WARN: Killing pending tasks (3) Error executing process > 'RunQC (S3_test)' in AMR++2

Question

[MSRS]

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

[German.M.Demidov]

Where are the errors?

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

[MSRS]

Thanks, How can I address it?

[Pierre Lindenbaum]

the error was dumped in

/home/shaminur/bioinfo/AMRplusplus/amrplusplus_v2/work/be/d0c5a65ad38ac92da34f79f9b75afc/S3_test.trimmomatic.stats.log

[MSRS]

.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

Answer 1

[Pierre Lindenbaum]

/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.

[MSRS]

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)'

[German.M.Demidov]

It is actually different error

[MSRS]

Are there any solutions? Thanks