Closed shreya1singh728 closed 1 year ago
The same right here.
(AMR++) pgen@pgen:~/sw/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity --pipeline demo
N E X T F L O W ~ version 22.10.1
Unable to parse config file: '/home/pgen/sw/AMRplusplus/nextflow.config'
Compile failed for sources FixedSetSources[name='/groovy/script/Script72BDC4EDE19221D16B6DAD882DE0C8A0']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/groovy/script/Script72BDC4EDE19221D16B6DAD882DE0C8A0: 18: Unexpected input: '{' @ line 18, column 9.
process {
^
1 error
Thank you very much.
config/singularity.config
file.process {
cpus = 4 // The maximum amount of CPUs to use
disk = '8 GB' // The maximum amount of disk space a single process is allowed to use
executor = 'local' // The type of system the processes are being run on (do not modify this)
maxForks = 4 // The maximum number of forks a single process is allowed to spawn
clusterOptions='--job-name=%j --ntasks=2 --partition=short'
container = **'enriquedoster/amrplusplus:latest'**
withLabel: 'qiime2' {
container = 'enriquedoster/qiime2:latest'
}
}
thank you very much for your quick response! Sorry but it does not seem to work...
(AMR++) pgen@pgen:~/sw/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity --pipeline demo
N E X T F L O W ~ version 22.10.1
Launching `main_AMR++.nf` [mighty_swartz] DSL2 - revision: 531e9acfee
A M R + + N F P I P E L I N E
===================================
reads : /home/pgen/sw/AMRplusplus/data/raw/*_R{1,2}.fastq.gz
output : test_results
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
ERROR ################################################################
Please choose a pipeline!!!
To test the pipeline, use the "demo" pipeline :
ERROR ################################################################
Exiting ...
Thanks in advance. María
thank you very much for your quick response! Sorry but it does not seem to work...
(AMR++) pgen@pgen:~/sw/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity --pipeline demo N E X T F L O W ~ version 22.10.1 Launching `main_AMR++.nf` [mighty_swartz] DSL2 - revision: 531e9acfee A M R + + N F P I P E L I N E =================================== reads : /home/pgen/sw/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process ERROR ################################################################ Please choose a pipeline!!! To test the pipeline, use the "demo" pipeline : ERROR ################################################################ Exiting ...
Thanks in advance. María
upsss...
Try removing the --pipeline demo
part of the nexflow run
code
there are several warnings but it seems to work, I attached to the screen output.
(AMR++) pgen@pgen:~/sw/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity
N E X T F L O W ~ version 22.10.1
Launching `main_AMR++.nf` [extravagant_bernard] DSL2 - revision: 531e9acfee
A M R + + N F P I P E L I N E
===================================
reads : /home/pgen/sw/AMRplusplus/data/raw/*_R{1,2}.fastq.gz
output : test_results
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process
Running a demonstration of AMR++
===================================
executor > local (21)
[a4/3e8b1e] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S3_test) [100%] 3 of 3 ✔
[ef/c5f5e8] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔
[e2/554f25] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S3_test) [100%] 3 of 3 ✔
[be/e51ba3] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔
[dc/e6a782] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null) [100%] 1 of 1 ✔
[1e/ddcae7] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔
[54/4d281c] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S3_test) [100%] 3 of 3 ✔
[c9/a7946d] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S3_test) [100%] 3 of 3 ✔
[59/2ce8a9] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults (null) [100%] 1 of 1 ✔
[8f/99b2e7] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S3_test) [100%] 3 of 3 ✔
[1a/74bf20] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction (null) [100%] 1 of 1 ✔
Pipeline completed!
Started at 2022-11-24T12:47:09.844675161+01:00
Finished at 2022-11-24T12:50:02.554790786+01:00
Time elapsed: 2m 53s
Execution status: OK
Completed at: 24-Nov-2022 12:50:02
Duration : 2m 53s
CPU hours : 0.3
Succeeded : 21
Interestingly enough, mine throws an error at run resistome
Mine results seem to be OK.
