[2023-06-05 23:46:12,249] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:46:12,254] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:46:12,254] [INFO] DQC Reference Directory: /var/lib/cwl/stgd798a8a5-ef6f-479c-b904-0f24b9fd28a0/dqc_reference
[2023-06-05 23:46:14,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:46:14,097] [INFO] Task started: Prodigal
[2023-06-05 23:46:14,097] [INFO] Running command: gunzip -c /var/lib/cwl/stgf95e2aff-e414-460c-bdb2-0663e1ec7b79/GCA_934255035.1_ERR7738597_bin.167_genomic.fna.gz | prodigal -d GCA_934255035.1_ERR7738597_bin.167_genomic.fna/cds.fna -a GCA_934255035.1_ERR7738597_bin.167_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:46:16,646] [INFO] Task succeeded: Prodigal
[2023-06-05 23:46:16,647] [INFO] Task started: HMMsearch
[2023-06-05 23:46:16,647] [INFO] Running command: hmmsearch --tblout GCA_934255035.1_ERR7738597_bin.167_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd798a8a5-ef6f-479c-b904-0f24b9fd28a0/dqc_reference/reference_markers.hmm GCA_934255035.1_ERR7738597_bin.167_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:46:16,803] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:46:16,805] [INFO] Found 6/6 markers.
[2023-06-05 23:46:16,821] [INFO] Query marker FASTA was written to GCA_934255035.1_ERR7738597_bin.167_genomic.fna/markers.fasta
[2023-06-05 23:46:16,821] [INFO] Task started: Blastn
[2023-06-05 23:46:16,821] [INFO] Running command: blastn -query GCA_934255035.1_ERR7738597_bin.167_genomic.fna/markers.fasta -db /var/lib/cwl/stgd798a8a5-ef6f-479c-b904-0f24b9fd28a0/dqc_reference/reference_markers.fasta -out GCA_934255035.1_ERR7738597_bin.167_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:46:18,262] [INFO] Task succeeded: Blastn
[2023-06-05 23:46:18,265] [INFO] Selected 17 target genomes.
[2023-06-05 23:46:18,265] [INFO] Target genome list was writen to GCA_934255035.1_ERR7738597_bin.167_genomic.fna/target_genomes.txt
[2023-06-05 23:46:18,271] [INFO] Task started: fastANI
[2023-06-05 23:46:18,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgf95e2aff-e414-460c-bdb2-0663e1ec7b79/GCA_934255035.1_ERR7738597_bin.167_genomic.fna.gz --refList GCA_934255035.1_ERR7738597_bin.167_genomic.fna/target_genomes.txt --output GCA_934255035.1_ERR7738597_bin.167_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:46:24,020] [INFO] Task succeeded: fastANI
[2023-06-05 23:46:24,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd798a8a5-ef6f-479c-b904-0f24b9fd28a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:46:24,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd798a8a5-ef6f-479c-b904-0f24b9fd28a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:46:24,032] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:46:24,032] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 23:46:24,033] [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=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	93.6231	313	352	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	93.535	315	352	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	93.5027	319	352	95	below_threshold
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	93.4715	324	352	95	below_threshold
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	82.1098	184	352	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	81.5144	194	352	95	below_threshold
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	81.4226	193	352	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	80.6718	178	352	95	below_threshold
Haemophilus influenzae	strain=NCTC8143	GCA_001457655.1	727	727	type	True	80.5193	182	352	95	below_threshold
Haemophilus aegyptius	strain=FDAARGOS_1478	GCA_019930905.1	197575	197575	type	True	80.5036	189	352	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	80.49	189	352	95	below_threshold
Rodentibacter mrazii	strain=Ppn418	GCA_001998825.1	1908257	1908257	type	True	78.2971	174	352	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	77.1775	51	352	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	77.079	53	352	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 23:46:24,034] [INFO] DFAST Taxonomy check result was written to GCA_934255035.1_ERR7738597_bin.167_genomic.fna/tc_result.tsv
[2023-06-05 23:46:24,035] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:46:24,035] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:46:24,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd798a8a5-ef6f-479c-b904-0f24b9fd28a0/dqc_reference/checkm_data
[2023-06-05 23:46:24,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:46:24,064] [INFO] Task started: CheckM
[2023-06-05 23:46:24,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934255035.1_ERR7738597_bin.167_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934255035.1_ERR7738597_bin.167_genomic.fna/checkm_input GCA_934255035.1_ERR7738597_bin.167_genomic.fna/checkm_result
[2023-06-05 23:46:38,856] [INFO] Task succeeded: CheckM
[2023-06-05 23:46:38,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:46:38,875] [INFO] ===== Completeness check finished =====
[2023-06-05 23:46:38,875] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:46:38,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934255035.1_ERR7738597_bin.167_genomic.fna/markers.fasta)
[2023-06-05 23:46:38,876] [INFO] Task started: Blastn
[2023-06-05 23:46:38,876] [INFO] Running command: blastn -query GCA_934255035.1_ERR7738597_bin.167_genomic.fna/markers.fasta -db /var/lib/cwl/stgd798a8a5-ef6f-479c-b904-0f24b9fd28a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_934255035.1_ERR7738597_bin.167_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:46:39,853] [INFO] Task succeeded: Blastn
[2023-06-05 23:46:39,857] [INFO] Selected 19 target genomes.
