[2024-01-24 12:21:44,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg63fb2900-3576-4160-b6ed-2a2f776373dc/dqc_reference
[2024-01-24 12:21:45,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,792] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a5f2bae-529c-4d03-bfc1-e6c996a16cb3/GCF_004340985.1_ASM434098v1_genomic.fna.gz | prodigal -d GCF_004340985.1_ASM434098v1_genomic.fna/cds.fna -a GCF_004340985.1_ASM434098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:52,386] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:52,386] [INFO] Task started: HMMsearch
[2024-01-24 12:21:52,386] [INFO] Running command: hmmsearch --tblout GCF_004340985.1_ASM434098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63fb2900-3576-4160-b6ed-2a2f776373dc/dqc_reference/reference_markers.hmm GCF_004340985.1_ASM434098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:52,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:52,650] [INFO] Found 6/6 markers.
[2024-01-24 12:21:52,674] [INFO] Query marker FASTA was written to GCF_004340985.1_ASM434098v1_genomic.fna/markers.fasta
[2024-01-24 12:21:52,675] [INFO] Task started: Blastn
[2024-01-24 12:21:52,675] [INFO] Running command: blastn -query GCF_004340985.1_ASM434098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63fb2900-3576-4160-b6ed-2a2f776373dc/dqc_reference/reference_markers.fasta -out GCF_004340985.1_ASM434098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:53,382] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:53,386] [INFO] Selected 24 target genomes.
[2024-01-24 12:21:53,386] [INFO] Target genome list was writen to GCF_004340985.1_ASM434098v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:53,395] [INFO] Task started: fastANI
[2024-01-24 12:21:53,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5f2bae-529c-4d03-bfc1-e6c996a16cb3/GCF_004340985.1_ASM434098v1_genomic.fna.gz --refList GCF_004340985.1_ASM434098v1_genomic.fna/target_genomes.txt --output GCF_004340985.1_ASM434098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:03,462] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:03,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63fb2900-3576-4160-b6ed-2a2f776373dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:03,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63fb2900-3576-4160-b6ed-2a2f776373dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:03,478] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:03,479] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:03,479] [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
Cricetibacter osteomyelitidis	strain=DSM 28404	GCA_004340985.1	1521931	1521931	type	True	100.0	873	876	95	conclusive
Pasteurella multocida subsp. gallicida	strain=NCTC10204	GCA_900636625.1	123812	747	type	True	78.0228	150	876	95	below_threshold
Pasteurella canis	strain=NCTC11621	GCA_900454865.1	753	753	type	True	78.0168	133	876	95	below_threshold
Pasteurella multocida	strain=NCTC10322	GCA_900187275.1	747	747	type	True	77.9726	148	876	95	below_threshold
Pasteurella multocida subsp. septica	strain=NCTC11995	GCA_900454845.1	115545	747	type	True	77.9684	157	876	95	below_threshold
Pasteurella multocida	strain=ATCC 43137	GCA_000754275.1	747	747	type	True	77.944	148	876	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_901764995.1	51048	51048	type	True	77.9067	192	876	95	below_threshold
Actinobacillus porcinus	strain=NM319	GCA_900773985.1	51048	51048	type	True	77.8887	193	876	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	77.8642	182	876	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	77.8469	181	876	95	below_threshold
Aggregatibacter aphrophilus	strain=NCTC5906	GCA_900636915.1	732	732	type	True	77.8464	208	876	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	77.8357	194	876	95	below_threshold
Aggregatibacter kilianii	strain=PN_528	GCA_003130255.1	2025884	2025884	type	True	77.8356	207	876	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	77.8302	191	876	95	below_threshold
Actinobacillus seminis	strain=NCTC10851	GCA_900460625.1	722	722	type	True	77.7588	196	876	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	77.7286	168	876	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	77.6742	168	876	95	below_threshold
Actinobacillus seminis	strain=ATCC 15768	GCA_002263215.1	722	722	type	True	77.6484	199	876	95	below_threshold
Mesocricetibacter intestinalis	strain=DSM 28403	GCA_004363295.1	1521930	1521930	type	True	77.3811	153	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:03,488] [INFO] DFAST Taxonomy check result was written to GCF_004340985.1_ASM434098v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:03,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:03,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:03,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63fb2900-3576-4160-b6ed-2a2f776373dc/dqc_reference/checkm_data
[2024-01-24 12:22:03,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:03,538] [INFO] Task started: CheckM
[2024-01-24 12:22:03,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340985.1_ASM434098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340985.1_ASM434098v1_genomic.fna/checkm_input GCF_004340985.1_ASM434098v1_genomic.fna/checkm_result
[2024-01-24 12:22:29,702] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:29,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:29,724] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:29,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:29,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340985.1_ASM434098v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:29,726] [INFO] Task started: Blastn
[2024-01-24 12:22:29,726] [INFO] Running command: blastn -query GCF_004340985.1_ASM434098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63fb2900-3576-4160-b6ed-2a2f776373dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340985.1_ASM434098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:30,795] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:30,798] [INFO] Selected 21 target genomes.