I have a similar issue when I run "nextflow run main_AMR++.nf -profile local" or "nextflow run main_AMR++.nf -profile local demo". I have installed AMR++ on a local computer follwing instruccions found in README.md file on AMRplusplus folder. Then I installed its dependencies in the same conda environment. Below I paste the error message
executor > local (13) [62/f54c71] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S3_test) [100%] 3 of 3 ✔ [c4/e3f6f0] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [37/5d51c8] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [100%] 3 of 3 ✔ [73/5b31a6] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [21/1d9e09] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [61/40fe4a] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S3_test) [ 33%] 1 of 3 executor > local (13) [62/f54c71] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S3_test) [100%] 3 of 3 ✔ [c4/e3f6f0] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [37/5d51c8] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [100%] 3 of 3 ✔ [73/5b31a6] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [21/1d9e09] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [61/40fe4a] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S3_test) [ 50%] 1 of 2 [3d/c2d285] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S1_test) [100%] 1 of 1, failed: 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [52/1aea20] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S1_test) [100%] 1 of 1, failed: 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S1_test)'
Caused by:
Process FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S1_test)
terminated with an error exit status (1)
Command executed:
resistome -ref_fp megares_database_v3.00.fasta -annot_fp megares_annotations_v3.00.csv -sam_fp S1_test.alignment.sam -gene_fp S1_test.AMR.gene.tsv -group_fp S1_test.AMR.group.tsv -mech_fp S1_test.AMR.mechanism.tsv -class_fp S1_test.AMR.class.tsv -type_fp S1_test.AMR.type.tsv -t 10
Command exit status: 1
Command output: (empty)
Command error:
Program: ResistomeAnalyzer Contact: Chris Dean cdean11@rams.colostate.edu
Usage: ./resistome [options]
Options:
-ref_fp STR/FILE Fasta formatted reference sequence
-annot_fp STR/FILE CSV formatted annotation database
rk dir-sam_fp STR/FILE SAM formatted alignment file /home/-gene_fpo/AMRpluSTR/FILErk/3d/c2Output name for gene level resistome -group_fp STR/FILE Output name for group level resistome p: whe-mech_fpve fixedSTR/FILEblem youOutput name for mechanism level resistome -class_fp STR/FILE Output name for class level resistome -t INT Gene fraction threshold
Work dir: /home/fulgencio/AMRplusplus/work/3d/c2d285ad0bc608ca2f0fba0326a179
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line
@pedres show me the out put of ls /home/fulgencio/AMRplusplus/work/3d/c2d285ad0bc608ca2f0fba0326a179
Mine results seem to be OK. @mdtorohernando Whats the version of your singularity?
singularity v3.8.6
singularity v3.8.6
And you simply git cloned this repo, not a different version of it right?
simply connecting to the repo, as the README file stated. Singularity is installed into the AMR++ conda environment, not works out of it.
Interesting, I'll redo the process and try
@pedres show me the out put of
ls /home/fulgencio/AMRplusplus/work/3d/c2d285ad0bc608ca2f0fba0326a179
Hi,
There are four direct access to files megares_annotations_v3.00.csv, megares_database_v3.00.fasta, resistome, S1_test_alignment.sam.
Manuel
Try removing the
--pipeline demo
part of thenexflow run
code
It didn't work for me.
main_AMR++.nf
[backstabbing_montalcini] DSL2 - revision: 531e9acfee
A M R + + N F P I P E L I N Ereads : /home/shreya/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results
executor > local (4) [ce/526c61] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [e9/b633ac] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [ 0%] 0 of 1 executor > local (4) [ce/526c61] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [e9/b633ac] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [ 50%] 1 of 2, failed: 1 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test)'
Caused by:
Process FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test)
terminated with an error exit status (127)
Command executed:
trimmomatic PE -threads 4 S1_test_R1.fastq.gz S1_test_R2.fastq.gz S1_test.1P.fastq.gz S1_test.1U.fastq.gz S1_test.2P.fastq.gz S1_test.2U.fastq.gz ILLUMINACLIP:/home/shreya/AMRplusplus/data/adapters/nextera.fa:2:30:10:3:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 2> S1_test.trimmomatic.stats.log
Command exit status: 127
Command output: (empty)
Work dir: /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$
@shreya1singh728
Do: less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/S1_test.trimmomatic.stats.log
and see what it tells you
I again tried the entire process and this time the error is :
main_AMR++.nf
[shrivelled_allen] DSL2 - revision: 531e9acfee
A M R + + N F P I P E L I N Ereads : /home/shreya/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results
