[2024-01-24 13:08:58,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,168] [INFO] DQC Reference Directory: /var/lib/cwl/stge1bde5af-8de8-452d-8fcd-fcb2b901aa10/dqc_reference
[2024-01-24 13:08:59,408] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,408] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,409] [INFO] Running command: gunzip -c /var/lib/cwl/stgca0f1925-bbc8-4d34-8dc2-9997891ac8a1/GCF_000007745.1_ASM774v1_genomic.fna.gz | prodigal -d GCF_000007745.1_ASM774v1_genomic.fna/cds.fna -a GCF_000007745.1_ASM774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:04,635] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:04,635] [INFO] Task started: HMMsearch
[2024-01-24 13:09:04,635] [INFO] Running command: hmmsearch --tblout GCF_000007745.1_ASM774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1bde5af-8de8-452d-8fcd-fcb2b901aa10/dqc_reference/reference_markers.hmm GCF_000007745.1_ASM774v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:04,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:04,869] [INFO] Found 6/6 markers.
[2024-01-24 13:09:04,893] [INFO] Query marker FASTA was written to GCF_000007745.1_ASM774v1_genomic.fna/markers.fasta
[2024-01-24 13:09:04,894] [INFO] Task started: Blastn
[2024-01-24 13:09:04,894] [INFO] Running command: blastn -query GCF_000007745.1_ASM774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1bde5af-8de8-452d-8fcd-fcb2b901aa10/dqc_reference/reference_markers.fasta -out GCF_000007745.1_ASM774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:05,583] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:05,587] [INFO] Selected 22 target genomes.
[2024-01-24 13:09:05,587] [INFO] Target genome list was writen to GCF_000007745.1_ASM774v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:05,768] [INFO] Task started: fastANI
[2024-01-24 13:09:05,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0f1925-bbc8-4d34-8dc2-9997891ac8a1/GCF_000007745.1_ASM774v1_genomic.fna.gz --refList GCF_000007745.1_ASM774v1_genomic.fna/target_genomes.txt --output GCF_000007745.1_ASM774v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:15,838] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:15,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1bde5af-8de8-452d-8fcd-fcb2b901aa10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:15,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1bde5af-8de8-452d-8fcd-fcb2b901aa10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:15,854] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:15,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:15,854] [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
Basfia succiniciproducens	strain=DSM 22022	GCA_900101275.1	653940	653940	suspected-type	True	98.8432	685	771	95	conclusive
Basfia succiniciproducens	strain=JF4016	GCA_011455875.1	653940	653940	suspected-type	True	98.8384	702	771	95	conclusive
Pasteurella canis	strain=NCTC11621	GCA_900454865.1	753	753	type	True	79.0189	117	771	95	below_threshold
Pasteurella bettyae	strain=NCTC10535	GCA_900454515.1	752	752	suspected-type	True	79.01	268	771	95	below_threshold
Pasteurella multocida subsp. septica	strain=NCTC11995	GCA_900454845.1	115545	747	type	True	79.0067	139	771	95	below_threshold
Pasteurella multocida subsp. gallicida	strain=NCTC10204	GCA_900636625.1	123812	747	type	True	78.9595	146	771	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.9471	152	771	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	78.8359	139	771	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	78.6684	196	771	95	below_threshold
Pasteurella bettyae	strain=CCUG 2042	GCA_000262245.1	752	752	suspected-type	True	78.4488	260	771	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.425	197	771	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	78.2607	223	771	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	78.2273	225	771	95	below_threshold
Mesocricetibacter intestinalis	strain=DSM 28403	GCA_004363295.1	1521930	1521930	type	True	77.9864	215	771	95	below_threshold
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	76.9852	106	771	95	below_threshold
Testudinibacter aquarius	strain=ELNT2X	GCA_009761355.1	1524974	1524974	type	True	76.8806	104	771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:15,856] [INFO] DFAST Taxonomy check result was written to GCF_000007745.1_ASM774v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:15,856] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:15,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:15,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1bde5af-8de8-452d-8fcd-fcb2b901aa10/dqc_reference/checkm_data
[2024-01-24 13:09:15,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:15,882] [INFO] Task started: CheckM
[2024-01-24 13:09:15,882] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000007745.1_ASM774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000007745.1_ASM774v1_genomic.fna/checkm_input GCF_000007745.1_ASM774v1_genomic.fna/checkm_result
[2024-01-24 13:09:37,974] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:37,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:37,994] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:37,994] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:37,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000007745.1_ASM774v1_genomic.fna/markers.fasta)
[2024-01-24 13:09:37,995] [INFO] Task started: Blastn
[2024-01-24 13:09:37,995] [INFO] Running command: blastn -query GCF_000007745.1_ASM774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1bde5af-8de8-452d-8fcd-fcb2b901aa10/dqc_reference/reference_markers_gtdb.fasta -out GCF_000007745.1_ASM774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:39,114] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:39,119] [INFO] Selected 21 target genomes.
