First attempt to run test job fails

[ghost]

I'm going to try looking into this, but in the meantime though I'd report it. Here's the output from my test run after following the documentation.

$ nextflow run companion -profile docker
N E X T F L O W ~ version 19.10.0
Launching companion/annot.nf [prickly_mcclintock] - revision: 63734f6d0c

C O M P A N I O N ~ version 1.0.2
query : /opt/companion/example-data/L_donovani.1.fasta
reference : LmjF.1
reference directory : /opt/companion/example-data/references
output directory : /opt/companion/example-output

[- ] process > truncate_input_headers -
[- ] process > truncate_input_headers -
[- ] process > sanitize_input -
executor > local (2)
[d4/a2f1c2] process > truncate_input_headers [ 0%] 0 of 1
[- ] process > sanitize_input -
[- ] process > contiguate_pseudochromosomes -
[- ] process > predict_tRNA -
[4e/8398aa] process > press_ncRNA_cms [ 0%] 0 of 1
[- ] process > predict_ncRNA -
[- ] process > merge_ncrnas -
[- ] process > exonerate_empty_hints -
[- ] process > ratt_make_ref_embl -
[- ] process > run_ratt -
[- ] process > ratt_to_gff3 -
[- ] process > transcript_empty_hints -
[- ] process > merge_hints -
executor > local (2)
[d4/a2f1c2] process > truncate_input_headers [ 0%] 0 of 1
[- ] process > sanitize_input -
executor > local (3)
[d4/a2f1c2] process > truncate_input_headers [ 0%] 0 of 1
[- ] process > sanitize_input -
[- ] process > contiguate_pseudochromosomes -
[- ] process > predict_tRNA -
[4e/8398aa] process > press_ncRNA_cms [ 0%] 0 of 1
[- ] process > predict_ncRNA -
[- ] process > merge_ncrnas -
[e2/7fdb92] process > exonerate_empty_hints [ 0%] 0 of 1
[- ] process > ratt_make_ref_embl -
[- ] process > run_ratt -
[- ] process > ratt_to_gff3 -
[- ] process > transcript_empty_hints -
[- ] process > merge_hints -
[- ] process > run_augustus_pseudo -
[- ] process > run_augustus_contigs -
[- ] process > run_snap -
[- ] process > merge_genemodels -
[- ] process > integrate_genemodels -
[- ] process > fix_polycistrons -
[- ] process > remove_exons -
[- ] process > pseudogene_indexing -
[- ] process > pseudogene_last -
[- ] process > pseudogene_calling -
[- ] process > merge_structural -
[- ] process > add_gap_features -
executor > local (3)
[d4/a2f1c2] process > truncate_input_headers [ 0%] 0 of 1
[- ] process > sanitize_input -
[- ] process > contiguate_pseudochromosomes -
[- ] process > predict_tRNA -
[4e/8398aa] process > press_ncRNA_cms [100%] 1 of 1, failed: 1 ✘
[- ] process > predict_ncRNA -
[- ] process > merge_ncrnas -
[e2/7fdb92] process > exonerate_empty_hints [ 0%] 0 of 1
[- ] process > ratt_make_ref_embl -
[- ] process > run_ratt -
[- ] process > ratt_to_gff3 -
[- ] process > transcript_empty_hints -
[- ] process > merge_hints -
[- ] process > run_augustus_pseudo -
[- ] process > run_augustus_contigs -
[- ] process > run_snap -
[- ] process > merge_genemodels -
[- ] process > integrate_genemodels -
[- ] process > fix_polycistrons -
[- ] process > remove_exons -
[- ] process > pseudogene_indexing -
[- ] process > pseudogene_last -
[- ] process > pseudogene_calling -
[- ] process > merge_structural -
[- ] process > add_gap_features -
executor > local (3)
[d4/a2f1c2] process > truncate_input_headers [100%] 1 of 1 ✔
[- ] process > sanitize_input -
[- ] process > contiguate_pseudochromosomes -
[- ] process > predict_tRNA -
[4e/8398aa] process > press_ncRNA_cms [100%] 1 of 1, failed: 1 ✘
[- ] process > predict_ncRNA -
[- ] process > merge_ncrnas -
[e2/7fdb92] process > exonerate_empty_hints [100%] 1 of 1, failed: 1
[- ] process > ratt_make_ref_embl -
[- ] process > run_ratt -
[- ] process > ratt_to_gff3 -
[- ] process > transcript_empty_hints -
[- ] process > merge_hints -
[- ] process > run_augustus_pseudo -
[- ] process > run_augustus_contigs -
[- ] process > run_snap -
[- ] process > merge_genemodels -
[- ] process > integrate_genemodels -
[- ] process > fix_polycistrons -
[- ] process > remove_exons -
[- ] process > pseudogene_indexing -
[- ] process > pseudogene_last -
[- ] process > pseudogene_calling -
[- ] process > merge_structural -
[- ] process > add_gap_features -
[- ] process > split_splice_models_at_gaps -
[- ] process > add_polypeptides -
[- ] process > get_proteins_for_orthomcl -
[- ] process > make_ref_input_for_orthomcl -
[- ] process > make_target_input_for_orthomcl -
[- ] process > blast_for_orthomcl_formatdb -
[- ] process > blast_for_orthomcl -
[- ] process > run_orthomcl -
[- ] process > annotate_orthologs -
[- ] process > run_pfam -
[- ] process > pfam_to_gff3 -
[- ] process > annotate_pfam -
[- ] process > make_distribution_gff -
[- ] process > make_distribution_gaf -
[- ] process > make_distribution_seqs -
[- ] process > make_genome_stats -
[- ] process > reference_compare -
[- ] process > make_tree -
[- ] process > blast_for_circos -
[- ] process > make_circos_inputs -
[- ] process > circos_run_chrs -
[- ] process > circos_run_bin -
[- ] process > merge_gff3_for_gff3toembl -
[- ] process > make_embl -
[- ] process > make_report -
[- ] process > make_genelist -
[- ] process > add_products_to_protein_fasta -
WARN: The operator first is useless when applied to a value channel which returns a single value by definition -- check channel ncrna_cmindex
WARN: Access to undefined parameter TRANSCRIPT_FILE -- Initialise it to a default value eg. params.TRANSCRIPT_FILE = some_value
WARN: The operator first is useless when applied to a value channel which returns a single value by definition -- check channel pseudochr_last_index
WARN: Killing pending tasks (1)
Error executing process > 'press_ncRNA_cms'

Caused by:
Process press_ncRNA_cms terminated with an error exit status (1)

Command executed:

cp /opt/data/cm/rnas.cm ./models.cm
cmpress -F models.cm

Command exit status:
1

Command output:
(empty)

Command error:
cp: cannot stat '/opt/data/cm/rnas.cm': No such file or directory

Work dir:
/opt/work/4e/8398aa9b63844d3e9e2108bcaf01e0

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line