Pipeline completed! > FAST_AMRplusplus:FASTQ_QC_WF:fastqc - Started at 2022-11-26T11:17:33.271775+05:30_QC_WF:multiqc - Finished at 2022-11-26T11:28:36.727112+05:30_TRIM_WF:runqc - Time elapsed: 11m 3s> FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - Execution status: failedST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies - [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc - [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc - [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc - [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null)'
Caused by: Failed to pull singularity image command: singularity pull --name enriquedoster-amrplusplus-latest.img.pulling.1669441659667 docker://enriquedoster/amrplusplus:latest > /dev/null status : 255 message: INFO: Converting OCI blobs to SIF format INFO: Starting build... Getting image source signatures Copying blob sha256:7a6db449b51b92eac5c81cdbd82917785343f1664b2be57b22337b0a40c5b29d Copying blob sha256:32e0667afc6985157fea1c1ee7cf3a118077c15f5dc11ca1468b919fc1c34c67 Copying blob sha256:8a8eae38ae9c29f7cff05033967a73dd10ef9bee5fafdc976a0a7559011acd4c FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: initializing source oci:/home/shreya/.singularity/cache/blob:3625f93a5188bb6769ce63a14bf055aeed0a24200f2d082852a7d272b6741e7f: writing blob: happened during read: unexpected EOF
@shreya1singh728
Do:
less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/S1_test.trimmomatic.stats.log
and see what it tells you
/home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/S1_test.trimmomatic.stats.log: No such file or directory
@shreya1singh728
Do: less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/
@shreya1singh728
Do:
less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/ /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/: No such file or directory
Hi, I have tried it with nextflow run main_AMR++.nf -profile conda and it worked.
Running a demonstration of AMR++
===================================
executor > local (20) [ad/52c5e2] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [100%] 3 of 3 ✔ [ca/832a3c] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [2c/48712c] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S3_test) [100%] 3 of 3 ✔ [d6/a86ccd] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [0e/8ba01e] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [2d/515ad8] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S1_test) [100%] 3 of 3 ✔ [20/47ebda] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S3_test) [100%] 3 of 3 ✔ [36/a5a122] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults (null) [100%] 1 of 1 ✔ [92/88b286] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S3_test) [100%] 3 of 3 ✔ [c7/9e2d38] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction (null) [100%] 1 of 1 ✔ Pipeline completed! Started at 2022-11-26T08:21:46.149649097+01:00 Finished at 2022-11-26T08:23:30.019478941+01:00 Time elapsed: 1m 44s Execution status: OK Completed at: 26-Nov-2022 08:23:30 Duration : 1m 44s CPU hours : 0.1 Succeeded : 20
@shreya1singh728 Do:
less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/ /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/: No such file or directory
Did you manage to fix this?
@shreya1singh728 Do:
less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/ /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/: No such file or directory
Did you manage to fix this?
there are several warnings but it seems to work, I attached to the screen output.
(AMR++) pgen@pgen:~/sw/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity N E X T F L O W ~ version 22.10.1 Launching `main_AMR++.nf` [extravagant_bernard] DSL2 - revision: 531e9acfee A M R + + N F P I P E L I N E =================================== reads : /home/pgen/sw/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/pgen/sw/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process Running a demonstration of AMR++ =================================== executor > local (21) [a4/3e8b1e] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S3_test) [100%] 3 of 3 ✔ [ef/c5f5e8] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [e2/554f25] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S3_test) [100%] 3 of 3 ✔ [be/e51ba3] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [dc/e6a782] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null) [100%] 1 of 1 ✔ [1e/ddcae7] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [54/4d281c] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S3_test) [100%] 3 of 3 ✔ [c9/a7946d] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S3_test) [100%] 3 of 3 ✔ [59/2ce8a9] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults (null) [100%] 1 of 1 ✔ [8f/99b2e7] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S3_test) [100%] 3 of 3 ✔ [1a/74bf20] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction (null) [100%] 1 of 1 ✔ Pipeline completed! Started at 2022-11-24T12:47:09.844675161+01:00 Finished at 2022-11-24T12:50:02.554790786+01:00 Time elapsed: 2m 53s Execution status: OK Completed at: 24-Nov-2022 12:50:02 Duration : 2m 53s CPU hours : 0.3 Succeeded : 21
Hi, could you send me your modules/Resistome/resistome.nf
file
Try removing the
--pipeline demo
part of thenexflow run
codeIt didn't work for me.
