[2024-01-24 11:12:58,028] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,032] [INFO] DQC Reference Directory: /var/lib/cwl/stg14dc2324-45ff-41ce-9cff-7a92985b6d3b/dqc_reference
[2024-01-24 11:12:59,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,572] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,572] [INFO] Running command: gunzip -c /var/lib/cwl/stg9781b148-9fb9-4cda-9cb9-be031fb01df6/GCF_004339625.1_ASM433962v1_genomic.fna.gz | prodigal -d GCF_004339625.1_ASM433962v1_genomic.fna/cds.fna -a GCF_004339625.1_ASM433962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:05,207] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:05,208] [INFO] Task started: HMMsearch
[2024-01-24 11:13:05,208] [INFO] Running command: hmmsearch --tblout GCF_004339625.1_ASM433962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14dc2324-45ff-41ce-9cff-7a92985b6d3b/dqc_reference/reference_markers.hmm GCF_004339625.1_ASM433962v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:05,461] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:05,463] [INFO] Found 6/6 markers.
[2024-01-24 11:13:05,492] [INFO] Query marker FASTA was written to GCF_004339625.1_ASM433962v1_genomic.fna/markers.fasta
[2024-01-24 11:13:05,493] [INFO] Task started: Blastn
[2024-01-24 11:13:05,493] [INFO] Running command: blastn -query GCF_004339625.1_ASM433962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14dc2324-45ff-41ce-9cff-7a92985b6d3b/dqc_reference/reference_markers.fasta -out GCF_004339625.1_ASM433962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:06,187] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:06,190] [INFO] Selected 21 target genomes.
[2024-01-24 11:13:06,190] [INFO] Target genome list was writen to GCF_004339625.1_ASM433962v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:06,216] [INFO] Task started: fastANI
[2024-01-24 11:13:06,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg9781b148-9fb9-4cda-9cb9-be031fb01df6/GCF_004339625.1_ASM433962v1_genomic.fna.gz --refList GCF_004339625.1_ASM433962v1_genomic.fna/target_genomes.txt --output GCF_004339625.1_ASM433962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:15,890] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:15,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14dc2324-45ff-41ce-9cff-7a92985b6d3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:15,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14dc2324-45ff-41ce-9cff-7a92985b6d3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:15,903] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:15,903] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:15,904] [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=DSM 10053	GCA_004339625.1	53417	53417	type	True	100.0	821	822	95	conclusive
Lonepinella koalarum	strain=ATCC 700131	GCA_004565475.1	53417	53417	type	True	99.9914	815	822	95	conclusive
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	78.0934	255	822	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	78.0784	257	822	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.0018	176	822	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.0007	132	822	95	below_threshold
Actinobacillus equuli	strain=NCTC8529	GCA_900636745.1	718	718	type	True	77.8991	126	822	95	below_threshold
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	77.8083	172	822	95	below_threshold
Avibacterium paragallinarum	strain=CCUG 12835	GCA_002921155.1	728	728	type	True	77.7257	158	822	95	below_threshold
Pasteurella bettyae	strain=NCTC10535	GCA_900454515.1	752	752	suspected-type	True	77.5854	198	822	95	below_threshold
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	77.537	190	822	95	below_threshold
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	77.436	195	822	95	below_threshold
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	77.4286	134	822	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	77.3367	180	822	95	below_threshold
Pasteurella dagmatis	strain=ATCC 43325	GCA_000163475.1	754	754	type	True	77.2937	176	822	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	77.191	177	822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:15,905] [INFO] DFAST Taxonomy check result was written to GCF_004339625.1_ASM433962v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:15,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:15,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:15,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14dc2324-45ff-41ce-9cff-7a92985b6d3b/dqc_reference/checkm_data
[2024-01-24 11:13:15,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:15,933] [INFO] Task started: CheckM
[2024-01-24 11:13:15,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339625.1_ASM433962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339625.1_ASM433962v1_genomic.fna/checkm_input GCF_004339625.1_ASM433962v1_genomic.fna/checkm_result
[2024-01-24 11:13:40,351] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:40,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:40,376] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:40,377] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:40,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339625.1_ASM433962v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:40,378] [INFO] Task started: Blastn
[2024-01-24 11:13:40,379] [INFO] Running command: blastn -query GCF_004339625.1_ASM433962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14dc2324-45ff-41ce-9cff-7a92985b6d3b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339625.1_ASM433962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:41,499] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:41,502] [INFO] Selected 22 target genomes.
[2024-01-24 11:13:41,503] [INFO] Target genome list was writen to GCF_004339625.1_ASM433962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:41,524] [INFO] Task started: fastANI
[2024-01-24 11:13:41,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg9781b148-9fb9-4cda-9cb9-be031fb01df6/GCF_004339625.1_ASM433962v1_genomic.fna.gz --refList GCF_004339625.1_ASM433962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339625.1_ASM433962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:50,174] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:50,199] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:50,199] [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	99.9914	815	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Lonepinella	95.0	99.41	98.83	0.96	0.92	3	conclusive
GCA_900444965.1	s__Basfia_A rossii	78.1204	235	822	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_901764995.1	s__Basfia_A porcinus	78.0924	256	822	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	78.0301	226	822	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_900450705.1	s__Avibacterium paragallinarum	77.8655	169	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	97.58	96.82	0.90	0.82	41	-
GCF_000210895.1	s__Haemophilus_D parainfluenzae_A	77.8426	178	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	-
GCA_905205995.1	s__Haemophilus_D sp905205995	77.8406	166	822	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_003252755.1	s__Haemophilus_D parainfluenzae_N	77.7751	180	822	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_014843355.1	s__Basfia_A sp014843355	77.6637	157	822	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_003493605.1	s__Haemophilus haemolyticus_J	77.5927	158	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999305.1	s__Rodentibacter myodis	77.5362	190	822	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	77.5041	140	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900756155.1	s__Haemophilus_D sp900756155	77.5032	179	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCA_001752465.1	s__Haemophilus quentini	77.4967	153	822	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	77.4966	112	822	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_003253005.1	s__Haemophilus_D parainfluenzae_M	77.4836	188	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCF_000262245.1	s__Basfia bettyae	77.436	195	822	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	77.4109	160	822	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	77.3317	178	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCA_905207935.1	s__Haemophilus_D sp905207935	77.3288	147	822	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_000379905.1	s__Rodentibacter pneumotropicus	77.2683	175	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
GCF_014202395.1	s__Histophilus somni	77.0424	144	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Histophilus	95.0	99.10	98.34	0.94	0.85	61	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:50,200] [INFO] GTDB search result was written to GCF_004339625.1_ASM433962v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:50,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:50,206] [INFO] DFAST_QC result json was written to GCF_004339625.1_ASM433962v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:50,206] [INFO] DFAST_QC completed!
[2024-01-24 11:13:50,206] [INFO] Total running time: 0h0m52s