First attempt to run test job fails

[jorvis]

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

[gooday92]

I get the same problem, do you have any advice?