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity
N E X T F L O W ~ version 22.10.1 Launching
main_AMR++.nf
[backstabbing_montalcini] DSL2 - revision: 531e9acfee A M R + + N F P I P E L I N E reads : /home/shreya/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_resultsWARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process Running a demonstration of AMR++ ===================================
executor > local (4) [ce/526c61] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [e9/b633ac] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [ 0%] 0 of 1 executor > local (4) [ce/526c61] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [e9/b633ac] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [ 50%] 1 of 2, failed: 1 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test)'
Caused by: Process
FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test)
terminated with an error exit status (127)Command executed:
trimmomatic PE -threads 4 S1_test_R1.fastq.gz S1_test_R2.fastq.gz S1_test.1P.fastq.gz S1_test.1U.fastq.gz S1_test.2P.fastq.gz S1_test.2U.fastq.gz ILLUMINACLIP:/home/shreya/AMRplusplus/data/adapters/nextera.fa:2:30:10:3:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 2> S1_test.trimmomatic.stats.log
Command exit status: 127
Command output: (empty)
Work dir: /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b
Tip: when you have fixed the problem you can continue the execution adding the option
-resume
to the run command line(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$
Have you solved this?
Try removing the
--pipeline demo
part of thenexflow run
codeIt didn't work for me.
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity
N E X T F L O W ~ version 22.10.1 Launching
main_AMR++.nf
[backstabbing_montalcini] DSL2 - revision: 531e9acfee A M R + + N F P I P E L I N E reads : /home/shreya/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_runsnp' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_resistomeresults' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process WARN: A process with name 'dedup_snpresults' is defined more than once in module script: /home/shreya/AMRplusplus/./subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process Running a demonstration of AMR++ =================================== executor > local (4) [ce/526c61] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [e9/b633ac] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [ 0%] 0 of 1 executor > local (4) [ce/526c61] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [e9/b633ac] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [ 50%] 1 of 2, failed: 1 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test)' Caused by: ProcessFAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test)
terminated with an error exit status (127) Command executed: trimmomatic PE -threads 4 S1_test_R1.fastq.gz S1_test_R2.fastq.gz S1_test.1P.fastq.gz S1_test.1U.fastq.gz S1_test.2P.fastq.gz S1_test.2U.fastq.gz ILLUMINACLIP:/home/shreya/AMRplusplus/data/adapters/nextera.fa:2:30:10:3:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 2> S1_test.trimmomatic.stats.log Command exit status: 127 Command output: (empty) Work dir: /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b Tip: when you have fixed the problem you can continue the execution adding the option-resume
to the run command line (AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$Have you solved this?
Hii, I reinstalled the pipeline and tried with nextflow run main_AMR++.nf -profile conda, there were many warnings but the result seems okay.
main_AMR++.nf
[cranky_bose] DSL2 - revision: 531e9acfee
A M R + + N F P I P E L I N Ereads : /home/shreya/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results
executor > local (16) executor > local (17) executor > local (17) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ executor > local (18) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ executor > local (19) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [82/fafbe3] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ executor > local (20) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [82/fafbe3] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [00/55b898] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 3 of 3 ✔ executor > local (21) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [82/fafbe3] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [00/55b898] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 3 of 3 ✔ [7f/f60318] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ executor > local (21) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [82/fafbe3] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [00/55b898] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 3 of 3 ✔ [7f/f60318] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ executor > local (21) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [82/fafbe3] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [00/55b898] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 