[2023-06-05 23:46:39,857] [INFO] Target genome list was writen to GCA_934255035.1_ERR7738597_bin.167_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:46:39,864] [INFO] Task started: fastANI
[2023-06-05 23:46:39,864] [INFO] Running command: fastANI --query /var/lib/cwl/stgf95e2aff-e414-460c-bdb2-0663e1ec7b79/GCA_934255035.1_ERR7738597_bin.167_genomic.fna.gz --refList GCA_934255035.1_ERR7738597_bin.167_genomic.fna/target_genomes_gtdb.txt --output GCA_934255035.1_ERR7738597_bin.167_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:46:46,655] [INFO] Task succeeded: fastANI
[2023-06-05 23:46:46,670] [INFO] Found 18 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-05 23:46:46,670] [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	95.6491	330	352	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
GCA_905205995.1	s__Haemophilus_D sp905205995	95.2443	311	352	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	95.1278	336	352	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_001679485.1	s__Haemophilus_D sp001679485	94.8258	310	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	95.82	95.82	0.90	0.90	2	-
GCA_905207935.1	s__Haemophilus_D sp905207935	94.3882	284	352	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_900756155.1	s__Haemophilus_D sp900756155	94.1745	310	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCF_001815355.1	s__Haemophilus_D sp001815355	94.0835	312	352	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_003253005.1	s__Haemophilus_D parainfluenzae_M	93.6751	305	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCA_905215245.1	s__Haemophilus_D sp905215245	93.6417	265	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCF_000191405.1	s__Haemophilus_D parainfluenzae	93.6231	313	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	-
GCA_900756875.1	s__Haemophilus_D sp900756875	93.5867	272	352	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_003252755.1	s__Haemophilus_D parainfluenzae_N	93.5537	317	352	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_003252795.1	s__Haemophilus_D parainfluenzae_K	93.3377	315	352	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_015255025.1	s__Haemophilus_D sp015255025	93.1896	277	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
GCA_018381425.1	s__Haemophilus_D parainfluenzae_O	92.2926	222	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.89	95.76	0.75	0.73	3	-
GCA_001752465.1	s__Haemophilus quentini	81.6304	183	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	99.94	99.85	0.97	0.94	5	-
GCF_000827595.2	s__Necropsobacter massiliensis	80.2847	64	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998825.1	s__Rodentibacter mrazii	78.2971	174	352	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-05 23:46:46,685] [INFO] GTDB search result was written to GCA_934255035.1_ERR7738597_bin.167_genomic.fna/result_gtdb.tsv
[2023-06-05 23:46:46,685] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:46:46,689] [INFO] DFAST_QC result json was written to GCA_934255035.1_ERR7738597_bin.167_genomic.fna/dqc_result.json
[2023-06-05 23:46:46,689] [INFO] DFAST_QC completed!
[2023-06-05 23:46:46,689] [INFO] Total running time: 0h0m34s