Question: WARN: Killing pending tasks (3) Error executing process > 'RunQC (S3_test)' in AMR++2
0
gravatar for Shaminur
12 months ago by
Shaminur80
Dhaka University
Shaminur80 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 • 311 views
ADD COMMENTlink modified 12 months ago by Pierre Lindenbaum131k • written 12 months ago by Shaminur80

Where are the errors?

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

ADD REPLYlink written 12 months ago by German.M.Demidov1.9k

Thanks, How can I address it?

ADD REPLYlink written 12 months ago by Shaminur80

the error was dumped in

/home/shaminur/bioinfo/AMRplusplus/amrplusplus_v2/work/be/d0c5a65ad38ac92da34f79f9b75afc/S3_test.trimmomatic.stats.log
ADD REPLYlink written 12 months ago by Pierre Lindenbaum131k

.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 12 months ago by Shaminur80
2
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k 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 12 months ago by Pierre Lindenbaum131k

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 12 months ago by Shaminur80

It is actually different error

ADD REPLYlink written 12 months ago by German.M.Demidov1.9k

Are there any solutions? Thanks

ADD REPLYlink modified 12 months ago • written 12 months ago by Shaminur80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1629 users visited in the last hour