[2023-03-15 17:56:53,187] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:56:53,187] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:56:53,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg5010cfa0-50d5-4347-8119-10307f3314d6/dqc_reference
[2023-03-15 17:56:57,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:56:57,419] [INFO] Task started: Prodigal
[2023-03-15 17:56:57,420] [INFO] Running command: cat /var/lib/cwl/stgdeafe257-e41c-491f-84cd-93029b989fba/OceanDNA-b38656.fa | prodigal -d OceanDNA-b38656/cds.fna -a OceanDNA-b38656/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:57:06,146] [INFO] Task succeeded: Prodigal
[2023-03-15 17:57:06,146] [INFO] Task started: HMMsearch
[2023-03-15 17:57:06,146] [INFO] Running command: hmmsearch --tblout OceanDNA-b38656/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5010cfa0-50d5-4347-8119-10307f3314d6/dqc_reference/reference_markers.hmm OceanDNA-b38656/protein.faa > /dev/null
[2023-03-15 17:57:06,400] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:57:06,401] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdeafe257-e41c-491f-84cd-93029b989fba/OceanDNA-b38656.fa]
[2023-03-15 17:57:06,437] [INFO] Query marker FASTA was written to OceanDNA-b38656/markers.fasta
[2023-03-15 17:57:06,437] [INFO] Task started: Blastn
[2023-03-15 17:57:06,437] [INFO] Running command: blastn -query OceanDNA-b38656/markers.fasta -db /var/lib/cwl/stg5010cfa0-50d5-4347-8119-10307f3314d6/dqc_reference/reference_markers.fasta -out OceanDNA-b38656/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:57:09,735] [INFO] Task succeeded: Blastn
[2023-03-15 17:57:09,736] [INFO] Selected 24 target genomes.
[2023-03-15 17:57:09,736] [INFO] Target genome list was writen to OceanDNA-b38656/target_genomes.txt
[2023-03-15 17:57:09,827] [INFO] Task started: fastANI
[2023-03-15 17:57:09,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeafe257-e41c-491f-84cd-93029b989fba/OceanDNA-b38656.fa --refList OceanDNA-b38656/target_genomes.txt --output OceanDNA-b38656/fastani_result.tsv --threads 1
[2023-03-15 17:57:27,858] [INFO] Task succeeded: fastANI
[2023-03-15 17:57:27,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5010cfa0-50d5-4347-8119-10307f3314d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:57:27,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5010cfa0-50d5-4347-8119-10307f3314d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:57:27,862] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 17:57:27,862] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 17:57:27,862] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Neptunomonas marina	strain=HPM-16	GCA_004005935.1	1815562	1815562	type	True	98.0532	451	465	95	conclusive
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	77.4289	57	465	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:57:27,862] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38656/tc_result.tsv
[2023-03-15 17:57:27,862] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:57:27,862] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:57:27,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5010cfa0-50d5-4347-8119-10307f3314d6/dqc_reference/checkm_data
[2023-03-15 17:57:27,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:57:27,867] [INFO] Task started: CheckM
[2023-03-15 17:57:27,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38656/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38656/checkm_input OceanDNA-b38656/checkm_result
[2023-03-15 17:58:00,423] [INFO] Task succeeded: CheckM
[2023-03-15 17:58:00,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:58:00,425] [INFO] ===== Completeness check finished =====
[2023-03-15 17:58:00,425] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:58:00,426] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38656/markers.fasta)
[2023-03-15 17:58:00,426] [INFO] Task started: Blastn
[2023-03-15 17:58:00,426] [INFO] Running command: blastn -query OceanDNA-b38656/markers.fasta -db /var/lib/cwl/stg5010cfa0-50d5-4347-8119-10307f3314d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38656/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:58:02,365] [INFO] Task succeeded: Blastn
[2023-03-15 17:58:02,366] [INFO] Selected 21 target genomes.
[2023-03-15 17:58:02,366] [INFO] Target genome list was writen to OceanDNA-b38656/target_genomes_gtdb.txt
[2023-03-15 17:58:02,619] [INFO] Task started: fastANI
[2023-03-15 17:58:02,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeafe257-e41c-491f-84cd-93029b989fba/OceanDNA-b38656.fa --refList OceanDNA-b38656/target_genomes_gtdb.txt --output OceanDNA-b38656/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:58:15,506] [INFO] Task succeeded: fastANI
[2023-03-15 17:58:15,508] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:58:15,508] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004005935.1	s__Neptunomonas marina	98.0532	451	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	97.03	97.03	0.93	0.93	2	conclusive
GCF_008630635.1	s__Neptunomonas concharum	77.4289	57	465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:58:15,508] [INFO] GTDB search result was written to OceanDNA-b38656/result_gtdb.tsv
[2023-03-15 17:58:15,509] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:58:15,511] [INFO] DFAST_QC result json was written to OceanDNA-b38656/dqc_result.json
[2023-03-15 17:58:15,511] [INFO] DFAST_QC completed!
[2023-03-15 17:58:15,511] [INFO] Total running time: 0h1m22s