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junaruga/nextflow-run-nanoseq-test-podman4.log

Created November 17, 2020 20:17
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nextflow-run-nanoseq-test-podman4.log
$ cat nextflow-run-nanoseq-test-podman4.log
N E X T F L O W ~ version 20.07.1
Launching `nf-core/nanoseq` [thirsty_montalcini] - revision: ad5b2bb7a3 [master]
[- ] process > GET_TEST_DATA -
[- ] process > CHECK_SAMPLESHEET -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : thirsty_montalcini
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)
[31/8f73c3] 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 : thirsty_montalcini
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)
[31/8f73c3] 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 -
[aa/5deb6e] process > OUTPUT_DOCUMENTATION [ 0%] 0 of 1
[- ] process > GET_SOFTWARE_VERSIONS -
[- ] process > MULTIQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : thirsty_montalcini
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)
[31/8f73c3] 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 -
[aa/5deb6e] process > OUTPUT_DOCUMENTATION [ 0%] 0 of 1
[- ] process > GET_SOFTWARE_VERSIONS -
[- ] process > MULTIQC -
----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/nanoseq v1.1.0
----------------------------------------------------
Pipeline Release : master
Run Name : thirsty_montalcini
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 (3)
[31/8f73c3] process > GET_TEST_DATA [ 0%] 0 of 1
[2c/236480] 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 -
[aa/5deb6e] process > OUTPUT_DOCUMENTATION [ 0%] 0 of 1
[- ] process > GET_SOFTWARE_VERSIONS -
[- ] process > MULTIQC -
executor > local (3)
[31/8f73c3] process > GET_TEST_DATA [ 0%] 0 of 1
[2c/236480] 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 -
[aa/5deb6e] process > OUTPUT_DOCUMENTATION [ 0%] 0 of 1
[- ] process > GET_SOFTWARE_VERSIONS -
[- ] process > MULTIQC -
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:
Trying to pull docker.io/nfcore/nanoseq:1.1.0...
Getting image source signatures
Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
Copying blob sha256:5019cfb0a680b922320d12e58ed76f322322992137372cf22d054279611b9696
Copying blob sha256:f68e4fbb98684405f26d85827952a832eb3519030cc208f0ed4e92266d1b8b16
Copying blob sha256:0dfc925e594668b1ae72a3916ea8b5a1878cf834a3b64efbf1813fc9a8f09111
Copying blob sha256:d62aaefe018042f379b11997e7c4745a7f51d4d859992853fe69c6f327637c97
Copying blob sha256:11b03534eb7b5779ea1619dbc134377ff65951ece643277442d38c053b744d8f
Copying blob sha256:3c724b26a4167f9c1af5e51f8498ca309fb169594c39de00ceec013e3d8bd241
Copying config sha256:8101584944a07eefaf1f6bac56317c7566843c75d0814bceb42042cc4f283fe5
Writing manifest to image destination
Storing signatures
Error: relabel failed "/home/jaruga": SELinux relabeling of /home/jaruga is not allowed
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/31/8f73c34e5ae4a7ef8d880a7ed8d931
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
executor > local (3)
[31/8f73c3] process > GET_TEST_DATA [100%] 1 of 1, failed: 1 ✘
[2c/236480] 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 -
[aa/5deb6e] 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 > '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:
Trying to pull docker.io/nfcore/nanoseq:1.1.0...
Getting image source signatures
Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
Copying blob sha256:5019cfb0a680b922320d12e58ed76f322322992137372cf22d054279611b9696
Copying blob sha256:f68e4fbb98684405f26d85827952a832eb3519030cc208f0ed4e92266d1b8b16
Copying blob sha256:0dfc925e594668b1ae72a3916ea8b5a1878cf834a3b64efbf1813fc9a8f09111
Copying blob sha256:d62aaefe018042f379b11997e7c4745a7f51d4d859992853fe69c6f327637c97
Copying blob sha256:11b03534eb7b5779ea1619dbc134377ff65951ece643277442d38c053b744d8f
Copying blob sha256:3c724b26a4167f9c1af5e51f8498ca309fb169594c39de00ceec013e3d8bd241
Copying config sha256:8101584944a07eefaf1f6bac56317c7566843c75d0814bceb42042cc4f283fe5
Writing manifest to image destination
Storing signatures
Error: relabel failed "/home/jaruga": SELinux relabeling of /home/jaruga is not allowed
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/31/8f73c34e5ae4a7ef8d880a7ed8d931
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
executor > local (3)
[31/8f73c3] process > GET_TEST_DATA [100%] 1 of 1, failed: 1 ✘
[2c/236480] 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 -
[aa/5deb6e] 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 > '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:
Trying to pull docker.io/nfcore/nanoseq:1.1.0...
Getting image source signatures
Copying blob sha256:96cf53b3a9dd496f4c91ab86eeadca2c8a31210c2e5c2a82badbb0dcf8c8f76b
Copying blob sha256:9c388eb6d33c40662539172f0d9a357287bd1cd171692ca5c08db2886bc527c3
Copying blob sha256:68ced04f60ab5c7a5f1d0b0b4e7572c5a4c8cce44866513d30d9df1a15277d6b
Copying blob sha256:5019cfb0a680b922320d12e58ed76f322322992137372cf22d054279611b9696
Copying blob sha256:f68e4fbb98684405f26d85827952a832eb3519030cc208f0ed4e92266d1b8b16
Copying blob sha256:0dfc925e594668b1ae72a3916ea8b5a1878cf834a3b64efbf1813fc9a8f09111
Copying blob sha256:d62aaefe018042f379b11997e7c4745a7f51d4d859992853fe69c6f327637c97
Copying blob sha256:11b03534eb7b5779ea1619dbc134377ff65951ece643277442d38c053b744d8f
Copying blob sha256:3c724b26a4167f9c1af5e51f8498ca309fb169594c39de00ceec013e3d8bd241
Copying config sha256:8101584944a07eefaf1f6bac56317c7566843c75d0814bceb42042cc4f283fe5
Writing manifest to image destination
Storing signatures
Error: relabel failed "/home/jaruga": SELinux relabeling of /home/jaruga is not allowed
Work dir:
/home/jaruga/git/nf-core/nanoseq/work/31/8f73c34e5ae4a7ef8d880a7ed8d931
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
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