[2023-06-04 21:08:48,587] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:08:48,589] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:08:48,589] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6407090-4cfc-4181-9004-dc18b4881ad5/dqc_reference
[2023-06-04 21:08:50,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:08:50,192] [INFO] Task started: Prodigal
[2023-06-04 21:08:50,192] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc6bde5-d4df-44de-8f53-bde424293296/GCA_934233085.1_ERR7745888_bin.73_genomic.fna.gz | prodigal -d GCA_934233085.1_ERR7745888_bin.73_genomic.fna/cds.fna -a GCA_934233085.1_ERR7745888_bin.73_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:08:53,645] [INFO] Task succeeded: Prodigal
[2023-06-04 21:08:53,646] [INFO] Task started: HMMsearch
[2023-06-04 21:08:53,646] [INFO] Running command: hmmsearch --tblout GCA_934233085.1_ERR7745888_bin.73_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6407090-4cfc-4181-9004-dc18b4881ad5/dqc_reference/reference_markers.hmm GCA_934233085.1_ERR7745888_bin.73_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:08:53,887] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:08:53,889] [INFO] Found 6/6 markers.
[2023-06-04 21:08:53,913] [INFO] Query marker FASTA was written to GCA_934233085.1_ERR7745888_bin.73_genomic.fna/markers.fasta
[2023-06-04 21:08:53,914] [INFO] Task started: Blastn
[2023-06-04 21:08:53,914] [INFO] Running command: blastn -query GCA_934233085.1_ERR7745888_bin.73_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6407090-4cfc-4181-9004-dc18b4881ad5/dqc_reference/reference_markers.fasta -out GCA_934233085.1_ERR7745888_bin.73_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:08:54,628] [INFO] Task succeeded: Blastn
[2023-06-04 21:08:54,632] [INFO] Selected 7 target genomes.
[2023-06-04 21:08:54,632] [INFO] Target genome list was writen to GCA_934233085.1_ERR7745888_bin.73_genomic.fna/target_genomes.txt
[2023-06-04 21:08:54,638] [INFO] Task started: fastANI
[2023-06-04 21:08:54,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc6bde5-d4df-44de-8f53-bde424293296/GCA_934233085.1_ERR7745888_bin.73_genomic.fna.gz --refList GCA_934233085.1_ERR7745888_bin.73_genomic.fna/target_genomes.txt --output GCA_934233085.1_ERR7745888_bin.73_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:08:58,185] [INFO] Task succeeded: fastANI
[2023-06-04 21:08:58,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6407090-4cfc-4181-9004-dc18b4881ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:08:58,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6407090-4cfc-4181-9004-dc18b4881ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:08:58,194] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-04 21:08:58,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 21:08:58,194] [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
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	95.0482	359	395	95	conclusive
Haemophilus parahaemolyticus	strain=FDAARGOS_1199	GCA_016889385.1	735	735	type	True	89.773	321	395	95	below_threshold
Haemophilus parahaemolyticus	strain=NCTC 8479	GCA_900450675.1	735	735	type	True	89.748	325	395	95	below_threshold
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	89.7034	324	395	95	below_threshold
Haemophilus parahaemolyticus	strain=HK385	GCA_000262265.1	735	735	type	True	89.6269	325	395	95	below_threshold
Haemophilus sputorum	strain=CCUG 13788	GCA_000238795.2	1078480	1078480	type	True	78.3173	155	395	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:08:58,198] [INFO] DFAST Taxonomy check result was written to GCA_934233085.1_ERR7745888_bin.73_genomic.fna/tc_result.tsv
[2023-06-04 21:08:58,199] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:08:58,199] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:08:58,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6407090-4cfc-4181-9004-dc18b4881ad5/dqc_reference/checkm_data
[2023-06-04 21:08:58,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:08:58,221] [INFO] Task started: CheckM
[2023-06-04 21:08:58,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934233085.1_ERR7745888_bin.73_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934233085.1_ERR7745888_bin.73_genomic.fna/checkm_input GCA_934233085.1_ERR7745888_bin.73_genomic.fna/checkm_result
[2023-06-04 21:09:16,364] [INFO] Task succeeded: CheckM
[2023-06-04 21:09:16,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:09:16,388] [INFO] ===== Completeness check finished =====
[2023-06-04 21:09:16,388] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:09:16,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934233085.1_ERR7745888_bin.73_genomic.fna/markers.fasta)
[2023-06-04 21:09:16,389] [INFO] Task started: Blastn
[2023-06-04 21:09:16,389] [INFO] Running command: blastn -query GCA_934233085.1_ERR7745888_bin.73_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6407090-4cfc-4181-9004-dc18b4881ad5/dqc_reference/reference_markers_gtdb.fasta -out GCA_934233085.1_ERR7745888_bin.73_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:09:17,421] [INFO] Task succeeded: Blastn
[2023-06-04 21:09:17,425] [INFO] Selected 14 target genomes.
[2023-06-04 21:09:17,425] [INFO] Target genome list was writen to GCA_934233085.1_ERR7745888_bin.73_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:09:17,706] [INFO] Task started: fastANI
[2023-06-04 21:09:17,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc6bde5-d4df-44de-8f53-bde424293296/GCA_934233085.1_ERR7745888_bin.73_genomic.fna.gz --refList GCA_934233085.1_ERR7745888_bin.73_genomic.fna/target_genomes_gtdb.txt --output GCA_934233085.1_ERR7745888_bin.73_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:09:24,483] [INFO] Task succeeded: fastANI
[2023-06-04 21:09:24,501] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:09:24,501] [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_002015045.1	s__Haemophilus_A paraphrohaemolyticus	95.0482	359	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	conclusive
GCF_002015035.1	s__Haemophilus_A parahaemolyticus	89.7657	322	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.50	95.62	0.95	0.88	11	-
GCA_018373095.1	s__Haemophilus_A parahaemolyticus_A	88.7926	295	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	78.9764	161	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_000175195.1	s__Actinobacillus_A minor	78.7266	159	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238795.1	s__Haemophilus_A sputorum	78.3004	155	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.57	96.93	0.93	0.88	6	-
GCF_014541205.1	s__Mannheimia bovis	77.9501	129	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901687125.1	s__Actinobacillus vicugnae	77.7359	146	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	77.6142	134	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCA_002002485.1	s__GCF-002002485 sp002002485	77.4795	101	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__GCF-002002485	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011455275.1	s__Frederiksenia sp011455275	77.3337	93	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002015115.1	s__Haemophilus_E paracuniculus	77.1644	106	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377995.1	s__Mannheimia pernigra	77.0792	118	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
GCF_004345745.1	s__Nicoletella semolina	75.9654	59	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Nicoletella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:09:24,506] [INFO] GTDB search result was written to GCA_934233085.1_ERR7745888_bin.73_genomic.fna/result_gtdb.tsv
[2023-06-04 21:09:24,507] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:09:24,513] [INFO] DFAST_QC result json was written to GCA_934233085.1_ERR7745888_bin.73_genomic.fna/dqc_result.json
[2023-06-04 21:09:24,513] [INFO] DFAST_QC completed!
[2023-06-04 21:09:24,513] [INFO] Total running time: 0h0m36s