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junaruga/gist:a490c33968bb0c7b21bb91d3affd45a9

Created November 6, 2020 14:31
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nextflow-run-nanoseq-test-podman.log
Raw
gistfile1.txt
$ cat /etc/fedora-release
Fedora release 32 (Thirty Two)
$ rpm -qf $(which podman)
podman-1.9.3-1.fc32.x86_64
$ nextflow run nf-core/nanoseq -profile test,podman 2>&1 | tee nextflow-run-nanoseq-test-podman.log
$ cat nextflow-run-nanoseq-test-podman.log
N E X T F L O W ~ version 20.07.1
Launching `nf-core/nanoseq` [nice_joliot] - revision: b88e1c9a77 [master]
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ad5b2bb7a3]
WARN: There's no process matching config selector: GUPPY
WARN: There's no process matching config selector: PYCOQC -- Did you mean: PycoQC?
WARN: There's no process matching config selector: UCSC_BEDGRAPHTOBIGWIG
WARN: There's no process matching config selector: UCSC_BED12TOBIGBED
WARN: There's no process matching config selector: GET_SOFTWARE_VERSIONS
[- ] process > GetTestData -
[- ] process > CheckSampleSheet -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : nice_joliot
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 : podman - nfcore/nanoseq:1.1.0
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,podman
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (1)
[55/5095f2] process > GetTestData [ 0%] 0 of 1
[- ] process > CheckSampleSheet -
[- ] 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 -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : nice_joliot
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 : podman - nfcore/nanoseq:1.1.0
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,podman
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (2)
[55/5095f2] process > GetTestData [ 0%] 0 of 1
[- ] process > CheckSampleSheet -
[- ] 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 -
[84/27f111] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : nice_joliot
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 : podman - nfcore/nanoseq:1.1.0
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,podman
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (2)
[55/5095f2] process > GetTestData [ 0%] 0 of 1
[- ] process > CheckSampleSheet [ 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 -
[84/27f111] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : nice_joliot
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 : podman - nfcore/nanoseq:1.1.0
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,podman
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (3)
[55/5095f2] process > GetTestData [ 0%] 0 of 1
[b6/0b947a] 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 -
[84/27f111] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
executor > local (3)
[55/5095f2] process > GetTestData [ 0%] 0 of 1
[b6/0b947a] 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 -
[84/27f111] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
Error executing process > 'output_documentation'
Caused by:
Process `output_documentation` terminated with an error exit status (126)
Command executed:
markdown_to_html.py output.md -o results_description.html
Command exit status:
126
Command output:
(empty)
Command error:
Trying to pull docker.io/nfcore/nanoseq:1.1.0...
Getting image source signatures
Copying blob sha256:f68e4fbb98684405f26d85827952a832eb3519030cc208f0ed4e92266d1b8b16
Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
Copying blob sha256:5019cfb0a680b922320d12e58ed76f322322992137372cf22d054279611b9696
Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
Copying blob sha256:0dfc925e594668b1ae72a3916ea8b5a1878cf834a3b64efbf1813fc9a8f09111
Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
Copying blob sha256:d62aaefe018042f379b11997e7c4745a7f51d4d859992853fe69c6f327637c97
Copying blob sha256:11b03534eb7b5779ea1619dbc134377ff65951ece643277442d38c053b744d8f
Copying blob sha256:3c724b26a4167f9c1af5e51f8498ca309fb169594c39de00ceec013e3d8bd241
Copying config sha256:8101584944a07eefaf1f6bac56317c7566843c75d0814bceb42042cc4f283fe5
Writing manifest to image destination
Storing signatures
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/84/27f1119b0702ccdb7477b0bbc24b06
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
executor > local (3)
[55/5095f2] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[b6/0b947a] 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 -
[84/27f111] process > output_documentation [100%] 1 of 1, failed: 1 ✘
[- ] process > get_software_versions -
[- ] process > MultiQC -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'output_documentation'
Caused by:
Process `output_documentation` terminated with an error exit status (126)
Command executed:
markdown_to_html.py output.md -o results_description.html
Command exit status:
126
Command output:
(empty)
Command error:
Trying to pull docker.io/nfcore/nanoseq:1.1.0...
