ERROR: Job runner bpipe.executor.SlurmCommandExecutor failed

[Michał T. Lorenc]

Hi,
I found this workflow (https://github.com/vlsci/bpipe-trinotate/blob/master/trinotate.groovy).

I removed all module commands from it because I want to run it on one server.

This is the modified version:
-----------------------------

//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}
-----------------------------------------------------


But for some reaons I always get bpipe run trinotate.groovy /home/lorencm/assembly27_85_remove0_final.fasta

====================================================================================================
| 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.
==========================================

Any Idea what I miss?

Thank you in advance.

Michal