[2024-01-24 13:09:39,119] [INFO] Target genome list was writen to GCF_000007745.1_ASM774v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:39,320] [INFO] Task started: fastANI
[2024-01-24 13:09:39,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0f1925-bbc8-4d34-8dc2-9997891ac8a1/GCF_000007745.1_ASM774v1_genomic.fna.gz --refList GCF_000007745.1_ASM774v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000007745.1_ASM774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:09:47,911] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:47,931] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:09:47,932] [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_011455875.1	s__Basfia succiniciproducens	98.8269	703	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	99.17	98.70	0.95	0.93	4	conclusive
GCF_014843355.1	s__Basfia_A sp014843355	79.9818	332	771	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_000017245.1	s__Basfia_A succinogenes	79.7252	314	771	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_000973525.1	s__Pasteurella multocida_A	79.3853	135	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900638025.1	s__Haemophilus_D parainfluenzae_J	78.9682	163	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.84	95.19	0.91	0.89	5	-
GCF_900454865.1	s__Pasteurella canis	78.9288	120	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.76	98.68	0.94	0.91	4	-
GCA_900444965.1	s__Basfia_A rossii	78.8913	197	771	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_900187275.1	s__Pasteurella multocida	78.8383	141	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.93	96.53	0.94	0.57	288	-
GCF_900186835.1	s__Pasteurella dagmatis	78.5918	145	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCF_003096995.1	s__Basfia_A langaaensis	78.4643	194	771	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_015356115.1	s__Rodentibacter sp015356115	78.4627	199	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262245.1	s__Basfia bettyae	78.4485	260	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia	95.0	98.65	97.30	0.95	0.89	3	-
GCF_002795405.1	s__Caviibacterium pharyngocola	78.3894	268	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901764995.1	s__Basfia_A porcinus	78.2785	222	771	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_000191405.1	s__Haemophilus_D parainfluenzae	78.2316	148	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	-
GCF_004363295.1	s__Mesocricetibacter intestinalis	77.9907	214	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130205.1	s__Aggregatibacter actinomycetemcomitans_A	77.9888	195	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.99	96.75	0.93	0.87	15	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	77.7338	197	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
GCA_905207935.1	s__Haemophilus_D sp905207935	77.7331	122	771	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_905373425.1	s__Mesocricetibacter sp905373425	77.6267	152	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342725.1	s__Chelonobacter aquarius	76.9852	106	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:09:47,935] [INFO] GTDB search result was written to GCF_000007745.1_ASM774v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:09:47,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:09:47,940] [INFO] DFAST_QC result json was written to GCF_000007745.1_ASM774v1_genomic.fna/dqc_result.json
[2024-01-24 13:09:47,940] [INFO] DFAST_QC completed!
[2024-01-24 13:09:47,940] [INFO] Total running time: 0h0m50s