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junaruga/nextflow-run-nanoseq-test-docker3.log

Created November 6, 2020 13:43
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nextflow-run-nanoseq-test-docker3.log
$ cat /etc/fedora-release
Fedora release 32 (Thirty Two)
$ nextflow -version
N E X T F L O W
version 20.07.1 build 5412
created 24-07-2020 15:18 UTC (17:18 CEST)
cite doi:10.1038/nbt.3820
http://nextflow.io
$ nextflow run nf-core/nanoseq -profile test,docker 2>&1 | tee nextflow-run-nanoseq-test-docker3.log
$ cat nextflow-run-nanoseq-test-docker3.log
N E X T F L O W ~ version 20.07.1
Launching `nf-core/nanoseq` [marvelous_darwin] - 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NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ad5b2bb7a3]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 : marvelous_darwin
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:1.1.0
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,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (1)
[6c/c0d730] 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 -
[- ] process > output_documentation -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : marvelous_darwin
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:1.1.0
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,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (2)
[6c/c0d730] 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 -
[80/c1ad27] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : marvelous_darwin
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:1.1.0
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,docker
Config Description : Minimal test dataset to check pipeline function
----------------------------------------------------
executor > local (3)
[6c/c0d730] process > GetTestData [ 0%] 0 of 1
[f1/c2296c] 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 -
[80/c1ad27] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
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:
Unable to find image 'nfcore/nanoseq:1.1.0' locally
1.1.0: Pulling from nfcore/nanoseq
68ced04f60ab: Pulling fs layer
9c388eb6d33c: Pulling fs layer
96cf53b3a9dd: Pulling fs layer
5019cfb0a680: Pulling fs layer
f68e4fbb9868: Pulling fs layer
0dfc925e5946: Pulling fs layer
d62aaefe0180: Pulling fs layer
11b03534eb7b: Pulling fs layer
3c724b26a416: Pulling fs layer
0dfc925e5946: Waiting
5019cfb0a680: Waiting
d62aaefe0180: Waiting
f68e4fbb9868: Waiting
11b03534eb7b: Waiting
3c724b26a416: Waiting
68ced04f60ab: Download complete
68ced04f60ab: Pull complete
5019cfb0a680: Verifying Checksum
5019cfb0a680: Download complete
f68e4fbb9868: Download complete
96cf53b3a9dd: Verifying Checksum
96cf53b3a9dd: Download complete
d62aaefe0180: Download complete
11b03534eb7b: Verifying Checksum
11b03534eb7b: Download complete
3c724b26a416: Verifying Checksum
3c724b26a416: Download complete
9c388eb6d33c: Verifying Checksum
9c388eb6d33c: Download complete
9c388eb6d33c: Pull complete
96cf53b3a9dd: Pull complete
5019cfb0a680: Pull complete
f68e4fbb9868: Pull complete
0dfc925e5946: Verifying Checksum
0dfc925e5946: Download complete
0dfc925e5946: Pull complete
d62aaefe0180: Pull complete
11b03534eb7b: Pull complete
3c724b26a416: Pull complete
Digest: sha256:787cb5b87d7f887cbbe992b804c16cb2e64902753e778bbcc4a1b20d34925506
Status: Image is up to date for nfcore/nanoseq:1.1.0
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/6c/c0d730e2afcf5d44e61a20a2b9821b
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
executor > local (3)
[6c/c0d730] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[f1/c2296c] 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 -
[80/c1ad27] process > output_documentation [100%] 1 of 1, failed: 1 ✘
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > MultiQC -
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:
Unable to find image 'nfcore/nanoseq:1.1.0' locally
1.1.0: Pulling from nfcore/nanoseq
68ced04f60ab: Pulling fs layer
9c388eb6d33c: Pulling fs layer
96cf53b3a9dd: Pulling fs layer
5019cfb0a680: Pulling fs layer
f68e4fbb9868: Pulling fs layer
0dfc925e5946: Pulling fs layer
d62aaefe0180: Pulling fs layer
11b03534eb7b: Pulling fs layer
3c724b26a416: Pulling fs layer
0dfc925e5946: Waiting
5019cfb0a680: Waiting
d62aaefe0180: Waiting
f68e4fbb9868: Waiting
11b03534eb7b: Waiting
3c724b26a416: Waiting
68ced04f60ab: Download complete
68ced04f60ab: Pull complete
5019cfb0a680: Verifying Checksum
5019cfb0a680: Download complete
f68e4fbb9868: Download complete
96cf53b3a9dd: Verifying Checksum
96cf53b3a9dd: Download complete
d62aaefe0180: Download complete
11b03534eb7b: Verifying Checksum
11b03534eb7b: Download complete
3c724b26a416: Verifying Checksum
3c724b26a416: Download complete
9c388eb6d33c: Verifying Checksum
9c388eb6d33c: Download complete
9c388eb6d33c: Pull complete
96cf53b3a9dd: Pull complete
5019cfb0a680: Pull complete
f68e4fbb9868: Pull complete
0dfc925e5946: Verifying Checksum
0dfc925e5946: Download complete
0dfc925e5946: Pull complete
d62aaefe0180: Pull complete
11b03534eb7b: Pull complete
3c724b26a416: Pull complete
Digest: sha256:787cb5b87d7f887cbbe992b804c16cb2e64902753e778bbcc4a1b20d34925506
Status: Image is up to date for nfcore/nanoseq:1.1.0
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/6c/c0d730e2afcf5d44e61a20a2b9821b
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
executor > local (3)
[6c/c0d730] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[f1/c2296c] 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 -
[80/c1ad27] process > output_documentation [100%] 1 of 1, failed: 1 ✘
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > MultiQC -
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:
Unable to find image 'nfcore/nanoseq:1.1.0' locally
1.1.0: Pulling from nfcore/nanoseq
68ced04f60ab: Pulling fs layer
9c388eb6d33c: Pulling fs layer
96cf53b3a9dd: Pulling fs layer
5019cfb0a680: Pulling fs layer
f68e4fbb9868: Pulling fs layer
0dfc925e5946: Pulling fs layer
d62aaefe0180: Pulling fs layer
11b03534eb7b: Pulling fs layer
3c724b26a416: Pulling fs layer
0dfc925e5946: Waiting
5019cfb0a680: Waiting
d62aaefe0180: Waiting
f68e4fbb9868: Waiting
11b03534eb7b: Waiting
3c724b26a416: Waiting
68ced04f60ab: Download complete
68ced04f60ab: Pull complete
5019cfb0a680: Verifying Checksum
5019cfb0a680: Download complete
f68e4fbb9868: Download complete
96cf53b3a9dd: Verifying Checksum
96cf53b3a9dd: Download complete
d62aaefe0180: Download complete
11b03534eb7b: Verifying Checksum
11b03534eb7b: Download complete
3c724b26a416: Verifying Checksum
3c724b26a416: Download complete
9c388eb6d33c: Verifying Checksum
9c388eb6d33c: Download complete
9c388eb6d33c: Pull complete
96cf53b3a9dd: Pull complete
5019cfb0a680: Pull complete
f68e4fbb9868: Pull complete
0dfc925e5946: Verifying Checksum
0dfc925e5946: Download complete
0dfc925e5946: Pull complete
d62aaefe0180: Pull complete
11b03534eb7b: Pull complete
3c724b26a416: Pull complete
Digest: sha256:787cb5b87d7f887cbbe992b804c16cb2e64902753e778bbcc4a1b20d34925506
Status: Image is up to date for nfcore/nanoseq:1.1.0
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/6c/c0d730e2afcf5d44e61a20a2b9821b
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
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