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junaruga/nextflow-run-nanoseq-test-podman2.log

Last active November 6, 2020 15:42
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Fedora 32 SELinux disabled
Raw
nextflow-run-nanoseq-test-podman2.log
$ cat /etc/fedora-release
Fedora release 32 (Thirty Two)
$ java -version
openjdk version "1.8.0_252"
OpenJDK Runtime Environment (build 1.8.0_252-b09)
OpenJDK 64-Bit Server VM (build 25.252-b09, mixed mode)
$ 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
$ git clean -fdx
$ podman system prune -a -f
Deleted Pods
Deleted Containers
Deleted Images
docker.io/nfcore/nanoseq:1.1.0
$ podman images
REPOSITORY TAG IMAGE ID CREATED SIZE
<none> <none> 3fbf5fe6450e 2 days ago 222 MB
<none> <none> e9d8ee5059a6 4 days ago 181 MB
<= some images remaining but it's not related to this issue. Maybe.
$ nextflow run nf-core/nanoseq -profile test,podman 2>&1 | tee nextflow-run-nanoseq-test-podman2.log
$ cat nextflow-run-nanoseq-test-podman2.log
N E X T F L O W ~ version 20.07.1
Launching `nf-core/nanoseq` [spontaneous_lamarr] - 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NOTE: Your local project version looks outdated - a different revision is available in the remote repository [ad5b2bb7a3]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 -
[- ] process > Guppy -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : spontaneous_lamarr
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)
[70/b1fb88] 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 -
[d4/f33520] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : spontaneous_lamarr
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)
[70/b1fb88] 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 -
[d4/f33520] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : spontaneous_lamarr
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)
[70/b1fb88] process > GetTestData [ 0%] 0 of 1
[aa/5ad355] 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 -
[d4/f33520] process > output_documentation [ 0%] 0 of 1
[- ] process > get_software_versions -
[- ] process > MultiQC -
executor > local (3)
[70/b1fb88] process > GetTestData [ 0%] 0 of 1
[aa/5ad355] 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 -
[d4/f33520] process > output_documentation [100%] 1 of 1 ✔
[- ] process > get_software_versions -
[- ] process > MultiQC -
executor > local (3)
[70/b1fb88] process > GetTestData [ 0%] 0 of 1
[aa/5ad355] 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 -
[d4/f33520] process > output_documentation [100%] 1 of 1 ✔
[- ] process > get_software_versions -
[- ] process > MultiQC -
Error executing process > 'CheckSampleSheet (samplesheet_bc_dx.csv)'
Caused by:
Process `CheckSampleSheet (samplesheet_bc_dx.csv)` terminated with an error exit status (1)
Command executed:
check_samplesheet.py samplesheet_bc_dx.csv samplesheet_reformat.csv
Command exit status:
1
Command output:
ERROR: Please check samplesheet header -> group,replicate,barcode,input_file,genome,transcriptome != sample,fastq,barcode,genome,transcriptome
Command wrapper:
ERROR: Please check samplesheet header -> group,replicate,barcode,input_file,genome,transcriptome != sample,fastq,barcode,genome,transcriptome
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/aa/5ad355a878baa1667658b761293df8
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
executor > local (3)
[70/b1fb88] process > GetTestData [ 0%] 0 of 1
[aa/5ad355] 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 -
[d4/f33520] process > output_documentation [100%] 1 of 1 ✔
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > MultiQC -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'CheckSampleSheet (samplesheet_bc_dx.csv)'
Caused by:
Process `CheckSampleSheet (samplesheet_bc_dx.csv)` terminated with an error exit status (1)
Command executed:
check_samplesheet.py samplesheet_bc_dx.csv samplesheet_reformat.csv
Command exit status:
1
Command output:
ERROR: Please check samplesheet header -> group,replicate,barcode,input_file,genome,transcriptome != sample,fastq,barcode,genome,transcriptome
Command wrapper:
ERROR: Please check samplesheet header -> group,replicate,barcode,input_file,genome,transcriptome != sample,fastq,barcode,genome,transcriptome
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/aa/5ad355a878baa1667658b761293df8
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
executor > local (3)
[70/b1fb88] process > GetTestData [100%] 1 of 1 ✔
[aa/5ad355] 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 -
[d4/f33520] process > output_documentation [100%] 1 of 1 ✔
[- ] process > get_software_versions [ 0%] 0 of 1
[- ] process > MultiQC -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'CheckSampleSheet (samplesheet_bc_dx.csv)'
Caused by:
Process `CheckSampleSheet (samplesheet_bc_dx.csv)` terminated with an error exit status (1)
Command executed:
check_samplesheet.py samplesheet_bc_dx.csv samplesheet_reformat.csv
Command exit status:
1
Command output:
ERROR: Please check samplesheet header -> group,replicate,barcode,input_file,genome,transcriptome != sample,fastq,barcode,genome,transcriptome
Command wrapper:
ERROR: Please check samplesheet header -> group,replicate,barcode,input_file,genome,transcriptome != sample,fastq,barcode,genome,transcriptome
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/aa/5ad355a878baa1667658b761293df8
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
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