[2024-01-25 18:43:52,560] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:52,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:52,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ddf4d0d-3dc2-41c7-943b-4ecbb5730cfe/dqc_reference
[2024-01-25 18:43:53,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:53,679] [INFO] Task started: Prodigal
[2024-01-25 18:43:53,679] [INFO] Running command: gunzip -c /var/lib/cwl/stgf898eb28-4906-46f0-bd43-c6c145dffa17/GCF_002795425.1_ASM279542v1_genomic.fna.gz | prodigal -d GCF_002795425.1_ASM279542v1_genomic.fna/cds.fna -a GCF_002795425.1_ASM279542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:58,637] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:58,637] [INFO] Task started: HMMsearch
[2024-01-25 18:43:58,637] [INFO] Running command: hmmsearch --tblout GCF_002795425.1_ASM279542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ddf4d0d-3dc2-41c7-943b-4ecbb5730cfe/dqc_reference/reference_markers.hmm GCF_002795425.1_ASM279542v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:58,842] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:58,843] [INFO] Found 6/6 markers.
[2024-01-25 18:43:58,865] [INFO] Query marker FASTA was written to GCF_002795425.1_ASM279542v1_genomic.fna/markers.fasta
[2024-01-25 18:43:58,866] [INFO] Task started: Blastn
[2024-01-25 18:43:58,866] [INFO] Running command: blastn -query GCF_002795425.1_ASM279542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ddf4d0d-3dc2-41c7-943b-4ecbb5730cfe/dqc_reference/reference_markers.fasta -out GCF_002795425.1_ASM279542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:59,456] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:59,459] [INFO] Selected 22 target genomes.
[2024-01-25 18:43:59,459] [INFO] Target genome list was writen to GCF_002795425.1_ASM279542v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:59,467] [INFO] Task started: fastANI
[2024-01-25 18:43:59,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgf898eb28-4906-46f0-bd43-c6c145dffa17/GCF_002795425.1_ASM279542v1_genomic.fna.gz --refList GCF_002795425.1_ASM279542v1_genomic.fna/target_genomes.txt --output GCF_002795425.1_ASM279542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:08,833] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:08,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ddf4d0d-3dc2-41c7-943b-4ecbb5730cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:08,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ddf4d0d-3dc2-41c7-943b-4ecbb5730cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:08,844] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:08,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:08,844] [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
Conservatibacter flavescens	strain=7.4	GCA_002795425.1	28161	28161	type	True	100.0	843	845	95	conclusive
Volucribacter psittacicida	strain=DSM 15534	GCA_004339025.1	203482	203482	type	True	77.9025	221	845	95	below_threshold
Pasteurella multocida subsp. gallicida	strain=NCTC10204	GCA_900636625.1	123812	747	type	True	77.8171	166	845	95	below_threshold
Pasteurella canis	strain=NCTC11621	GCA_900454865.1	753	753	type	True	77.7924	177	845	95	below_threshold
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	77.7903	128	845	95	below_threshold
Canicola haemoglobinophilus	strain=CCUG 3714	GCA_002015075.1	733	733	type	True	77.6786	169	845	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	77.6695	153	845	95	below_threshold
Aggregatibacter segnis	strain=NCTC10977	GCA_900476035.1	739	739	type	True	77.6561	129	845	95	below_threshold
Aggregatibacter segnis	strain=FDAARGOS_987	GCA_016127115.1	739	739	type	True	77.5996	132	845	95	below_threshold
Canicola haemoglobinophilus	strain=NCTC1659	GCA_900450725.1	733	733	type	True	77.5811	177	845	95	below_threshold
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	77.5255	163	845	95	below_threshold
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	77.5207	130	845	95	below_threshold
Basfia succiniciproducens	strain=DSM 22022	GCA_900101275.1	653940	653940	suspected-type	True	77.4797	120	845	95	below_threshold
Basfia succiniciproducens	strain=JF4016	GCA_011455875.1	653940	653940	suspected-type	True	77.4715	115	845	95	below_threshold
Bisgaardia hudsonensis	strain=DSM 28231	GCA_004345785.1	109472	109472	type	True	77.2822	149	845	95	below_threshold
Actinobacillus ureae	strain=ATCC 25976	GCA_000188255.1	723	723	type	True	77.278	106	845	95	below_threshold