Getting image source signatures
Copying blob sha256:f68e4fbb98684405f26d85827952a832eb3519030cc208f0ed4e92266d1b8b16
Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
Copying blob sha256:5019cfb0a680b922320d12e58ed76f322322992137372cf22d054279611b9696
Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
Copying blob sha256:0dfc925e594668b1ae72a3916ea8b5a1878cf834a3b64efbf1813fc9a8f09111
Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
Copying blob sha256:d62aaefe018042f379b11997e7c4745a7f51d4d859992853fe69c6f327637c97
Copying blob sha256:11b03534eb7b5779ea1619dbc134377ff65951ece643277442d38c053b744d8f
Copying blob sha256:3c724b26a4167f9c1af5e51f8498ca309fb169594c39de00ceec013e3d8bd241
Copying config sha256:8101584944a07eefaf1f6bac56317c7566843c75d0814bceb42042cc4f283fe5
Writing manifest to image destination
Storing signatures
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/84/27f1119b0702ccdb7477b0bbc24b06
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
executor > local (3)
[55/5095f2] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[b6/0b947a] 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 -
[84/27f111] process > output_documentation [100%] 1 of 1, failed: 1 ✘
[- ] process > get_software_versions -
[- ] process > MultiQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/nanoseq] Pipeline completed with errors-
Error executing process > 'output_documentation'
Caused by:
Process `output_documentation` terminated with an error exit status (126)
Command executed:
markdown_to_html.py output.md -o results_description.html
Command exit status:
126
Command output:
(empty)
Command error:
Trying to pull docker.io/nfcore/nanoseq:1.1.0...
Getting image source signatures
Copying blob sha256:f68e4fbb98684405f26d85827952a832eb3519030cc208f0ed4e92266d1b8b16
Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
Copying blob sha256:5019cfb0a680b922320d12e58ed76f322322992137372cf22d054279611b9696
Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
Copying blob sha256:0dfc925e594668b1ae72a3916ea8b5a1878cf834a3b64efbf1813fc9a8f09111
Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
Copying blob sha256:d62aaefe018042f379b11997e7c4745a7f51d4d859992853fe69c6f327637c97
Copying blob sha256:11b03534eb7b5779ea1619dbc134377ff65951ece643277442d38c053b744d8f
Copying blob sha256:3c724b26a4167f9c1af5e51f8498ca309fb169594c39de00ceec013e3d8bd241
Copying config sha256:8101584944a07eefaf1f6bac56317c7566843c75d0814bceb42042cc4f283fe5
Writing manifest to image destination
Storing signatures
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/84/27f1119b0702ccdb7477b0bbc24b06
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
executor > local (3)
[55/5095f2] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[b6/0b947a] 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 -
[84/27f111] process > output_documentation [100%] 1 of 1, failed: 1 ✘
[- ] process > get_software_versions -
[- ] process > MultiQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/nanoseq] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'output_documentation'
Caused by:
Process `output_documentation` terminated with an error exit status (126)
Command executed:
markdown_to_html.py output.md -o results_description.html
Command exit status:
126
Command output:
(empty)
Command error:
Trying to pull docker.io/nfcore/nanoseq:1.1.0...
Getting image source signatures
Copying blob sha256:f68e4fbb98684405f26d85827952a832eb3519030cc208f0ed4e92266d1b8b16
Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
Copying blob sha256:5019cfb0a680b922320d12e58ed76f322322992137372cf22d054279611b9696
Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
Copying blob sha256:0dfc925e594668b1ae72a3916ea8b5a1878cf834a3b64efbf1813fc9a8f09111
Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
Copying blob sha256:d62aaefe018042f379b11997e7c4745a7f51d4d859992853fe69c6f327637c97
Copying blob sha256:11b03534eb7b5779ea1619dbc134377ff65951ece643277442d38c053b744d8f
Copying blob sha256:3c724b26a4167f9c1af5e51f8498ca309fb169594c39de00ceec013e3d8bd241
Copying config sha256:8101584944a07eefaf1f6bac56317c7566843c75d0814bceb42042cc4f283fe5
Writing manifest to image destination
Storing signatures
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/84/27f1119b0702ccdb7477b0bbc24b06
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
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