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Microbial-Ecology-Group / AMRplusplus

AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
https://www.meglab.org/
GNU General Public License v3.0
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Unable to parse nextflow config file #4

Closed shreya1singh728 closed 1 year ago

shreya1singh728 commented 1 year ago

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

mdtorohernando commented 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.

EorgeKit commented 1 year ago

This is due to the config/singularity.config file.

In this piece of code add single quotes in the starred (don't add the stars, I put them for directive purposes to where the problem is) part.

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'
  }
}
mdtorohernando commented 1 year ago

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

EorgeKit commented 1 year ago

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

Yeah I am getting the same error

mdtorohernando commented 1 year ago

upsss...

EorgeKit commented 1 year ago

Try removing the --pipeline demo part of the nexflow run code

mdtorohernando commented 1 year ago

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
EorgeKit commented 1 year ago

Interestingly enough, mine throws an error at run resistome

mdtorohernando commented 1 year ago

Mine results seem to be OK.

pedres commented 1 year ago

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

EorgeKit commented 1 year ago

@pedres show me the out put of ls /home/fulgencio/AMRplusplus/work/3d/c2d285ad0bc608ca2f0fba0326a179

EorgeKit commented 1 year ago

Mine results seem to be OK. @mdtorohernando Whats the version of your singularity?

mdtorohernando commented 1 year ago

singularity v3.8.6

EorgeKit commented 1 year ago

singularity v3.8.6

And you simply git cloned this repo, not a different version of it right?

mdtorohernando commented 1 year ago

simply connecting to the repo, as the README file stated. Singularity is installed into the AMR++ conda environment, not works out of it.

EorgeKit commented 1 year ago

Interesting, I'll redo the process and try

pedres commented 1 year ago

@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

shreya1singh728 commented 1 year ago

Try removing the --pipeline demo part of the nexflow run code

It 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: 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$

EorgeKit commented 1 year ago

@shreya1singh728

Do: less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/S1_test.trimmomatic.stats.log

and see what it tells you

shreya1singh728 commented 1 year ago

I again tried the entire process and this time the error is :

(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 [shrivelled_allen] 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++

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 commented 1 year ago

@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

EorgeKit commented 1 year ago

@shreya1singh728

Do: less /home/shreya/AMRplusplus/work/c0/716119b3fe3b69720a9359d988374b/

shreya1singh728 commented 1 year ago

@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

pedres commented 1 year ago

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

Kauthar-Omar commented 1 year ago

@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?

Kauthar-Omar commented 1 year ago

@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?

Kauthar-Omar commented 1 year ago

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

EorgeKit commented 1 year ago

Try removing the --pipeline demo part of the nexflow run code

It 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: 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?

shreya1singh728 commented 1 year ago

Try removing the --pipeline demo part of the nexflow run code

It 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: 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?

Hii, I reinstalled the pipeline and tried with nextflow run main_AMR++.nf -profile conda, there were many warnings but the result seems okay.

(AMR++) shreya@DESKTOP-D417TM9:~/AMRplusplus$ nextflow run main_AMR++.nf -profile conda N E X T F L O W ~ version 22.10.1 Launching main_AMR++.nf [cranky_bose] 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 (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 commented 1 year ago

@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.

shreya1singh728 commented 1 year ago

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!

EorgeKit commented 1 year ago

@shreya1singh728 okay that is great

Hope0713 commented 1 year ago

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

Hope0713 commented 1 year ago

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

WARN: A process with name 'dedup_snpresults' 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 (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

EnriqueDoster commented 1 year ago

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!

renxinzhao commented 1 year ago

How can I solve the following problem? Thanks.

nextflow run main_AMR++.nf -profile singularity N E X T F L O W ~ version 22.10.4 Launching main_AMR++.nf [desperate_easley] DSL2 - revision: c52e346ad8 A M R + + N F P I P E L I N E

reads : /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 sys.exit(run_multiqc()) File "/opt/conda/lib/python3.8/site-packages/multiqc/main.py", line 22, in run_multiqc multiqc.run_cli(prog_name="multiqc") File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1130, in call return self.main(*args, kwargs) File "/opt/conda/lib/python3.8/site-packages/rich_click/rich_command.py", line 19, in main rv = super().main(args, standalone_mode=False, kwargs) File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 760, in invoke return __callback(args, kwargs) File "/opt/conda/lib/python3.8/site-packages/multiqc/multiqc.py", line 286, in run_cli multiqc_run = run(*kwargs) File "/opt/conda/lib/python3.8/site-packages/multiqc/multiqc.py", line 612, in run template_mod = config.avail_templates[config.template].load() File "/home/rxzhao/.local/lib/python3.8/site-packages/pkg_resources/init.py", line 2470, in load self.require(args, **kwargs) File "/home/rxzhao/.local/lib/python3.8/site-packages/pkg_resources/init.py", line 2493, in require items = working_set.resolve(reqs, env, installer, extras=self.extras) File "/home/rxzhao/.local/lib/python3.8/site-packages/pkg_resources/init.py", line 800, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (typing-extensions 3.7.4.3 (/home/rxzhao/.local/lib/python3.8/site-packages), Requirement.parse('typing-extensions<5.0,>=4.0.0; python_version < "3.9"'), {'rich'}) INFO: Cleaning up image...

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