[2024-01-25 17:41:20,622] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:20,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:20,623] [INFO] DQC Reference Directory: /var/lib/cwl/stge0d8ef20-53a8-4ff5-ae04-842224535586/dqc_reference
[2024-01-25 17:41:21,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:21,738] [INFO] Task started: Prodigal
[2024-01-25 17:41:21,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a466c5a-2414-4f61-b973-59768d745d5c/GCF_002015115.1_ASM201511v1_genomic.fna.gz | prodigal -d GCF_002015115.1_ASM201511v1_genomic.fna/cds.fna -a GCF_002015115.1_ASM201511v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:26,646] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:26,647] [INFO] Task started: HMMsearch
[2024-01-25 17:41:26,647] [INFO] Running command: hmmsearch --tblout GCF_002015115.1_ASM201511v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0d8ef20-53a8-4ff5-ae04-842224535586/dqc_reference/reference_markers.hmm GCF_002015115.1_ASM201511v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:26,847] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:26,848] [INFO] Found 6/6 markers.
[2024-01-25 17:41:26,868] [INFO] Query marker FASTA was written to GCF_002015115.1_ASM201511v1_genomic.fna/markers.fasta
[2024-01-25 17:41:26,868] [INFO] Task started: Blastn
[2024-01-25 17:41:26,868] [INFO] Running command: blastn -query GCF_002015115.1_ASM201511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0d8ef20-53a8-4ff5-ae04-842224535586/dqc_reference/reference_markers.fasta -out GCF_002015115.1_ASM201511v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:27,476] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:27,479] [INFO] Selected 21 target genomes.
[2024-01-25 17:41:27,479] [INFO] Target genome list was writen to GCF_002015115.1_ASM201511v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:27,515] [INFO] Task started: fastANI
[2024-01-25 17:41:27,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a466c5a-2414-4f61-b973-59768d745d5c/GCF_002015115.1_ASM201511v1_genomic.fna.gz --refList GCF_002015115.1_ASM201511v1_genomic.fna/target_genomes.txt --output GCF_002015115.1_ASM201511v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:37,819] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:37,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0d8ef20-53a8-4ff5-ae04-842224535586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:37,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0d8ef20-53a8-4ff5-ae04-842224535586/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:37,829] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:37,830] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:37,830] [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 paracuniculus	strain=CCUG 43573	GCA_002015115.1	734	734	type	True	100.0	669	670	95	conclusive
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	78.6736	230	670	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.6574	170	670	95	below_threshold
Actinobacillus suis	strain=ATCC 33415	GCA_000739435.1	716	716	type	True	78.561	187	670	95	below_threshold
Actinobacillus lignieresii	strain=NCTC4189	GCA_900444945.1	720	720	type	True	78.4836	187	670	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	78.3914	190	670	95	below_threshold
Bibersteinia trehalosi	strain=DSM 23101	GCA_004346205.1	47735	47735	type	True	78.3873	159	670	95	below_threshold
Mannheimia haemolytica	strain=NCTC9380	GCA_900452985.1	75985	75985	type	True	78.3512	233	670	95	below_threshold
Mannheimia haemolytica	strain=DSM 10531	GCA_004342115.1	75985	75985	type	True	78.3027	230	670	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	78.2593	180	670	95	below_threshold
Muribacter muris	strain=Ackerman80-443D	GCA_001038205.1	67855	67855	type	True	78.2186	253	670	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	78.1685	216	670	95	below_threshold
Haemophilus parahaemolyticus	strain=FDAARGOS_1199	GCA_016889385.1	735	735	type	True	78.125	198	670	95	below_threshold
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	78.0893	199	670	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000167095.1	715	715	type	True	78.0754	182	670	95	below_threshold
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	78.0283	197	670	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:37,831] [INFO] DFAST Taxonomy check result was written to GCF_002015115.1_ASM201511v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:37,832] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:37,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:37,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0d8ef20-53a8-4ff5-ae04-842224535586/dqc_reference/checkm_data
[2024-01-25 17:41:37,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:37,855] [INFO] Task started: CheckM
[2024-01-25 17:41:37,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002015115.1_ASM201511v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002015115.1_ASM201511v1_genomic.fna/checkm_input GCF_002015115.1_ASM201511v1_genomic.fna/checkm_result
[2024-01-25 17:41:57,358] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:57,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:57,375] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:57,375] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:57,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002015115.1_ASM201511v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:57,376] [INFO] Task started: Blastn
[2024-01-25 17:41:57,376] [INFO] Running command: blastn -query GCF_002015115.1_ASM201511v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0d8ef20-53a8-4ff5-ae04-842224535586/dqc_reference/reference_markers_gtdb.fasta -out GCF_002015115.1_ASM201511v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:58,276] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:58,280] [INFO] Selected 20 target genomes.
[2024-01-25 17:41:58,280] [INFO] Target genome list was writen to GCF_002015115.1_ASM201511v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:58,303] [INFO] Task started: fastANI
[2024-01-25 17:41:58,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a466c5a-2414-4f61-b973-59768d745d5c/GCF_002015115.1_ASM201511v1_genomic.fna.gz --refList GCF_002015115.1_ASM201511v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002015115.1_ASM201511v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:07,724] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:07,734] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:07,735] [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_002015115.1	s__Haemophilus_E paracuniculus	100.0	669	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013377235.1	s__Mannheimia varigena	78.7116	228	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_000374285.1	s__Actinobacillus capsulatus	78.6591	168	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739435.1	s__Actinobacillus suis	78.5835	186	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.85	99.75	0.98	0.94	7	-
GCF_900444945.1	s__Actinobacillus lignieresii	78.505	186	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_004346205.1	s__Bibersteinia trehalosi	78.4113	158	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bibersteinia	95.0	98.14	97.86	0.95	0.93	7	-
GCF_901764975.1	s__Glaesserella indolica	78.4002	225	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000521605.1	s__Mannheimia sp000521605	78.3262	221	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342115.1	s__Mannheimia haemolytica	78.268	232	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	99.19	95.33	0.93	0.85	196	-
GCF_900636745.1	s__Actinobacillus equuli	78.2584	180	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_001038205.1	s__Muribacter muris	78.2281	253	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Muribacter	95.0	96.52	96.51	0.85	0.84	5	-
GCF_014541205.1	s__Mannheimia bovis	78.1576	216	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	78.0526	201	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	-
GCA_012221805.1	s__RH1A sp012221805	78.0499	156	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__RH1A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002015035.1	s__Haemophilus_A parahaemolyticus	78.0257	195	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.50	95.62	0.95	0.88	11	-
GCF_001999285.1	s__Rodentibacter sp001999285	77.7974	90	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	97.96	97.96	0.90	0.90	3	-
GCA_006228005.1	s__Chelonobacter sp006228005	76.7998	84	670	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.89	99.87	0.94	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:07,736] [INFO] GTDB search result was written to GCF_002015115.1_ASM201511v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:07,737] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:07,740] [INFO] DFAST_QC result json was written to GCF_002015115.1_ASM201511v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:07,741] [INFO] DFAST_QC completed!
[2024-01-25 17:42:07,741] [INFO] Total running time: 0h0m47s