This repository was archived by the owner on May 5, 2020. It is now read-only.
This repository was archived by the owner on May 5, 2020. It is now read-only.
Error when run pipeline with docker file #28
Description
Hi, when I ran this command :
nextflow run nf-core/vipr -params-file vi.yaml -profile docker
I met this error:
N E X T F L O W ~ version 0.31.1
Launching `nf-core/vipr` [gloomy_almeida] - revision: 1ca3412b9d [master]
==================================================
nf-core/vipr : Viral amplicon/enrichment analysis and intrahost variant calling: v1.0-dev
==================================================
List of samples: PDH203_GTGGCC
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trim_and_combine = <value>` with a process selector
[warm up] executor > local
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$decont = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$kraken = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$tadpole = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$gap_fill_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$polish_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$final_mapping = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$var_calling = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$genomecov = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$vipr_tools = <value>` with a process selector
[c6/04f746] Submitted process > trim_and_combine (Preprocessing of 1 read pairs for PDH203_GTGGCC)
ERROR ~ Error executing process > 'trim_and_combine (Preprocessing of 1 read pairs for PDH203_GTGGCC)'
Caused by:
Process `trim_and_combine (Preprocessing of 1 read pairs for PDH203_GTGGCC)` terminated with an error exit status (125)
Command executed:
# loop over readunits in pairs per sample
pairno=0
echo 425-N706-S517_S6_L001_R1_001.fastq 425-N706-S517_S6_L001_R2_001.fastq | xargs -n2 | while read fq1 fq2; do
let pairno=pairno+1
# note: don't make reads smaller than assembler kmer length
skewer --quiet -t 4 -m pe -q 3 -n -l 31 -z -o pair${pairno}-skewer-out $fq1 $fq2;
cat *-trimmed-pair1.fastq.gz >> PDH203_GTGGCC_R1-trimmed.fastq.gz;
cat *-trimmed-pair2.fastq.gz >> PDH203_GTGGCC_R2-trimmed.fastq.gz;
rm *-trimmed-pair[12].fastq.gz;
done
fastqc -t {task.cpus} PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz;
Command exit status:
125
Command output:
(empty)
Command error:
Unable to find image 'nfcore/vipr:1.0-dev' locally
docker: Error response from daemon: manifest for nfcore/vipr:1.0-dev not found.
See 'docker run --help'.
Work dir:
/home/vi/work/c6/04f746274f2e2baec8dcb1b457ba47
Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option `-resume`
-- Check '.nextflow.log' file for details
Oops... Pipeline execution stopped with the following message: Unable to find image 'nfcore/vipr:1.0-dev' locally
docker: Error response from daemon: manifest for nfcore/vipr:1.0-dev not found.
See 'docker run --help'.
Pipeline execution summary
---------------------------
Completed at : Mon Sep 24 03:55:39 UTC 2018
Duration : 5.6s
Success : false
Work Dir : /home/vi/work
Exit status : 125
Error report : Error executing process > 'trim_and_combine (Preprocessing of 1 read pairs for PDH203_GTGGCC)'
Caused by:
Process `trim_and_combine (Preprocessing of 1 read pairs for PDH203_GTGGCC)` terminated with an error exit status (125)
Command executed:
# loop over readunits in pairs per sample
pairno=0
echo 425-N706-S517_S6_L001_R1_001.fastq 425-N706-S517_S6_L001_R2_001.fastq | xargs -n2 | while read fq1 fq2; do
let pairno=pairno+1
# note: don't make reads smaller than assembler kmer length
skewer --quiet -t 4 -m pe -q 3 -n -l 31 -z -o pair${pairno}-skewer-out $fq1 $fq2;
cat *-trimmed-pair1.fastq.gz >> PDH203_GTGGCC_R1-trimmed.fastq.gz;
cat *-trimmed-pair2.fastq.gz >> PDH203_GTGGCC_R2-trimmed.fastq.gz;
rm *-trimmed-pair[12].fastq.gz;
done
fastqc -t {task.cpus} PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz;
Command exit status:
125
Command output:
(empty)
Command error:
Unable to find image 'nfcore/vipr:1.0-dev' locally
docker: Error response from daemon: manifest for nfcore/vipr:1.0-dev not found.