3 of 3 ✔ [7f/f60318] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ executor > local (21) [41/6ec00f] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [82/fafbe3] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [00/55b898] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 3 of 3 ✔ [7f/f60318] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [a6/b32666] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null) [100%] 1 of 1 ✔ [1e/ab09d1] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [67/cc08ff] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S1_test) [100%] 3 of 3 ✔ [65/8e8be2] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S3_test) [100%] 3 of 3 ✔ [72/808386] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults (null) [100%] 1 of 1 ✔ [c5/b8c681] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S3_test) [100%] 3 of 3 ✔ [32/cb0f23] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction (null) [100%] 1 of 1 ✔ Pipeline completed! Started at 2022-11-26T14:58:59.015123100+05:30 Finished at 2022-11-26T15:53:07.427126400+05:30 Time elapsed: 54m 8s Execution status: OK WARN: Failed to publish file: /home/shreya/AMRplusplus/work/41/94a2fd97c324216aa8f73ab47832cd/S2_test.mech.tsv; to: /home/shreya/AMRplusplus/test_results/ResistomeAnalysis/Rarefaction/Counts/S2_test.mech.tsv [copy] -- See log file for details WARN: Failed to publish file: /home/shreya/AMRplusplus/work/b2/22a0ecabe5cd86ea73e077cfea9b30/S1_test.mech.tsv; to: /home/shreya/AMRplusplus/test_results/ResistomeAnalysis/Rarefaction/Counts/S1_test.mech.tsv [copy] -- See log file for details WARN: Failed to publish file: /home/shreya/AMRplusplus/work/c5/b8c6818b723bdc2a4e0e5db7846274/S3_test.group.tsv; to: /home/shreya/AMRplusplus/test_results/ResistomeAnalysis/Rarefaction/Counts/S3_test.group.tsv [copy] -- See log file for details WARN: Failed to publish file: /home/shreya/AMRplusplus/work/65/8e8be2b394c8c5319605e7e080a65e/S3_test.AMR.group.tsv; to: /home/shreya/AMRplusplus/test_results/ResistomeAnalysis/ResistomeCounts/S3_test.AMR.group.tsv [copy] -- See log file for details
Completed at: 26-Nov-2022 15:53:07 Duration : 54m 8s CPU hours : 4.6 Succeeded : 21
Thanks!
@shreya1singh728 Do:
less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/ /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/: No such file or directory
Did you manage to fix this?
Hii, I reinstalled the pipeline and tried with nextflow run main_AMR++.nf -profile conda, there were many warnings but the result seems okay.
Hi, I have tried it with nextflow run main_AMR++.nf -profile conda and it worked.
Running a demonstration of AMR++ ===================================
executor > local (20) [ad/52c5e2] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test) [100%] 3 of 3 ✔ [ca/832a3c] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [2c/48712c] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S3_test) [100%] 3 of 3 ✔ [d6/a86ccd] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [0e/8ba01e] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [2d/515ad8] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S1_test) [100%] 3 of 3 ✔ [20/47ebda] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S3_test) [100%] 3 of 3 ✔ [36/a5a122] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults (null) [100%] 1 of 1 ✔ [92/88b286] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S3_test) [100%] 3 of 3 ✔ [c7/9e2d38] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction (null) [100%] 1 of 1 ✔ Pipeline completed! Started at 2022-11-26T08:21:46.149649097+01:00 Finished at 2022-11-26T08:23:30.019478941+01:00 Time elapsed: 1m 44s Execution status: OK Completed at: 26-Nov-2022 08:23:30 Duration : 1m 44s CPU hours : 0.1 Succeeded : 20
Thanks!
@shreya1singh728 okay that is great
Hi, I am using conda to install AMR++ pipeline but with the following error:
$ nextflow run main_AMR++.nf -profile conda
N E X T F L O W ~ version 22.10.1
Launching main_AMR++.nf
[sleepy_cray] DSL2 - revision: 531e9acfee
A M R + + N F P I P E L I N E
reads : /public/hpz/02.software/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results
WARN: A process with name 'dedup_runresistome' is defined more than once in module script: /public/hpz/02.software/AMRplusplus/subworkflows/fastq_resistome.nf -- Make sure to not define the same function as process ... Running a demonstration of AMR++
executor > local (13) [82/b7ece6] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [69/b1527f] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [9c/05828e] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 3 of 3 ✔ [60/a94a63] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [52/a2706b] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [94/c716fa] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S2_test) [ 33%] 1 of 3 [13/3e9958] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S2_test) [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S2_test)'
