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junaruga/nextflow-run-nanoseq-test-podman5.log

Created November 17, 2020 20:19
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nextflow-run-nanoseq-test-podman5.log
$ cat nextflow-run-nanoseq-test-podman5.log
N E X T F L O W ~ version 20.07.1
Launching `nf-core/nanoseq` [mighty_engelbart] - revision: ad5b2bb7a3 [master]
[- ] process > GET_TEST_DATA -
[- ] process > CHECK_SAMPLESHEET -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : mighty_engelbart
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
Barcode Both Ends : No
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 Profile Description: Minimal test dataset to check pipeline function
Config Files : /home/jaruga/.nextflow/assets/nf-core/nanoseq/nextflow.config, /home/jaruga/git/nf-core/nanoseq/nextflow.config
----------------------------------------------------
executor > local (1)
[c1/55cb35] process > GET_TEST_DATA [ 0%] 0 of 1
[- ] process > CHECK_SAMPLESHEET -
[- ] process > GUPPY -
[- ] process > PYCOQC -
[- ] process > NANOPLOT_SUMMARY -
[- ] process > NANOPLOT_FASTQ -
[- ] process > FASTQC -
[- ] process > GET_CHROM_SIZES -
[- ] process > GTF_TO_BED -
[- ] process > MINIMAP2_INDEX -
[- ] process > MINIMAP2_ALIGN -
[- ] process > SAMTOOLS_SORT -
[- ] process > BEDTOOLS_GENOMECOV -
[- ] process > UCSC_BEDGRAPHTOBIGWIG -
[- ] process > BEDTOOLS_BAMTOBED -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : mighty_engelbart
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
Barcode Both Ends : No
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 Profile Description: Minimal test dataset to check pipeline function
Config Files : /home/jaruga/.nextflow/assets/nf-core/nanoseq/nextflow.config, /home/jaruga/git/nf-core/nanoseq/nextflow.config
----------------------------------------------------
executor > local (2)
[c1/55cb35] process > GET_TEST_DATA [ 0%] 0 of 1
[- ] process > CHECK_SAMPLESHEET -
[- ] process > GUPPY -
[- ] process > PYCOQC -
[- ] process > NANOPLOT_SUMMARY -
[- ] process > NANOPLOT_FASTQ -
[- ] process > FASTQC -
[- ] process > GET_CHROM_SIZES -
[- ] process > GTF_TO_BED -
[- ] process > MINIMAP2_INDEX -
[- ] process > MINIMAP2_ALIGN -
[- ] process > SAMTOOLS_SORT -
[- ] process > BEDTOOLS_GENOMECOV -
[- ] process > UCSC_BEDGRAPHTOBIGWIG -
[- ] process > BEDTOOLS_BAMTOBED -
[- ] process > UCSC_BED12TOBIGBED -
[f0/ad80d2] process > OUTPUT_DOCUMENTATION [ 0%] 0 of 1
[- ] process > GET_SOFTWARE_VERSIONS -
[- ] process > MULTIQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : mighty_engelbart
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
Barcode Both Ends : No
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 Profile Description: Minimal test dataset to check pipeline function
Config Files : /home/jaruga/.nextflow/assets/nf-core/nanoseq/nextflow.config, /home/jaruga/git/nf-core/nanoseq/nextflow.config
----------------------------------------------------
executor > local (2)
[c1/55cb35] process > GET_TEST_DATA [ 0%] 0 of 1
[- ] process > CHECK_SAMPLESHEET [ 0%] 0 of 1
[- ] process > GUPPY -
[- ] process > PYCOQC -
[- ] process > NANOPLOT_SUMMARY -
[- ] process > NANOPLOT_FASTQ -
[- ] process > FASTQC -
[- ] process > GET_CHROM_SIZES -
[- ] process > GTF_TO_BED -
[- ] process > MINIMAP2_INDEX -
[- ] process > MINIMAP2_ALIGN -
[- ] process > SAMTOOLS_SORT -
[- ] process > BEDTOOLS_GENOMECOV -
[- ] process > UCSC_BEDGRAPHTOBIGWIG -
[- ] process > BEDTOOLS_BAMTOBED -
[- ] process > UCSC_BED12TOBIGBED -
[f0/ad80d2] process > OUTPUT_DOCUMENTATION [ 0%] 0 of 1
[- ] process > GET_SOFTWARE_VERSIONS -
[- ] process > MULTIQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : mighty_engelbart
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
Barcode Both Ends : No
