[2024-01-24 13:22:02,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,103] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,103] [INFO] DQC Reference Directory: /var/lib/cwl/stge1ad717e-0a2d-4ad7-9a3a-a49df7003eb9/dqc_reference
[2024-01-24 13:22:03,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,508] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bb65e61-c100-4083-8613-58638ab5ba8a/GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna.gz | prodigal -d GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/cds.fna -a GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:09,946] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:09,946] [INFO] Task started: HMMsearch
[2024-01-24 13:22:09,946] [INFO] Running command: hmmsearch --tblout GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1ad717e-0a2d-4ad7-9a3a-a49df7003eb9/dqc_reference/reference_markers.hmm GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:10,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:10,222] [INFO] Found 6/6 markers.
[2024-01-24 13:22:10,246] [INFO] Query marker FASTA was written to GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/markers.fasta
[2024-01-24 13:22:10,246] [INFO] Task started: Blastn
[2024-01-24 13:22:10,246] [INFO] Running command: blastn -query GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/markers.fasta -db /var/lib/cwl/stge1ad717e-0a2d-4ad7-9a3a-a49df7003eb9/dqc_reference/reference_markers.fasta -out GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:10,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:10,901] [INFO] Selected 35 target genomes.
[2024-01-24 13:22:10,902] [INFO] Target genome list was writen to GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/target_genomes.txt
[2024-01-24 13:22:10,930] [INFO] Task started: fastANI
[2024-01-24 13:22:10,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb65e61-c100-4083-8613-58638ab5ba8a/GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna.gz --refList GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/target_genomes.txt --output GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:25,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:25,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1ad717e-0a2d-4ad7-9a3a-a49df7003eb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:25,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1ad717e-0a2d-4ad7-9a3a-a49df7003eb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:25,745] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:25,745] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:25,746] [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
Actinobacillus seminis	strain=ATCC 15768	GCA_002263215.1	722	722	type	True	78.3274	222	815	95	below_threshold
Actinobacillus seminis	strain=NCTC10851	GCA_900460625.1	722	722	type	True	78.3045	224	815	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.2384	57	815	95	below_threshold
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	78.1912	215	815	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	78.0849	56	815	95	below_threshold
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	78.0048	213	815	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	77.9454	143	815	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	77.9426	218	815	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	77.9214	144	815	95	below_threshold
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	77.9049	198	815	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	77.8954	224	815	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	77.8562	87	815	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	77.8045	214	815	95	below_threshold
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	77.6943	178	815	95	below_threshold
Aggregatibacter segnis	strain=FDAARGOS_987	GCA_016127115.1	739	739	type	True	77.6905	184	815	95	below_threshold
Aggregatibacter segnis	strain=NCTC10977	GCA_900476035.1	739	739	type	True	77.6761	181	815	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	77.6059	137	815	95	below_threshold
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	77.5145	88	815	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	77.451	219	815	95	below_threshold
Pasteurella testudinis	strain=NCTC12150	GCA_900454705.1	761	761	type	True	77.4466	187	815	95	below_threshold
Rodentibacter rarus	strain=CCUG 17206	GCA_001998965.1	1908260	1908260	type	True	77.4362	151	815	95	below_threshold
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	77.4189	92	815	95	below_threshold
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	77.4069	133	815	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	77.3512	149	815	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_019633665.1	761	761	type	True	77.1866	184	815	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_900176075.1	761	761	type	True	77.1592	186	815	95	below_threshold
Spirabiliibacterium mucosae	strain=20609_3	GCA_014884965.1	28156	28156	type	True	76.9444	79	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:25,747] [INFO] DFAST Taxonomy check result was written to GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/tc_result.tsv
[2024-01-24 13:22:25,747] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:25,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:25,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1ad717e-0a2d-4ad7-9a3a-a49df7003eb9/dqc_reference/checkm_data
[2024-01-24 13:22:25,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:25,775] [INFO] Task started: CheckM
[2024-01-24 13:22:25,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/checkm_input GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/checkm_result
[2024-01-24 13:22:52,887] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:52,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:52,912] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:52,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:52,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/markers.fasta)
[2024-01-24 13:22:52,913] [INFO] Task started: Blastn
[2024-01-24 13:22:52,914] [INFO] Running command: blastn -query GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/markers.fasta -db /var/lib/cwl/stge1ad717e-0a2d-4ad7-9a3a-a49df7003eb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:53,912] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:53,915] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:53,915] [INFO] Target genome list was writen to GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:53,939] [INFO] Task started: fastANI
[2024-01-24 13:22:53,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb65e61-c100-4083-8613-58638ab5ba8a/GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna.gz --refList GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/target_genomes_gtdb.txt --output GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:02,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:02,131] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:02,132] [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_000827595.2	s__Necropsobacter massiliensis	100.0	814	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000752995.2	s__Necropsobacter massiliensis_B	93.5651	707	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000751835.1	s__Necropsobacter rosorum	84.7736	637	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018381425.1	s__Haemophilus_D parainfluenzae_O	81.8798	77	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.89	95.76	0.75	0.73	3	-
GCF_000210895.1	s__Haemophilus_D parainfluenzae_A	80.7457	127	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	-
GCF_002795405.1	s__Caviibacterium pharyngocola	79.1469	380	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263215.1	s__Actinobacillus_B seminis	78.3271	222	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	99.95	99.95	1.00	1.00	2	-
GCF_900635775.1	s__Avibacterium volantium	78.1969	214	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCA_900637275.1	s__Actinobacillus_B aerogenes	78.1582	245	815	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_003129965.1	s__Aggregatibacter kilianii_A	77.9271	248	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002921145.1	s__Avibacterium endocarditidis	77.9049	198	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	-
GCA_000017245.1	s__Basfia_A succinogenes	77.7384	196	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001998825.1	s__Rodentibacter mrazii	77.708	160	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
GCF_004363295.1	s__Mesocricetibacter intestinalis	77.6455	219	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373425.1	s__Mesocricetibacter sp905373425	77.603	137	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901420285.1	s__Rodentibacter sp901420285	77.559	158	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176075.1	s__Chelonobacter testudinis	77.1703	185	815	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:02,134] [INFO] GTDB search result was written to GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:02,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:02,140] [INFO] DFAST_QC result json was written to GCF_000827595.2_Necropsobacter_senegalensis_FF6_genomic.fna/dqc_result.json
[2024-01-24 13:23:02,140] [INFO] DFAST_QC completed!
[2024-01-24 13:23:02,141] [INFO] Total running time: 0h1m0s