executor > local (13) [82/b7ece6] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3 ✔ [69/b1527f] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1 ✔ [9c/05828e] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 3 of 3 ✔ [60/a94a63] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [52/a2706b] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [2b/5b0c0f] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S3_test) [100%] 1 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome (S2_test) - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction (S2_test)'
Caused by: No such variable: bam -- Check script './subworkflows/../modules/Resistome/resistome.nf' at line: 155
Source block: """ samtools view -h ${bam} > converted.sam
$rarefaction \ -ref_fp ${amr} \ -sam_fp converted.sam \ -annot_fp ${annotation} \ -gene_fp ${sample_id}.gene.tsv \ -group_fp ${sample_id}.group.tsv \ -mech_fp ${sample_id}.mech.tsv \ -class_fp ${sample_id}.class.tsv \ -type_fp ${sample_id}.type.tsv \ -min ${min} \ -max ${max} \ -skip ${skip} \ -samples ${samples} \ -t ${threshold}
rm converted.sam """
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
When I run 'nextflow run main_AMR++.nf -profile singularity'. the error was as follows:
$ nextflow run main_AMR++.nf -profile singularity
N E X T F L O W ~ version 22.10.1
Launching main_AMR++.nf
[cheeky_chandrasekhar] DSL2 - revision: 531e9acfee
A M R + + N F P I P E L I N E
reads : /public/hpz/02.software/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results
executor > local (7) [99/3b4943] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [0d/d8f649] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S2_test) [ 0%] 0 of 3 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [73/6f0856] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [ 0%] 0 of 1 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - executor > local (7) [99/3b4943] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S1_test) [100%] 3 of 3, failed: 3 ✘ [- ] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc - [75/268768] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S1_test) [100%] 2 of 2, failed: 2 [- ] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats - [73/6f0856] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1, failed: 1 ✘ [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test)'
Caused by:
Process FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S2_test)
terminated with an error exit status (255)
Command executed:
mkdir S2_test_fastqc_logs fastqc -o S2_test_fastqc_logs -f fastq -q S2_test_R1.fastq.gz S2_test_R2.fastq.gz
Command exit status: 255
Command output: (empty)
Command error: INFO: Converting SIF file to temporary sandbox... FATAL: while extracting /public/hpz/02.software/AMRplusplus/envs/enriquedoster-amrplusplus-latest.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled : exit status 1
Work dir: /public/hpz/02.software/AMRplusplus/work/6c/ebffa4a8ec8b84d8d7e9ceabc3b616
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line
Hello everyone,
Thank you for bringing this to our attention. Could you please try downloading the latest AMR++ updates and try again?
I think we addressed the warnings you keep seeing, but the singularity error might have to do with your computing cluster and I would like to investigate that further. Have you by chance tried downloading the container first, as outlined here. Because we've fixed the config file error, I'll close this thread but please try that out and report back with a new issue, thanks!
How can I solve the following problem? Thanks.
main_AMR++.nf
[desperate_easley] DSL2 - revision: c52e346ad8
A M R + + N F P I P E L I N Ereads : /home/rxzhao/software/AMRplusplus/data/raw/*_R{1,2}.fastq.gz output : test_results
Running a demonstration of AMR++
===================================
To include SNP analysis, add `--snp Y` to your command.
===================================
To include deduplicated count analysis, add `--deduped Y` to your command.
Please be aware that adding deduplicated counts will significantly increase run time and temp file storage requirements.
===================================
executor > local (13) [b9/f51aa8] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S3_test) [100%] 3 of 3 ✔ [8e/65917b] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [ 0%] 0 of 1 [d3/eee701] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S3_test) [100%] 3 of 3 ✔ [44/b579d2] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [49/855f69] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null) [ 0%] 0 of 1 [61/58f780] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [9c/2fbbb7] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S3_test) [ 66%] 2 of 3 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_QC_WF:multiqc'
Caused by:
Process FAST_AMRplusplus:FASTQ_QC_WF:multiqc
terminated with an error exit status (1)
Command executed:
cp multiqc/* . multiqc -v . mv multiqc_data/multiqc_general_stats.txt .
Command exit status: 1
Command output: (empty)
Command error: INFO: Converting SIF file to temporary sandbox...
