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

Created August 31, 2020 08:14
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nextflow-run-nanoseq-test-docker
Raw
nextflow-run-nanoseq-test-docker.log
$ cat nextflow-run-nanoseq-test-docker.log
N E X T F L O W ~ version 20.07.1
Launching `nf-core/nanoseq` [zen_newton] - revision: b88e1c9a77 [master]
[- ] process > GetTestData -
[- ] process > CheckSampleSheet -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : zen_newton
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)
[23/164397] 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 -
[7f/48ee82] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : zen_newton
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)
[23/164397] 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 -
[7f/48ee82] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.0.0
----------------------------------------------------
Pipeline Release : master
Run Name : zen_newton
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)
[23/164397] process > GetTestData [ 0%] 0 of 1
[b1/9dba2a] 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 -
[7f/48ee82] 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:
Unable to find image 'nfcore/nanoseq:1.0.0' locally
1.0.0: Pulling from nfcore/nanoseq
b8f262c62ec6: Pulling fs layer
0a43c0154f16: Pulling fs layer
906d7b5da8fb: Pulling fs layer
067a79e18102: Pulling fs layer
36fc3626871f: Pulling fs layer
729bc6013bfd: Pulling fs layer
2697eae415b4: Pulling fs layer
36fc3626871f: Waiting
2697eae415b4: Waiting
729bc6013bfd: Waiting
067a79e18102: Waiting
b8f262c62ec6: Verifying Checksum
b8f262c62ec6: Download complete
b8f262c62ec6: Pull complete
067a79e18102: Verifying Checksum
067a79e18102: Download complete
36fc3626871f: Verifying Checksum
36fc3626871f: Download complete
906d7b5da8fb: Verifying Checksum
906d7b5da8fb: Download complete
2697eae415b4: Verifying Checksum
2697eae415b4: Download complete
0a43c0154f16: Download complete
0a43c0154f16: Pull complete
906d7b5da8fb: Pull complete
067a79e18102: Pull complete
36fc3626871f: Pull complete
729bc6013bfd: Verifying Checksum
729bc6013bfd: Download complete
729bc6013bfd: Pull complete
2697eae415b4: Pull complete
Digest: sha256:4beda04d1f9da552f508cc2903539a12a5116e6dad38f9ca1ed5246c8414c72c
Status: Image is up to date for nfcore/nanoseq:1.0.0
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/7f/48ee820291acfcbfa6fc35f1c27139
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
executor > local (3)
[23/164397] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[b1/9dba2a] 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 -
[7f/48ee82] 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:
Unable to find image 'nfcore/nanoseq:1.0.0' locally
1.0.0: Pulling from nfcore/nanoseq
b8f262c62ec6: Pulling fs layer
0a43c0154f16: Pulling fs layer
906d7b5da8fb: Pulling fs layer
067a79e18102: Pulling fs layer
36fc3626871f: Pulling fs layer
729bc6013bfd: Pulling fs layer
2697eae415b4: Pulling fs layer
36fc3626871f: Waiting
2697eae415b4: Waiting
729bc6013bfd: Waiting
067a79e18102: Waiting
b8f262c62ec6: Verifying Checksum
b8f262c62ec6: Download complete
b8f262c62ec6: Pull complete
067a79e18102: Verifying Checksum
067a79e18102: Download complete
36fc3626871f: Verifying Checksum
36fc3626871f: Download complete
906d7b5da8fb: Verifying Checksum
906d7b5da8fb: Download complete
2697eae415b4: Verifying Checksum
2697eae415b4: Download complete
0a43c0154f16: Download complete
0a43c0154f16: Pull complete
906d7b5da8fb: Pull complete
067a79e18102: Pull complete