[2024-01-24 12:22:30,798] [INFO] Target genome list was writen to GCF_004340985.1_ASM434098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:30,815] [INFO] Task started: fastANI
[2024-01-24 12:22:30,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5f2bae-529c-4d03-bfc1-e6c996a16cb3/GCF_004340985.1_ASM434098v1_genomic.fna.gz --refList GCF_004340985.1_ASM434098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340985.1_ASM434098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:40,428] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:40,445] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:40,445] [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_004340985.1	s__Cricetibacter osteomyelitidis	100.0	873	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Cricetibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_901420285.1	s__Rodentibacter sp901420285	78.0441	173	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637275.1	s__Actinobacillus_B aerogenes	77.9925	213	876	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_001999305.1	s__Rodentibacter myodis	77.9872	224	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454865.1	s__Pasteurella canis	77.9837	135	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.76	98.68	0.94	0.91	4	-
GCF_900187275.1	s__Pasteurella multocida	77.9742	148	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.93	96.53	0.94	0.57	288	-
GCF_017160915.1	s__Aggregatibacter actinomycetemcomitans_B	77.9539	227	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002015125.1	s__Pasteurella felis	77.9348	140	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.37	98.52	0.96	0.90	4	-
GCF_003129965.1	s__Aggregatibacter kilianii_A	77.9264	211	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901764995.1	s__Basfia_A porcinus	77.9067	192	876	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_000973525.1	s__Pasteurella multocida_A	77.8925	157	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	77.887	182	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
GCF_003130255.1	s__Aggregatibacter kilianii	77.8472	205	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.97	97.13	0.96	0.90	14	-
GCF_900444945.1	s__Actinobacillus lignieresii	77.8378	166	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	96.69	96.41	0.91	0.89	35	-
GCF_002921135.1	s__Avibacterium gallinarum	77.8242	192	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	77.761	168	876	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_003130205.1	s__Aggregatibacter actinomycetemcomitans_A	77.7191	199	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.99	96.75	0.93	0.87	15	-
GCF_002000485.1	s__Rodentibacter ratti	77.6742	180	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	96.24	96.11	0.85	0.81	4	-
GCF_002263215.1	s__Actinobacillus_B seminis	77.6641	198	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	99.95	99.95	1.00	1.00	2	-
GCA_000017245.1	s__Basfia_A succinogenes	77.5791	202	876	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_004363295.1	s__Mesocricetibacter intestinalis	77.3894	154	876	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:40,447] [INFO] GTDB search result was written to GCF_004340985.1_ASM434098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:40,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:40,464] [INFO] DFAST_QC result json was written to GCF_004340985.1_ASM434098v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:40,465] [INFO] DFAST_QC completed!
[2024-01-24 12:22:40,465] [INFO] Total running time: 0h0m56s