[2023-06-29 13:25:42,148] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:25:42,151] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:25:42,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg682bb2b5-21a2-4e85-9c53-cec1cfb1ac52/dqc_reference
[2023-06-29 13:25:43,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:25:43,404] [INFO] Task started: Prodigal
[2023-06-29 13:25:43,404] [INFO] Running command: gunzip -c /var/lib/cwl/stgf21e22f5-a2c9-4c7c-8db8-3180a7faf8ab/GCA_023265175.1_ASM2326517v1_genomic.fna.gz | prodigal -d GCA_023265175.1_ASM2326517v1_genomic.fna/cds.fna -a GCA_023265175.1_ASM2326517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:25:56,311] [INFO] Task succeeded: Prodigal
[2023-06-29 13:25:56,311] [INFO] Task started: HMMsearch
[2023-06-29 13:25:56,312] [INFO] Running command: hmmsearch --tblout GCA_023265175.1_ASM2326517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg682bb2b5-21a2-4e85-9c53-cec1cfb1ac52/dqc_reference/reference_markers.hmm GCA_023265175.1_ASM2326517v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:25:56,606] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:25:56,607] [INFO] Found 6/6 markers.
[2023-06-29 13:25:56,649] [INFO] Query marker FASTA was written to GCA_023265175.1_ASM2326517v1_genomic.fna/markers.fasta
[2023-06-29 13:25:56,649] [INFO] Task started: Blastn
[2023-06-29 13:25:56,650] [INFO] Running command: blastn -query GCA_023265175.1_ASM2326517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg682bb2b5-21a2-4e85-9c53-cec1cfb1ac52/dqc_reference/reference_markers.fasta -out GCA_023265175.1_ASM2326517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:25:57,312] [INFO] Task succeeded: Blastn
[2023-06-29 13:25:57,316] [INFO] Selected 23 target genomes.
[2023-06-29 13:25:57,317] [INFO] Target genome list was writen to GCA_023265175.1_ASM2326517v1_genomic.fna/target_genomes.txt
[2023-06-29 13:25:57,320] [INFO] Task started: fastANI
[2023-06-29 13:25:57,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgf21e22f5-a2c9-4c7c-8db8-3180a7faf8ab/GCA_023265175.1_ASM2326517v1_genomic.fna.gz --refList GCA_023265175.1_ASM2326517v1_genomic.fna/target_genomes.txt --output GCA_023265175.1_ASM2326517v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:26:14,644] [INFO] Task succeeded: fastANI
[2023-06-29 13:26:14,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg682bb2b5-21a2-4e85-9c53-cec1cfb1ac52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:26:14,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg682bb2b5-21a2-4e85-9c53-cec1cfb1ac52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:26:14,663] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:26:14,664] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:26:14,664] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	76.7491	164	1477	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.4863	52	1477	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.3403	131	1477	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.2054	103	1477	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	75.174	108	1477	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.1618	101	1477	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.1415	69	1477	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	75.1034	67	1477	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.0838	52	1477	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.0778	65	1477	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.9899	74	1477	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.9887	74	1477	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.807	104	1477	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	74.7845	91	1477	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.766	107	1477	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:26:14,666] [INFO] DFAST Taxonomy check result was written to GCA_023265175.1_ASM2326517v1_genomic.fna/tc_result.tsv
[2023-06-29 13:26:14,667] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:26:14,667] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:26:14,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg682bb2b5-21a2-4e85-9c53-cec1cfb1ac52/dqc_reference/checkm_data
[2023-06-29 13:26:14,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:26:14,724] [INFO] Task started: CheckM
[2023-06-29 13:26:14,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023265175.1_ASM2326517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023265175.1_ASM2326517v1_genomic.fna/checkm_input GCA_023265175.1_ASM2326517v1_genomic.fna/checkm_result
[2023-06-29 13:26:55,401] [INFO] Task succeeded: CheckM
[2023-06-29 13:26:55,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:26:55,432] [INFO] ===== Completeness check finished =====
[2023-06-29 13:26:55,432] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:26:55,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023265175.1_ASM2326517v1_genomic.fna/markers.fasta)
[2023-06-29 13:26:55,433] [INFO] Task started: Blastn
[2023-06-29 13:26:55,433] [INFO] Running command: blastn -query GCA_023265175.1_ASM2326517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg682bb2b5-21a2-4e85-9c53-cec1cfb1ac52/dqc_reference/reference_markers_gtdb.fasta -out GCA_023265175.1_ASM2326517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:26:56,450] [INFO] Task succeeded: Blastn
[2023-06-29 13:26:56,455] [INFO] Selected 9 target genomes.
[2023-06-29 13:26:56,455] [INFO] Target genome list was writen to GCA_023265175.1_ASM2326517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:26:56,460] [INFO] Task started: fastANI
[2023-06-29 13:26:56,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgf21e22f5-a2c9-4c7c-8db8-3180a7faf8ab/GCA_023265175.1_ASM2326517v1_genomic.fna.gz --refList GCA_023265175.1_ASM2326517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023265175.1_ASM2326517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:27:05,358] [INFO] Task succeeded: fastANI
[2023-06-29 13:27:05,370] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:27:05,370] [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
GCA_017883165.1	s__JADGOC01 sp017883165	79.0417	409	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JADGOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	78.4299	483	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_001917905.1	s__Gp6-AA45 sp001917905	78.2967	407	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.03	98.94	0.79	0.79	3	-
GCA_003222395.1	s__Gp6-AA45 sp003222395	78.2868	479	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.74	99.72	0.98	0.98	4	-
GCA_001767495.1	s__2-12-FULL-65-11 sp001767495	78.2591	288	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__2-12-FULL-65-11	95.0	99.89	99.89	0.97	0.97	2	-
GCA_016195265.1	s__Gp6-AA45 sp016195265	78.1705	403	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195295.1	s__Gp6-AA45 sp016195295	77.9217	312	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223775.1	s__Gp6-AA45 sp003223775	77.7889	333	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268955.1	s__WHSN01 sp018268955	77.6276	240	1477	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:27:05,372] [INFO] GTDB search result was written to GCA_023265175.1_ASM2326517v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:27:05,372] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:27:05,376] [INFO] DFAST_QC result json was written to GCA_023265175.1_ASM2326517v1_genomic.fna/dqc_result.json
[2023-06-29 13:27:05,376] [INFO] DFAST_QC completed!
[2023-06-29 13:27:05,377] [INFO] Total running time: 0h1m23s