecified
Guppy GPU Mode : No
Guppy GPU Runners : 6
Guppy CPU Threads : 1
Guppy GPU Device : auto
Guppy GPU Options : Unspecified
Aligner : minimap2
Save Intermeds : No
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - nfcore/nanoseq:1.0.0
Output dir : ./results
Launch dir : /home/jaruga/git/nf-core/nanoseq
Working dir : /home/jaruga/git/nf-core/nanoseq/work
Script dir : /home/jaruga/.nextflow/assets/nf-core/nanoseq
User : jaruga
Config Profile : test,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
Error executing process > 'GetTestData'
Caused by:
Process `GetTestData` terminated with an error exit status (126)
Command executed:
git clone https://github.com/nf-core/test-datasets.git --branch nanoseq --single-branch
Command exit status:
126
Command output:
(empty)
Command error:
+ nxf_launch
++ id -u
++ id -g
++ nxf_container_env
++ cat
+ docker run -i --memory 6144m -e NXF_DEBUG=1 -v /home/jaruga:/home/jaruga -v /home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8:/home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8 -w /home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8 --entrypoint /bin/bash -u 1000:1000 --name nxf-VKAUvCi30ASP1Ed89jy58fJm nfcore/nanoseq:1.0.0 -c 'eval export PYTHONNOUSERSITE="1"
export PATH="/home/jaruga/.nextflow/assets/nf-core/nanoseq/bin:$PATH"; /bin/bash .command.run nxf_trace'
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
executor > local (3)
[5e/b6a6a4] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[00/4fd003] process > CheckSampleSheet (samplesheet_bc_dx.csv) [100%] 1 of 1, failed: 1 ✘
[- ] process > Guppy -
[- ] process > PycoQC -
[- ] process > NanoPlotSummary -
[- ] process > NanoPlotFastQ -
[- ] process > FastQC -
[- ] process > GetChromSizes -
[- ] process > GTFToBED -
[- ] process > MiniMap2Index -
[- ] process > MiniMap2Align -
[- ] process > SortBAM -
[- ] process > BAMToBedGraph -
[- ] process > BedGraphToBigWig -
[- ] process > BAMToBed12 -
[- ] process > Bed12ToBigBed -
[79/18fb1a] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : angry_yalow
Samplesheet : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/samplesheet_bc_dx.csv
Protocol : cDNA
Stranded : No
Skip Basecalling : No
Skip Demultiplexing: No
Run Dir : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/fast5/barcoded/
Flowcell ID : FLO-MIN106
Kit ID : SQK-DCS109
Barcode Kit ID : EXP-NBD103
Guppy Config File : Unspecified
Guppy Model File : Unspecified
Guppy GPU Mode : No
Guppy GPU Runners : 6
Guppy CPU Threads : 1
Guppy GPU Device : auto
Guppy GPU Options : Unspecified
Aligner : minimap2
Save Intermeds : No
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - nfcore/nanoseq:1.0.0
Output dir : ./results
Launch dir : /home/jaruga/git/nf-core/nanoseq
Working dir : /home/jaruga/git/nf-core/nanoseq/work
Script dir : /home/jaruga/.nextflow/assets/nf-core/nanoseq
User : jaruga
Config Profile : test,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'GetTestData'
Caused by:
Process `GetTestData` terminated with an error exit status (126)
Command executed:
git clone https://github.com/nf-core/test-datasets.git --branch nanoseq --single-branch
Command exit status:
126
Command output:
(empty)
Command error:
+ nxf_launch
++ id -u
++ id -g
++ nxf_container_env
++ cat
+ docker run -i --memory 6144m -e NXF_DEBUG=1 -v /home/jaruga:/home/jaruga -v /home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8:/home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8 -w /home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8 --entrypoint /bin/bash -u 1000:1000 --name nxf-VKAUvCi30ASP1Ed89jy58fJm nfcore/nanoseq:1.0.0 -c 'eval export PYTHONNOUSERSITE="1"
export PATH="/home/jaruga/.nextflow/assets/nf-core/nanoseq/bin:$PATH"; /bin/bash .command.run nxf_trace'
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
executor > local (3)
[5e/b6a6a4] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[00/4fd003] process > CheckSampleSheet (samplesheet_bc_dx.csv) [100%] 1 of 1, failed: 1 ✘
[- ] process > Guppy -
[- ] process > PycoQC -
[- ] process > NanoPlotSummary -
[- ] process > NanoPlotFastQ -
[- ] process > FastQC -
[- ] process > GetChromSizes -
[- ] process > GTFToBED -
[- ] process > MiniMap2Index -
[- ] process > MiniMap2Align -
[- ] process > SortBAM -
[- ] process > BAMToBedGraph -
[- ] process > BedGraphToBigWig -
[- ] process > BAMToBed12 -
[- ] process > Bed12ToBigBed -
[79/18fb1a] process > output_documentation [100%] 1 of 1, failed: 1 ✘
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : angry_yalow
Samplesheet : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/samplesheet_bc_dx.csv
Protocol : cDNA
Stranded : No
Skip Basecalling : No
Skip Demultiplexing: No
Run Dir : https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/fast5/barcoded/
Flowcell ID : FLO-MIN106
Kit ID : SQK-DCS109
Barcode Kit ID : EXP-NBD103
Guppy Config File : Unspecified
Guppy Model File : Unspecified
Guppy GPU Mode : No
Guppy GPU Runners : 6
Guppy CPU Threads : 1
Guppy GPU Device : auto
Guppy GPU Options : Unspecified
Aligner : minimap2
Save Intermeds : No
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - nfcore/nanoseq:1.0.0
Output dir : ./results
Launch dir : /home/jaruga/git/nf-core/nanoseq
Working dir : /home/jaruga/git/nf-core/nanoseq/work
Script dir : /home/jaruga/.nextflow/assets/nf-core/nanoseq
User : jaruga
Config Profile : test,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'GetTestData'
Caused by:
Process `GetTestData` terminated with an error exit status (126)
Command executed:
git clone https://github.com/nf-core/test-datasets.git --branch nanoseq --single-branch
Command exit status:
126
Command output:
(empty)
Command error:
+ nxf_launch
++ id -u
++ id -g
++ nxf_container_env
++ cat
+ docker run -i --memory 6144m -e NXF_DEBUG=1 -v /home/jaruga:/home/jaruga -v /home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8:/home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8 -w /home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8 --entrypoint /bin/bash -u 1000:1000 --name nxf-VKAUvCi30ASP1Ed89jy58fJm nfcore/nanoseq:1.0.0 -c 'eval export PYTHONNOUSERSITE="1"
export PATH="/home/jaruga/.nextflow/assets/nf-core/nanoseq/bin:$PATH"; /bin/bash .command.run nxf_trace'
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/5e/b6a6a4be85fe31167de575fc0aa2d8
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
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