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 Profile Description: Minimal test dataset to check pipeline function
Config Files : /home/jaruga/.nextflow/assets/nf-core/nanoseq/nextflow.config, /home/jaruga/git/nf-core/nanoseq/nextflow.config
----------------------------------------------------
Error executing process > 'GET_TEST_DATA'
Caused by:
Process `GET_TEST_DATA` 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:
Error: relabel failed "/home/jaruga": SELinux relabeling of /home/jaruga is not allowed
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/c1/55cb352bc2f37646abd734dcef1915
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)
[c1/55cb35] process > GET_TEST_DATA [100%] 1 of 1, failed: 1 ✘
[a4/ce6d39] process > CHECK_SAMPLESHEET (samplesheet_bc_dx.csv) [ 0%] 0 of 1
[- ] process > GUPPY -
[- ] process > PYCOQC -
[- ] process > NANOPLOT_SUMMARY -
[- ] process > NANOPLOT_FASTQ -
[- ] process > FASTQC -
[- ] process > GET_CHROM_SIZES -
[- ] process > GTF_TO_BED -
[- ] process > MINIMAP2_INDEX -
[- ] process > MINIMAP2_ALIGN -
[- ] process > SAMTOOLS_SORT -
[- ] process > BEDTOOLS_GENOMECOV -
[- ] process > UCSC_BEDGRAPHTOBIGWIG -
[- ] process > BEDTOOLS_BAMTOBED -
[- ] process > UCSC_BED12TOBIGBED -
[f0/ad80d2] process > OUTPUT_DOCUMENTATION [100%] 1 of 1, failed: 1 ✘
[- ] process > GET_SOFTWARE_VERSIONS [ 0%] 0 of 1
[- ] process > MULTIQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : mighty_engelbart
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
Barcode Both Ends : No
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 Profile Description: Minimal test dataset to check pipeline function
Config Files : /home/jaruga/.nextflow/assets/nf-core/nanoseq/nextflow.config, /home/jaruga/git/nf-core/nanoseq/nextflow.config
----------------------------------------------------
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'GET_TEST_DATA'
Caused by:
Process `GET_TEST_DATA` 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:
Error: relabel failed "/home/jaruga": SELinux relabeling of /home/jaruga is not allowed
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/c1/55cb352bc2f37646abd734dcef1915
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)
[c1/55cb35] process > GET_TEST_DATA [100%] 1 of 1, failed: 1 ✘
[a4/ce6d39] process > CHECK_SAMPLESHEET (samplesheet_bc_dx.csv) [100%] 1 of 1, failed: 1 ✘
[- ] process > GUPPY -
[- ] process > PYCOQC -
[- ] process > NANOPLOT_SUMMARY -
[- ] process > NANOPLOT_FASTQ -
[- ] process > FASTQC -
[- ] process > GET_CHROM_SIZES -
[- ] process > GTF_TO_BED -
[- ] process > MINIMAP2_INDEX -
[- ] process > MINIMAP2_ALIGN -
[- ] process > SAMTOOLS_SORT -
[- ] process > BEDTOOLS_GENOMECOV -
[- ] process > UCSC_BEDGRAPHTOBIGWIG -
[- ] process > BEDTOOLS_BAMTOBED -
[- ] process > UCSC_BED12TOBIGBED -
[f0/ad80d2] process > OUTPUT_DOCUMENTATION [100%] 1 of 1, failed: 1 ✘
[- ] process > GET_SOFTWARE_VERSIONS [ 0%] 0 of 1
[- ] process > MULTIQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : mighty_engelbart
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
Barcode Both Ends : No
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 Profile Description: Minimal test dataset to check pipeline function
Config Files : /home/jaruga/.nextflow/assets/nf-core/nanoseq/nextflow.config, /home/jaruga/git/nf-core/nanoseq/nextflow.config
----------------------------------------------------
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'GET_TEST_DATA'
Caused by:
Process `GET_TEST_DATA` 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:
Error: relabel failed "/home/jaruga": SELinux relabeling of /home/jaruga is not allowed
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/c1/55cb352bc2f37646abd734dcef1915
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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