36fc3626871f: Pull complete
729bc6013bfd: Verifying Checksum
729bc6013bfd: Download complete
729bc6013bfd: Pull complete
2697eae415b4: Pull complete
Digest: sha256:4beda04d1f9da552f508cc2903539a12a5116e6dad38f9ca1ed5246c8414c72c
Status: Image is up to date for nfcore/nanoseq:1.0.0
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/7f/48ee820291acfcbfa6fc35f1c27139
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
executor > local (3)
[23/164397] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[b1/9dba2a] 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 -
[7f/48ee82] 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:
Unable to find image 'nfcore/nanoseq:1.0.0' locally
1.0.0: Pulling from nfcore/nanoseq
b8f262c62ec6: Pulling fs layer
0a43c0154f16: Pulling fs layer
906d7b5da8fb: Pulling fs layer
067a79e18102: Pulling fs layer
36fc3626871f: Pulling fs layer
729bc6013bfd: Pulling fs layer
2697eae415b4: Pulling fs layer
36fc3626871f: Waiting
2697eae415b4: Waiting
729bc6013bfd: Waiting
067a79e18102: Waiting
b8f262c62ec6: Verifying Checksum
b8f262c62ec6: Download complete
b8f262c62ec6: Pull complete
067a79e18102: Verifying Checksum
067a79e18102: Download complete
36fc3626871f: Verifying Checksum
36fc3626871f: Download complete
906d7b5da8fb: Verifying Checksum
906d7b5da8fb: Download complete
2697eae415b4: Verifying Checksum
2697eae415b4: Download complete
0a43c0154f16: Download complete
0a43c0154f16: Pull complete
906d7b5da8fb: Pull complete
067a79e18102: Pull complete
36fc3626871f: Pull complete
729bc6013bfd: Verifying Checksum
729bc6013bfd: Download complete
729bc6013bfd: Pull complete
2697eae415b4: Pull complete
Digest: sha256:4beda04d1f9da552f508cc2903539a12a5116e6dad38f9ca1ed5246c8414c72c
Status: Image is up to date for nfcore/nanoseq:1.0.0
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/7f/48ee820291acfcbfa6fc35f1c27139
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
executor > local (3)
[23/164397] process > GetTestData [100%] 1 of 1, failed: 1 ✘
[b1/9dba2a] 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 -
[7f/48ee82] 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:
Unable to find image 'nfcore/nanoseq:1.0.0' locally
1.0.0: Pulling from nfcore/nanoseq
b8f262c62ec6: Pulling fs layer
0a43c0154f16: Pulling fs layer
906d7b5da8fb: Pulling fs layer
067a79e18102: Pulling fs layer
36fc3626871f: Pulling fs layer
729bc6013bfd: Pulling fs layer
2697eae415b4: Pulling fs layer
36fc3626871f: Waiting
2697eae415b4: Waiting
729bc6013bfd: Waiting
067a79e18102: Waiting
b8f262c62ec6: Verifying Checksum
b8f262c62ec6: Download complete
b8f262c62ec6: Pull complete
067a79e18102: Verifying Checksum
067a79e18102: Download complete
36fc3626871f: Verifying Checksum
36fc3626871f: Download complete
906d7b5da8fb: Verifying Checksum
906d7b5da8fb: Download complete
2697eae415b4: Verifying Checksum
2697eae415b4: Download complete
0a43c0154f16: Download complete
0a43c0154f16: Pull complete
906d7b5da8fb: Pull complete
067a79e18102: Pull complete
36fc3626871f: Pull complete
729bc6013bfd: Verifying Checksum
729bc6013bfd: Download complete
729bc6013bfd: Pull complete
2697eae415b4: Pull complete
Digest: sha256:4beda04d1f9da552f508cc2903539a12a5116e6dad38f9ca1ed5246c8414c72c
Status: Image is up to date for nfcore/nanoseq:1.0.0
/bin/bash: .command.run: Permission denied
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/7f/48ee820291acfcbfa6fc35f1c27139
Tip: view the complete command output by changing to the process work dir and entering the command `ct .command.out`
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