Question: WARN: Killing pending tasks (3) Error executing process > 'RunQC (S3_test)' in AMR++2
0
gravatar for mdshaminurrahman95
26 days ago by
mdshaminurrahman950 wrote:

I am trying to run MEGARes (AMR++2) test according to their instructions (https://github.com/meglab-metagenomics/amrplusplus_v2/blob/master/docs/installation.md) and getting the error below...

nextflow run main_AmrPlusPlus_v2.nf -profile singularity --output test_results
N E X T F L O W  ~  version 19.10.0
Launching `main_AmrPlusPlus_v2.nf` [golden_chandrasekhar] - revision: 3de94d2cc3
executor >  local (5)
[6b/cb6591] process > RunQC (S2_test)                                 [  0%] 0 of 3
[-        ] process > QCStats                                         -
[28/df325f] process > BuildHostIndex (chr21.fasta)                    [  0%] 0 of 1
[-        ] process > AlignReadsToHost                                -
[-        ] process > RemoveHostDNA                                   -
[-        ] process > HostRemovalStats                                -
[-        ] process > NonHostReads                                    -
[28/adbb5e] process > BuildAMRIndex (megares_modified_database_v2.00) [  0%] 0 of 1
[-        ] process > AlignToAMR                                      -
[-        ] process > RunResistome                                    -
[-        ] process > ResistomeResults                                -
[-        ] process > SamDedupRunResistome                            -
[-        ] process > SamDedupResistomeResults                        -
executor >  local (5)
[6b/cb6591] process > RunQC (S2_test)                                 [100%] 3 of 3, failed: 3
[-        ] process > QCStats                                         -
[28/df325f] process > BuildHostIndex (chr21.fasta)                    [100%] 1 of 1, failed: 1
[-        ] process > AlignReadsToHost                                -
[-        ] process > RemoveHostDNA                                   -
[-        ] process > HostRemovalStats                                -
[-        ] process > NonHostReads                                    -
[28/adbb5e] process > BuildAMRIndex (megares_modified_database_v2.00) [100%] 1 of 1, failed: 1
[-        ] process > AlignToAMR                                      -
[-        ] process > RunResistome                                    -
[-        ] process > ResistomeResults                                -
[-        ] process > SamDedupRunResistome                            -
[-        ] process > SamDedupResistomeResults                        -
[-        ] process > RunRarefaction                                  -
WARN: Killing pending tasks (3)
Error executing process > 'RunQC (S3_test)'

Caused by:
  Process `RunQC (S3_test)` terminated with an error exit status (1)

Command executed:

  /usr/local/envs/AmrPlusPlus/bin/java -jar /usr/local/envs/AmrPlusPlus/share/trimmomatic/trimmomatic.jar       PE       -threads 10       S3_test_R1.fastq.gz S3_test_R2.fastq.gz S3_test.1P.fastq.gz S3_test.1U.fastq.gz S3_test.2P.fastq.gz S3_test.2U.fastq.gz       ILLUMINACLIP:/home/shaminur/bioinfo/AMRplusplus/amrplusplus_v2/data/adapters/nextera.fa:2:30:10:3:TRUE       LEADING:3       TRAILING:3       SLIDINGWINDOW:4:15       MINLEN:36       2> S3_test.trimmomatic.stats.log

Command exit status:
  1

Command output:
  (empty)

Work dir:
  /home/shaminur/bioinfo/AMRplusplus/amrplusplus_v2/work/be/d0c5a65ad38ac92da34f79f9b75afc

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Where are the errors? How can I solve it?

Thanks in advances

nextflow • 130 views
ADD COMMENTlink modified 26 days ago by Pierre Lindenbaum124k • written 26 days ago by mdshaminurrahman950

Where are the errors?

Error executing process > 'RunQC (S3_test)' - I think here

ADD REPLYlink written 26 days ago by German.M.Demidov1.0k

Thanks, How can I address it?

ADD REPLYlink written 26 days ago by mdshaminurrahman950

the error was dumped in

/home/shaminur/bioinfo/AMRplusplus/amrplusplus_v2/work/be/d0c5a65ad38ac92da34f79f9b75afc/S3_test.trimmomatic.stats.log
ADD REPLYlink written 26 days ago by Pierre Lindenbaum124k

.log file like this /home/shaminur/bioinfo/AMRplusplus/amrplusplus_v2/work/be/ba4fc350d99e164f5c3191ca41e5a1/.command.sh: line 2: /usr/local/envs/AmrPlusPlus/bin/java: No such file or directory

ADD REPLYlink written 26 days ago by mdshaminurrahman950
2
gravatar for Pierre Lindenbaum
26 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:
/usr/local/envs/AmrPlusPlus/bin/java: No such file or directory

the error is here, there is something wrong with your PATH to the java command.

ADD COMMENTlink written 26 days ago by Pierre Lindenbaum124k

here is my java....

Singularity> which java /usr/local/envs/AmrPlusPlus_env/bin/java but getting the same error..

WARN: Killing pending tasks (3) Error executing process > 'RunQC (S1_test)'

ADD REPLYlink written 25 days ago by mdshaminurrahman950

It is actually different error

ADD REPLYlink written 25 days ago by German.M.Demidov1.0k

Are there any solutions? Thanks

ADD REPLYlink modified 25 days ago • written 25 days ago by mdshaminurrahman950
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