melbournebioinformatics / bpipe-trinotate Goto Github PK

==================================================================================================== 
|                              Starting Pipeline at 2017-08-02 10:02                               | 
==================================================================================================== 

======================================== Stage transdecoder ======================================== 
ERROR: Job runner bpipe.executor.SlurmCommandExecutor failed to return a job id for job 2 (transdecoder) despite reporting success exit code for command: 

bash /lustre/work-lustre/waterhouse_team/miniconda2/opt/bpipe-0.9.9.2/bin/../bin/bpipe-slurm.sh start 

Raw output was:[ 
] 

========================================= Pipeline Failed ========================================== 

Job runner bpipe.executor.SlurmCommandExecutor failed to return a job id for job 2 (transdecoder) despite reporting success exit code for command: 

bash /lustre/work-lustre/waterhouse_team/miniconda2/opt/bpipe-0.9.9.2/bin/../bin/bpipe-slurm.sh start 

Raw output was:[ 
] 

Use 'bpipe errors' to see output from failed commands.

//load 'bpipe.config' 
NCPU="10" 
SWISSPROTDB="/work/lorencm/bpipe-trinotate/db/uniprot_sprot" 
RNAMMER_PATH="/work/lorencm/apps/rnammer-1.2.src/rnammer" 
PFAM_DB="/work/lorencm/bpipe-trinotate/db/Pfam-A.hmm" 

transdecoder = { 
        transform("fasta.transdecoder.pep","fasta.transdecoder.cds","fasta.transdecoder.bed","fasta.transdecoder.gff3"){ 
                exec """ 
                TransDecoder -t $input.fasta -m 100 --search_pfam $PFAM_DB --CPU $NCPU 
                """ 
        } 
} 

blastx = { 
        exec """ 
        blastx -query $input.fasta -db $SWISSPROTDB -num_threads $NCPU -max_target_seqs 1 -outfmt 6 > $output 
        """ 
} 

blastp = { 
        exec """ 
        blastp -query $input.pep -db $SWISSPROTDB -num_threads $NCPU -max_target_seqs 1 -outfmt 6 > $output 
        """ 
} 

hmmscan = { 
        produce("hmmscan.out"){ 
        exec """ 
        hmmscan --cpu $NCPU --domtblout hmmscan.out  $PFAM_DB $input.pep > pfam.log 
        """ 
        }         
} 

signalp = { 
        produce("signalp.out"){ 
                exec """ 
                signalp -f short -n signalp.out $input.pep 
                """ 
        } 
} 
         
tmhmm = { 
        produce("tmhmm.out"){ 
                exec """ 
                tmhmm --short < $input.pep > tmhmm.out 
                """ 
        } 
} 


// This stage invariably fails with exit code 999 
rnammmer = { 
        produce(input.prefix+".rnammer.gff"){ 
                exec """ 
                RnammerTranscriptome.pl --transcriptome $input.fasta --path_to_rnammer $RNAMMER_PATH 
                """ 
        } 
} 

download_sqlite_template = { 
        exec """ 
        cp \$TRINOTATE_DB . 
        """ 
} 

create_transmap = { 
        exec """ 
        get_Trinity_gene_to_trans_map.pl $input.fasta >  Trinity.fasta.gene_trans_map 
        """ 
} 

load_data = { 
        exec """ 
        Trinotate Trinotate.sqlite init --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta Trinity.fasta --transdecoder_pep Trinity.fasta.transdecoder.pep 

        Trinotate Trinotate.sqlite LOAD_swissprot_blastp Trinity.fasta.transdecoder.pep.blastp 

        Trinotate Trinotate.sqlite LOAD_swissprot_blastx Trinity.fasta.blastx 

        Trinotate Trinotate.sqlite LOAD_pfam hmmscan.out 

        Trinotate Trinotate.sqlite LOAD_tmhmm tmhmm.out 

        Trinotate Trinotate.sqlite LOAD_signalp signalp.out 
        """ 
} 

load_rnammer = { 
        exec """ 
        Trinotate Trinotate.sqlite LOAD_rnammer Trinity.fasta.rnammmer.gff 
        """ 
} 

//run { transdecoder+[blastx,blastp,hmmscan,signalp,tmhmm] } 
run { transdecoder+[blastx,blastp,hmmscan,signalp,tmhmm]+download_sqlite_template+create_transmap+load_data+rnammmer+load_rnammer}