[2023-06-05 03:38:20,167] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:38:20,169] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:38:20,169] [INFO] DQC Reference Directory: /var/lib/cwl/stga55b95b8-5a04-48e2-98c0-d774204fa57b/dqc_reference
[2023-06-05 03:38:22,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:38:22,123] [INFO] Task started: Prodigal
[2023-06-05 03:38:22,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f079d09-1e80-421b-8da3-4ce88d2f71a4/GCA_934229845.1_ERR7746219_bin.155_genomic.fna.gz | prodigal -d GCA_934229845.1_ERR7746219_bin.155_genomic.fna/cds.fna -a GCA_934229845.1_ERR7746219_bin.155_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:38:25,127] [INFO] Task succeeded: Prodigal
[2023-06-05 03:38:25,128] [INFO] Task started: HMMsearch
[2023-06-05 03:38:25,128] [INFO] Running command: hmmsearch --tblout GCA_934229845.1_ERR7746219_bin.155_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga55b95b8-5a04-48e2-98c0-d774204fa57b/dqc_reference/reference_markers.hmm GCA_934229845.1_ERR7746219_bin.155_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:38:25,307] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:38:25,309] [INFO] Found 6/6 markers.
[2023-06-05 03:38:25,327] [INFO] Query marker FASTA was written to GCA_934229845.1_ERR7746219_bin.155_genomic.fna/markers.fasta
[2023-06-05 03:38:25,328] [INFO] Task started: Blastn
[2023-06-05 03:38:25,328] [INFO] Running command: blastn -query GCA_934229845.1_ERR7746219_bin.155_genomic.fna/markers.fasta -db /var/lib/cwl/stga55b95b8-5a04-48e2-98c0-d774204fa57b/dqc_reference/reference_markers.fasta -out GCA_934229845.1_ERR7746219_bin.155_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:38:26,048] [INFO] Task succeeded: Blastn
[2023-06-05 03:38:26,051] [INFO] Selected 17 target genomes.
[2023-06-05 03:38:26,051] [INFO] Target genome list was writen to GCA_934229845.1_ERR7746219_bin.155_genomic.fna/target_genomes.txt
[2023-06-05 03:38:26,056] [INFO] Task started: fastANI
[2023-06-05 03:38:26,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f079d09-1e80-421b-8da3-4ce88d2f71a4/GCA_934229845.1_ERR7746219_bin.155_genomic.fna.gz --refList GCA_934229845.1_ERR7746219_bin.155_genomic.fna/target_genomes.txt --output GCA_934229845.1_ERR7746219_bin.155_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:38:33,084] [INFO] Task succeeded: fastANI
[2023-06-05 03:38:33,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga55b95b8-5a04-48e2-98c0-d774204fa57b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:38:33,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga55b95b8-5a04-48e2-98c0-d774204fa57b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:38:33,095] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:38:33,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:38:33,095] [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
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	93.4597	341	368	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	93.3999	344	368	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	93.3634	345	368	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	93.3544	340	368	95	below_threshold
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	83.3034	204	368	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	81.9216	220	368	95	below_threshold
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	81.8977	215	368	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	81.1244	198	368	95	below_threshold
Haemophilus aegyptius	strain=FDAARGOS_1478	GCA_019930905.1	197575	197575	type	True	81.0874	198	368	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	81.0239	204	368	95	below_threshold
Haemophilus influenzae	strain=NCTC8143	GCA_001457655.1	727	727	type	True	80.8335	208	368	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.3916	189	368	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:38:33,097] [INFO] DFAST Taxonomy check result was written to GCA_934229845.1_ERR7746219_bin.155_genomic.fna/tc_result.tsv
[2023-06-05 03:38:33,098] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:38:33,098] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:38:33,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga55b95b8-5a04-48e2-98c0-d774204fa57b/dqc_reference/checkm_data
[2023-06-05 03:38:33,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:38:33,118] [INFO] Task started: CheckM
[2023-06-05 03:38:33,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934229845.1_ERR7746219_bin.155_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934229845.1_ERR7746219_bin.155_genomic.fna/checkm_input GCA_934229845.1_ERR7746219_bin.155_genomic.fna/checkm_result
[2023-06-05 03:38:49,461] [INFO] Task succeeded: CheckM
[2023-06-05 03:38:49,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:38:49,480] [INFO] ===== Completeness check finished =====
[2023-06-05 03:38:49,480] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:38:49,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934229845.1_ERR7746219_bin.155_genomic.fna/markers.fasta)
[2023-06-05 03:38:49,480] [INFO] Task started: Blastn
[2023-06-05 03:38:49,480] [INFO] Running command: blastn -query GCA_934229845.1_ERR7746219_bin.155_genomic.fna/markers.fasta -db /var/lib/cwl/stga55b95b8-5a04-48e2-98c0-d774204fa57b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934229845.1_ERR7746219_bin.155_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:38:50,608] [INFO] Task succeeded: Blastn
[2023-06-05 03:38:50,612] [INFO] Selected 13 target genomes.
[2023-06-05 03:38:50,612] [INFO] Target genome list was writen to GCA_934229845.1_ERR7746219_bin.155_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:38:50,617] [INFO] Task started: fastANI
[2023-06-05 03:38:50,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f079d09-1e80-421b-8da3-4ce88d2f71a4/GCA_934229845.1_ERR7746219_bin.155_genomic.fna.gz --refList GCA_934229845.1_ERR7746219_bin.155_genomic.fna/target_genomes_gtdb.txt --output GCA_934229845.1_ERR7746219_bin.155_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:38:55,084] [INFO] Task succeeded: fastANI
[2023-06-05 03:38:55,096] [INFO] Found 13 fastANI hits (4 hits with ANI > circumscription radius)
[2023-06-05 03:38:55,096] [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_014931275.1	s__Haemophilus_D sp900755445	96.0922	351	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	inconclusive
GCF_001679485.1	s__Haemophilus_D sp001679485	95.2262	344	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	95.82	95.82	0.90	0.90	2	inconclusive
GCA_905205995.1	s__Haemophilus_D sp905205995	95.1774	335	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000210895.1	s__Haemophilus_D parainfluenzae_A	95.1647	356	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	inconclusive
GCF_003252725.1	s__Haemophilus_D parainfluenzae_L	94.7683	337	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.33	95.18	0.90	0.88	7	-
GCA_900756155.1	s__Haemophilus_D sp900756155	94.258	332	368	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_905207935.1	s__Haemophilus_D sp905207935	94.2438	295	368	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_001815355.1	s__Haemophilus_D sp001815355	94.1668	342	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.35	95.20	0.94	0.91	8	-
GCA_900756875.1	s__Haemophilus_D sp900756875	93.8303	296	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.91	95.91	0.89	0.89	2	-
GCA_905214375.1	s__Haemophilus_D sp905214375	93.8049	290	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	93.6344	337	368	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_003252795.1	s__Haemophilus_D parainfluenzae_K	93.5934	336	368	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_018381425.1	s__Haemophilus_D parainfluenzae_O	92.0024	240	368	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.89	95.76	0.75	0.73	3	-
--------------------------------------------------------------------------------
[2023-06-05 03:38:55,098] [INFO] GTDB search result was written to GCA_934229845.1_ERR7746219_bin.155_genomic.fna/result_gtdb.tsv
[2023-06-05 03:38:55,099] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:38:55,102] [INFO] DFAST_QC result json was written to GCA_934229845.1_ERR7746219_bin.155_genomic.fna/dqc_result.json
[2023-06-05 03:38:55,103] [INFO] DFAST_QC completed!
[2023-06-05 03:38:55,103] [INFO] Total running time: 0h0m35s