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4.9 years ago
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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
Error executing process > 'RunQC (S3_test)'
- I think hereThanks, How can I address it?
the error was dumped in
.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