/// MultiQC 🔍 | v1.13
[2023-02-01 10:52:45,796] multiqc [DEBUG ] This is MultiQC v1.13 [2023-02-01 10:52:45,797] multiqc [DEBUG ] Loading config settings from: multiqc_config.yaml [2023-02-01 10:52:45,798] multiqc [DEBUG ] New config: {'title': 'AMR++ Bioinformatic pipeline', 'subtitle': 'A pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.', 'report_header_info': [{'Contact E-mail': 'meglab.metagenomics@gmail.com'}, {'Application Type': 'AMR++'}, {'Project Type': 'FastQC analysis'}], 'custom_logo_url': 'https://www.nextflow.io', 'custom_logo_title': 'Center for Genomic Regulation'} executor > local (13) [b9/f51aa8] process > FAST_AMRplusplus:FASTQ_QC_WF:fastqc (FASTQC on S3_test) [100%] 3 of 3 ✔ [8e/65917b] process > FAST_AMRplusplus:FASTQ_QC_WF:multiqc [100%] 1 of 1, failed: 1 ✘ [d3/eee701] process > FAST_AMRplusplus:FASTQ_TRIM_WF:runqc (S3_test) [100%] 3 of 3 ✔ [44/b579d2] process > FAST_AMRplusplus:FASTQ_TRIM_WF:QCstats (null) [100%] 1 of 1 ✔ [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:build_dependencies (null) - [61/58f780] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:index [100%] 1 of 1 ✔ [c8/50ec8b] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:bwa_align (S1_test) [100%] 2 of 2 [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runresistome - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:resistomeresults - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:runrarefaction - [- ] process > FAST_AMRplusplus:FASTQ_RESISTOME_WF:plotrarefaction - Error executing process > 'FAST_AMRplusplus:FASTQ_QC_WF:multiqc'
Caused by:
Process FAST_AMRplusplus:FASTQ_QC_WF:multiqc
terminated with an error exit status (1)
Command executed:
cp multiqc/* . multiqc -v . mv multiqc_data/multiqc_general_stats.txt .
Command exit status: 1
Command output: (empty)
Command error: INFO: Converting SIF file to temporary sandbox...
/// MultiQC 🔍 | v1.13
[2023-02-01 10:52:45,796] multiqc [DEBUG ] This is MultiQC v1.13
[2023-02-01 10:52:45,797] multiqc [DEBUG ] Loading config settings from: multiqc_config.yaml
[2023-02-01 10:52:45,798] multiqc [DEBUG ] New config: {'title': 'AMR++ Bioinformatic pipeline', 'subtitle': 'A pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.', 'report_header_info': [{'Contact E-mail': 'meglab.metagenomics@gmail.com'}, {'Application Type': 'AMR++'}, {'Project Type': 'FastQC analysis'}], 'custom_logo_url': 'https://www.nextflow.io', 'custom_logo_title': 'Center for Genomic Regulation'}
[2023-02-01 10:52:45,798] multiqc [DEBUG ] Command used: /opt/conda/bin/multiqc -v .
[2023-02-01 10:52:47,957] multiqc [WARNING] MultiQC Version v1.14 now available!
[2023-02-01 10:52:47,957] multiqc [DEBUG ] Working dir : /home/rxzhao/software/AMRplusplus/work/8e/65917b2bff186bd401c3316f2f3a7f
[2023-02-01 10:52:47,957] multiqc [DEBUG ] Template : default
[2023-02-01 10:52:47,957] multiqc [DEBUG ] Running Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18) [GCC 10.3.0]
[2023-02-01 10:52:47,957] multiqc [INFO ] Report title: AMR++ Bioinformatic pipeline
[2023-02-01 10:52:47,957] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, sambamba, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, pbmarkdup, damageprofiler, biobambam2, jcvi, mtnucratio, picard, vep, sentieon, prokka, qc3C, nanostat, samblaster, samtools, sexdeterrmine, eigenstratdatabasetools, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, odgi, pangolin, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pychopper, pycoqc, minionqc, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap
[2023-02-01 10:52:47,957] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp9q_478xy
Traceback (most recent call last):
File "/opt/conda/bin/multiqc", line 10, in
Work dir: /home/rxzhao/software/AMRplusplus/work/8e/65917b2bff186bd401c3316f2f3a7f
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
Hello,
I am using conda to install AMR++ pipeline but the demo crashed while parsing nextflow.config with the following error:
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ nextflow run main_AMR++.nf -profile singularity --pipeline demo N E X T F L O W ~ version 22.10.1 Unable to parse config file: '/home/shreya/AMRplusplus/nextflow.config'
Compile failed for sources FixedSetSources[name='/groovy/script/Script72BDC4EDE19221D16B6DAD882DE0C8A0']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: /groovy/script/Script72BDC4EDE19221D16B6DAD882DE0C8A0: 18: Unexpected input: '{' @ line 18, column 9. process { ^
1 error
(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$
Please suggest the solution. Thankyou