[2024-01-24 12:21:56,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:56,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:56,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a073077-2ce9-4611-bcbd-01532a0649d9/dqc_reference
[2024-01-24 12:21:57,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:57,921] [INFO] Task started: Prodigal
[2024-01-24 12:21:57,921] [INFO] Running command: gunzip -c /var/lib/cwl/stgac3ae1ab-428f-49c0-a56a-452eb3d2684c/GCF_004565475.1_UNH_Lko_1.0_genomic.fna.gz | prodigal -d GCF_004565475.1_UNH_Lko_1.0_genomic.fna/cds.fna -a GCF_004565475.1_UNH_Lko_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:03,884] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:03,884] [INFO] Task started: HMMsearch
[2024-01-24 12:22:03,884] [INFO] Running command: hmmsearch --tblout GCF_004565475.1_UNH_Lko_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a073077-2ce9-4611-bcbd-01532a0649d9/dqc_reference/reference_markers.hmm GCF_004565475.1_UNH_Lko_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:04,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:04,205] [INFO] Found 6/6 markers.
[2024-01-24 12:22:04,232] [INFO] Query marker FASTA was written to GCF_004565475.1_UNH_Lko_1.0_genomic.fna/markers.fasta
[2024-01-24 12:22:04,233] [INFO] Task started: Blastn
[2024-01-24 12:22:04,233] [INFO] Running command: blastn -query GCF_004565475.1_UNH_Lko_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a073077-2ce9-4611-bcbd-01532a0649d9/dqc_reference/reference_markers.fasta -out GCF_004565475.1_UNH_Lko_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:04,953] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:04,956] [INFO] Selected 21 target genomes.
[2024-01-24 12:22:04,956] [INFO] Target genome list was writen to GCF_004565475.1_UNH_Lko_1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:22:05,016] [INFO] Task started: fastANI
[2024-01-24 12:22:05,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3ae1ab-428f-49c0-a56a-452eb3d2684c/GCF_004565475.1_UNH_Lko_1.0_genomic.fna.gz --refList GCF_004565475.1_UNH_Lko_1.0_genomic.fna/target_genomes.txt --output GCF_004565475.1_UNH_Lko_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:16,356] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:16,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a073077-2ce9-4611-bcbd-01532a0649d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:16,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a073077-2ce9-4611-bcbd-01532a0649d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:16,377] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:16,377] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:16,377] [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
Lonepinella koalarum	strain=ATCC 700131	GCA_004565475.1	53417	53417	type	True	100.0	819	819	95	conclusive
Lonepinella koalarum	strain=DSM 10053	GCA_004339625.1	53417	53417	type	True	99.995	817	819	95	conclusive
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	78.1486	249	819	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	78.1334	250	819	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	77.9431	178	819	95	below_threshold
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	77.7522	179	819	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	77.733	134	819	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	77.7132	133	819	95	below_threshold
Pasteurella bettyae	strain=NCTC10535	GCA_900454515.1	752	752	suspected-type	True	77.584	194	819	95	below_threshold
Avibacterium paragallinarum	strain=CCUG 12835	GCA_002921155.1	728	728	type	True	77.5752	166	819	95	below_threshold
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	77.4786	138	819	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	77.4424	189	819	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	77.3788	174	819	95	below_threshold
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	77.3648	193	819	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	77.3233	180	819	95	below_threshold
Pasteurella dagmatis	strain=ATCC 43325	GCA_000163475.1	754	754	type	True	77.2054	175	819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:16,379] [INFO] DFAST Taxonomy check result was written to GCF_004565475.1_UNH_Lko_1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:22:16,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:16,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:16,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a073077-2ce9-4611-bcbd-01532a0649d9/dqc_reference/checkm_data
[2024-01-24 12:22:16,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:16,413] [INFO] Task started: CheckM
[2024-01-24 12:22:16,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004565475.1_UNH_Lko_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004565475.1_UNH_Lko_1.0_genomic.fna/checkm_input GCF_004565475.1_UNH_Lko_1.0_genomic.fna/checkm_result
[2024-01-24 12:22:40,490] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:40,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:40,518] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:40,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:40,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004565475.1_UNH_Lko_1.0_genomic.fna/markers.fasta)
[2024-01-24 12:22:40,519] [INFO] Task started: Blastn
[2024-01-24 12:22:40,520] [INFO] Running command: blastn -query GCF_004565475.1_UNH_Lko_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a073077-2ce9-4611-bcbd-01532a0649d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004565475.1_UNH_Lko_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:41,590] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:41,594] [INFO] Selected 22 target genomes.
[2024-01-24 12:22:41,594] [INFO] Target genome list was writen to GCF_004565475.1_UNH_Lko_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:41,609] [INFO] Task started: fastANI
[2024-01-24 12:22:41,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3ae1ab-428f-49c0-a56a-452eb3d2684c/GCF_004565475.1_UNH_Lko_1.0_genomic.fna.gz --refList GCF_004565475.1_UNH_Lko_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_004565475.1_UNH_Lko_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:51,041] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:51,064] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:51,065] [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_004565475.1	s__Lonepinella koalarum	100.0	819	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Lonepinella	95.0	99.41	98.83	0.96	0.92	3	conclusive
GCF_901764995.1	s__Basfia_A porcinus	78.1334	250	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003096995.1	s__Basfia_A langaaensis	78.0375	226	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900444965.1	s__Basfia_A rossii	77.9375	240	819	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_014843355.1	s__Basfia_A sp014843355	77.8304	151	819	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_000210895.1	s__Haemophilus_D parainfluenzae_A	77.743	178	819	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_900450705.1	s__Avibacterium paragallinarum	77.7161	181	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	97.58	96.82	0.90	0.82	41	-
GCF_003252755.1	s__Haemophilus_D parainfluenzae_N	77.6953	183	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.46	95.02	0.94	0.93	5	-
GCF_003493605.1	s__Haemophilus haemolyticus_J	77.6715	152	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	77.558	186	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCA_905205995.1	s__Haemophilus_D sp905205995	77.5495	176	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001752465.1	s__Haemophilus quentini	77.5411	155	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	99.94	99.85	0.97	0.94	5	-
GCA_018381425.1	s__Haemophilus_D parainfluenzae_O	77.5041	112	819	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_001999305.1	s__Rodentibacter myodis	77.4767	189	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521605.1	s__Mannheimia sp000521605	77.4314	139	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379905.1	s__Rodentibacter pneumotropicus	77.4061	169	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
GCA_900756155.1	s__Haemophilus_D sp900756155	77.3739	181	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCF_000262245.1	s__Basfia bettyae	77.3616	193	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	-
GCA_900756875.1	s__Haemophilus_D sp900756875	77.3564	164	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.91	95.91	0.89	0.89	2	-
GCF_900186835.1	s__Pasteurella dagmatis	77.3356	182	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCF_014202395.1	s__Histophilus somni	77.1066	153	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Histophilus	95.0	99.10	98.34	0.94	0.85	61	-
GCA_905207935.1	s__Haemophilus_D sp905207935	76.9766	152	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:51,066] [INFO] GTDB search result was written to GCF_004565475.1_UNH_Lko_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:51,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:51,071] [INFO] DFAST_QC result json was written to GCF_004565475.1_UNH_Lko_1.0_genomic.fna/dqc_result.json
[2024-01-24 12:22:51,071] [INFO] DFAST_QC completed!
[2024-01-24 12:22:51,071] [INFO] Total running time: 0h0m54s