Rodentibacter mrazii	strain=Ppn418	GCA_001998825.1	1908257	1908257	type	True	77.2492	152	845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:08,846] [INFO] DFAST Taxonomy check result was written to GCF_002795425.1_ASM279542v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:08,846] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:08,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:08,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ddf4d0d-3dc2-41c7-943b-4ecbb5730cfe/dqc_reference/checkm_data
[2024-01-25 18:44:08,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:08,874] [INFO] Task started: CheckM
[2024-01-25 18:44:08,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002795425.1_ASM279542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002795425.1_ASM279542v1_genomic.fna/checkm_input GCF_002795425.1_ASM279542v1_genomic.fna/checkm_result
[2024-01-25 18:44:29,040] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:29,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:29,056] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:29,056] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:29,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002795425.1_ASM279542v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:29,057] [INFO] Task started: Blastn
[2024-01-25 18:44:29,057] [INFO] Running command: blastn -query GCF_002795425.1_ASM279542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ddf4d0d-3dc2-41c7-943b-4ecbb5730cfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_002795425.1_ASM279542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:29,908] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:29,910] [INFO] Selected 22 target genomes.
[2024-01-25 18:44:29,911] [INFO] Target genome list was writen to GCF_002795425.1_ASM279542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:29,923] [INFO] Task started: fastANI
[2024-01-25 18:44:29,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgf898eb28-4906-46f0-bd43-c6c145dffa17/GCF_002795425.1_ASM279542v1_genomic.fna.gz --refList GCF_002795425.1_ASM279542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002795425.1_ASM279542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:39,261] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:39,272] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:39,272] [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_002795425.1	s__Conservatibacter flavescens	100.0	843	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Conservatibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900637275.1	s__Actinobacillus_B aerogenes	77.9985	162	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339025.1	s__Volucribacter psittacicida	77.9025	221	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Volucribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454865.1	s__Pasteurella canis	77.8096	176	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.76	98.68	0.94	0.91	4	-
GCF_002850605.1	s__Pasteurella oralis	77.7276	180	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002015075.1	s__Canicola haemoglobinophilus	77.6991	168	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Canicola	95.0	99.15	98.65	0.96	0.92	4	-
GCF_900454535.1	s__Avibacterium avium	77.6704	152	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_900635775.1	s__Avibacterium volantium	77.5483	163	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCA_905205995.1	s__Haemophilus_D sp905205995	77.4619	146	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096995.1	s__Basfia_A langaaensis	77.4561	160	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455875.1	s__Basfia succiniciproducens	77.4462	116	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	99.17	98.70	0.95	0.93	4	-
GCF_013377195.1	s__Bisgaardia hudsonensis	77.2328	152	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000379905.1	s__Rodentibacter pneumotropicus	77.1757	149	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
GCF_001999425.1	s__Rodentibacter sp001999425	77.116	145	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202395.1	s__Histophilus somni	77.0786	154	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Histophilus	95.0	99.10	98.34	0.94	0.85	61	-
GCF_001678475.1	s__Gallibacterium sp001678475	77.0552	130	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	96.69	96.63	0.86	0.84	3	-
GCA_015255025.1	s__Haemophilus_D sp015255025	76.7011	118	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:39,281] [INFO] GTDB search result was written to GCF_002795425.1_ASM279542v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:39,281] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:39,285] [INFO] DFAST_QC result json was written to GCF_002795425.1_ASM279542v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:39,285] [INFO] DFAST_QC completed!
[2024-01-25 18:44:39,285] [INFO] Total running time: 0h0m47s