See 'docker run --help'.
Work dir:
/home/vi/work/c6/04f746274f2e2baec8dcb1b457ba47
Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option `-resume`
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
After that, I think I have prolem with the url of docker, So I edited the nextflow.config from
container = "nfcore/vipr:${version}" // for GIS translated into conda env name!
to
container = "nfcore/vipr
So the pipeline worked on first process. But it error on the second process
>N E X T F L O W ~ version 0.31.1
Launching `nf-core/vipr` [ridiculous_boyd] - revision: 1ca3412b9d [master]
==================================================
nf-core/vipr : Viral amplicon/enrichment analysis and intrahost variant calling: v1.0-dev
==================================================
List of samples: PDH203_GTGGCC
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trim_and_combine = <value>` with a process selector
[warm up] executor > local
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$decont = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$kraken = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$tadpole = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$gap_fill_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$polish_assembly = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$final_mapping = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$var_calling = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$genomecov = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$vipr_tools = <value>` with a process selector
[f8/88c7c1] Submitted process > trim_and_combine (Preprocessing of 1 read pairs for PDH203_GTGGCC)
[42/27852b] Submitted process > decont (Decontaminating PDH203_GTGGCC)
ERROR ~ Error executing process > 'decont (Decontaminating PDH203_GTGGCC)'
Caused by:
Process `decont (Decontaminating PDH203_GTGGCC)` terminated with an error exit status (1)
Command executed:
decont.py -i PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz -t 4 -c 0.5 -r human_g1k_v37.fasta -o PDH203_GTGGCC_trimmed_decont;
# since this is the last fastqc processing step, let's run fastqc here
fastqc -t {task.cpus} PDH203_GTGGCC_trimmed_decont_1.fastq.gz PDH203_GTGGCC_trimmed_decont_2.fastq.gz;
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/decont.py", line 449, in <module>
assert shutil.which('bwa') and shutil.which('samtools')
AttributeError: 'module' object has no attribute 'which'
Work dir:
/home/vi/.nextflow/assets/nf-core/vipr/work/42/27852be75b8444b072ea29c2bbaa61
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Oops... Pipeline execution stopped with the following message: WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/decont.py", line 449, in <module>
assert shutil.which('bwa') and shutil.which('samtools')
AttributeError: 'module' object has no attribute 'which'
Pipeline execution summary
---------------------------
Completed at : Mon Sep 24 04:09:36 UTC 2018
Duration : 24.8s
Success : false
Work Dir : /home/vi/.nextflow/assets/nf-core/vipr/work
Exit status : 1
Error report : Error executing process > 'decont (Decontaminating PDH203_GTGGCC)'
Caused by:
Process `decont (Decontaminating PDH203_GTGGCC)` terminated with an error exit status (1)
Command executed:
decont.py -i PDH203_GTGGCC_R1-trimmed.fastq.gz PDH203_GTGGCC_R2-trimmed.fastq.gz -t 4 -c 0.5 -r human_g1k_v37.fasta -o PDH203_GTGGCC_trimmed_decont;
# since this is the last fastqc processing step, let's run fastqc here
fastqc -t {task.cpus} PDH203_GTGGCC_trimmed_decont_1.fastq.gz PDH203_GTGGCC_trimmed_decont_2.fastq.gz;
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/decont.py", line 449, in <module>
assert shutil.which('bwa') and shutil.which('samtools')
AttributeError: 'module' object has no attribute 'which'
Work dir:
/home/vi/.nextflow/assets/nf-core/vipr/work/42/27852be75b8444b072ea29c2bbaa61
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
I think, i had problem with the docker file. Do you recommend I will use docker or using conda for software dependencies ?.
Kiên