[2024-01-24 10:47:22,635] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:22,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:22,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a1bf9da-bb09-4bf0-a541-5b708443c7b2/dqc_reference
[2024-01-24 10:47:26,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,184] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,185] [INFO] Running command: gunzip -c /var/lib/cwl/stga983d429-4578-49fc-a193-f42bc94c0f89/GCF_900454845.1_50465_C01_genomic.fna.gz | prodigal -d GCF_900454845.1_50465_C01_genomic.fna/cds.fna -a GCF_900454845.1_50465_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:31,496] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:31,496] [INFO] Task started: HMMsearch
[2024-01-24 10:47:31,496] [INFO] Running command: hmmsearch --tblout GCF_900454845.1_50465_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a1bf9da-bb09-4bf0-a541-5b708443c7b2/dqc_reference/reference_markers.hmm GCF_900454845.1_50465_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:31,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:31,756] [INFO] Found 6/6 markers.
[2024-01-24 10:47:31,782] [INFO] Query marker FASTA was written to GCF_900454845.1_50465_C01_genomic.fna/markers.fasta
[2024-01-24 10:47:31,783] [INFO] Task started: Blastn
[2024-01-24 10:47:31,783] [INFO] Running command: blastn -query GCF_900454845.1_50465_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a1bf9da-bb09-4bf0-a541-5b708443c7b2/dqc_reference/reference_markers.fasta -out GCF_900454845.1_50465_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:32,468] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:32,471] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:32,471] [INFO] Target genome list was writen to GCF_900454845.1_50465_C01_genomic.fna/target_genomes.txt
[2024-01-24 10:47:32,490] [INFO] Task started: fastANI
[2024-01-24 10:47:32,490] [INFO] Running command: fastANI --query /var/lib/cwl/stga983d429-4578-49fc-a193-f42bc94c0f89/GCF_900454845.1_50465_C01_genomic.fna.gz --refList GCF_900454845.1_50465_C01_genomic.fna/target_genomes.txt --output GCF_900454845.1_50465_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:39,882] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:39,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a1bf9da-bb09-4bf0-a541-5b708443c7b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:39,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a1bf9da-bb09-4bf0-a541-5b708443c7b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:39,895] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:47:39,895] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:39,895] [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
Pasteurella multocida subsp. septica	strain=NCTC11995	GCA_900454845.1	115545	747	type	True	100.0	756	758	95	conclusive
Pasteurella multocida subsp. gallicida	strain=NCTC10204	GCA_900636625.1	123812	747	type	True	96.6447	701	758	95	conclusive
Pasteurella multocida	strain=NCTC10322	GCA_900187275.1	747	747	type	True	96.583	704	758	95	conclusive
Pasteurella multocida	strain=ATCC 43137	GCA_000754275.1	747	747	type	True	96.5474	706	758	95	conclusive
Pasteurella canis	strain=NCTC11621	GCA_900454865.1	753	753	type	True	80.751	455	758	95	below_threshold
Pasteurella dagmatis	strain=NCTC11617	GCA_900186835.1	754	754	type	True	80.5551	431	758	95	below_threshold
Rodentibacter trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	77.4711	174	758	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:39,897] [INFO] DFAST Taxonomy check result was written to GCF_900454845.1_50465_C01_genomic.fna/tc_result.tsv
[2024-01-24 10:47:39,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:39,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:39,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a1bf9da-bb09-4bf0-a541-5b708443c7b2/dqc_reference/checkm_data
[2024-01-24 10:47:39,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:39,927] [INFO] Task started: CheckM
[2024-01-24 10:47:39,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900454845.1_50465_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900454845.1_50465_C01_genomic.fna/checkm_input GCF_900454845.1_50465_C01_genomic.fna/checkm_result
[2024-01-24 10:48:02,856] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:02,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:02,878] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:02,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:02,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900454845.1_50465_C01_genomic.fna/markers.fasta)
[2024-01-24 10:48:02,879] [INFO] Task started: Blastn
[2024-01-24 10:48:02,880] [INFO] Running command: blastn -query GCF_900454845.1_50465_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a1bf9da-bb09-4bf0-a541-5b708443c7b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900454845.1_50465_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:04,037] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:04,041] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:04,042] [INFO] Target genome list was writen to GCF_900454845.1_50465_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:04,113] [INFO] Task started: fastANI
[2024-01-24 10:48:04,113] [INFO] Running command: fastANI --query /var/lib/cwl/stga983d429-4578-49fc-a193-f42bc94c0f89/GCF_900454845.1_50465_C01_genomic.fna.gz --refList GCF_900454845.1_50465_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900454845.1_50465_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:11,858] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:11,873] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:11,873] [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_900187275.1	s__Pasteurella multocida	96.5772	702	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.93	96.53	0.94	0.57	288	conclusive
GCF_000973525.1	s__Pasteurella multocida_A	80.9941	433	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850605.1	s__Pasteurella oralis	80.7804	466	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454865.1	s__Pasteurella canis	80.6797	453	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.76	98.68	0.94	0.91	4	-
GCF_900186835.1	s__Pasteurella dagmatis	80.5694	430	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.39	98.82	0.98	0.96	3	-
GCF_014931275.1	s__Haemophilus_D sp900755445	79.1169	206	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCA_002015125.1	s__Pasteurella felis	79.0212	227	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	99.37	98.52	0.96	0.90	4	-
GCF_900638025.1	s__Haemophilus_D parainfluenzae_J	78.7427	196	758	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_003252725.1	s__Haemophilus_D parainfluenzae_L	78.6	178	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.33	95.18	0.90	0.88	7	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	78.3658	176	758	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_002795405.1	s__Caviibacterium pharyngocola	78.3228	172	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	78.2312	182	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCA_905205995.1	s__Haemophilus_D sp905205995	78.1476	185	758	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_000191405.1	s__Haemophilus_D parainfluenzae	78.1349	199	758	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_002989035.1	s__Haemophilus influenzae_F	78.0595	160	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9474	98.22	97.14	0.92	0.83	74	-
GCF_001815355.1	s__Haemophilus_D sp001815355	78.015	194	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.35	95.20	0.94	0.91	8	-
GCF_003129965.1	s__Aggregatibacter kilianii_A	77.98	142	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	77.6664	133	758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:11,875] [INFO] GTDB search result was written to GCF_900454845.1_50465_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:11,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:11,879] [INFO] DFAST_QC result json was written to GCF_900454845.1_50465_C01_genomic.fna/dqc_result.json
[2024-01-24 10:48:11,879] [INFO] DFAST_QC completed!
[2024-01-24 10:48:11,879] [INFO] Total running time: 0h0m49s