[2023-06-19 10:05:30,448] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:05:30,450] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:05:30,450] [INFO] DQC Reference Directory: /var/lib/cwl/stga2a66bb4-a4ab-4e54-9847-8fa8ae5425b7/dqc_reference
[2023-06-19 10:05:32,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:05:32,060] [INFO] Task started: Prodigal
[2023-06-19 10:05:32,061] [INFO] Running command: gunzip -c /var/lib/cwl/stg464f90d4-ecef-498f-a6d4-64fa2f27edfd/GCA_018819845.1_ASM1881984v1_genomic.fna.gz | prodigal -d GCA_018819845.1_ASM1881984v1_genomic.fna/cds.fna -a GCA_018819845.1_ASM1881984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:05:41,151] [INFO] Task succeeded: Prodigal
[2023-06-19 10:05:41,152] [INFO] Task started: HMMsearch
[2023-06-19 10:05:41,152] [INFO] Running command: hmmsearch --tblout GCA_018819845.1_ASM1881984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2a66bb4-a4ab-4e54-9847-8fa8ae5425b7/dqc_reference/reference_markers.hmm GCA_018819845.1_ASM1881984v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:05:41,409] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:05:41,411] [INFO] Found 6/6 markers.
[2023-06-19 10:05:41,448] [INFO] Query marker FASTA was written to GCA_018819845.1_ASM1881984v1_genomic.fna/markers.fasta
[2023-06-19 10:05:41,449] [INFO] Task started: Blastn
[2023-06-19 10:05:41,449] [INFO] Running command: blastn -query GCA_018819845.1_ASM1881984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2a66bb4-a4ab-4e54-9847-8fa8ae5425b7/dqc_reference/reference_markers.fasta -out GCA_018819845.1_ASM1881984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:05:42,466] [INFO] Task succeeded: Blastn
[2023-06-19 10:05:42,471] [INFO] Selected 23 target genomes.
[2023-06-19 10:05:42,472] [INFO] Target genome list was writen to GCA_018819845.1_ASM1881984v1_genomic.fna/target_genomes.txt
[2023-06-19 10:05:42,473] [INFO] Task started: fastANI
[2023-06-19 10:05:42,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg464f90d4-ecef-498f-a6d4-64fa2f27edfd/GCA_018819845.1_ASM1881984v1_genomic.fna.gz --refList GCA_018819845.1_ASM1881984v1_genomic.fna/target_genomes.txt --output GCA_018819845.1_ASM1881984v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:05:58,940] [INFO] Task succeeded: fastANI
[2023-06-19 10:05:58,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2a66bb4-a4ab-4e54-9847-8fa8ae5425b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:05:58,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2a66bb4-a4ab-4e54-9847-8fa8ae5425b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:05:58,963] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:05:58,963] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:05:58,964] [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
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	85.0688	658	977	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	84.2082	641	977	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	78.1648	258	977	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	78.0963	246	977	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.0905	228	977	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	77.775	224	977	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.7277	276	977	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.6577	261	977	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.6231	252	977	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.5313	213	977	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	77.5015	199	977	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.4818	216	977	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	77.4502	212	977	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	77.2864	185	977	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	77.1911	189	977	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	76.9327	171	977	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.7756	197	977	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.7446	234	977	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	76.7353	212	977	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	76.6582	239	977	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.6101	198	977	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.4302	196	977	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.3929	198	977	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:05:58,966] [INFO] DFAST Taxonomy check result was written to GCA_018819845.1_ASM1881984v1_genomic.fna/tc_result.tsv
[2023-06-19 10:05:58,968] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:05:58,968] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:05:58,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2a66bb4-a4ab-4e54-9847-8fa8ae5425b7/dqc_reference/checkm_data
[2023-06-19 10:05:58,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:05:59,004] [INFO] Task started: CheckM
[2023-06-19 10:05:59,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018819845.1_ASM1881984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018819845.1_ASM1881984v1_genomic.fna/checkm_input GCA_018819845.1_ASM1881984v1_genomic.fna/checkm_result
[2023-06-19 10:06:29,760] [INFO] Task succeeded: CheckM
[2023-06-19 10:06:29,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:06:29,787] [INFO] ===== Completeness check finished =====
[2023-06-19 10:06:29,787] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:06:29,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018819845.1_ASM1881984v1_genomic.fna/markers.fasta)
[2023-06-19 10:06:29,788] [INFO] Task started: Blastn
[2023-06-19 10:06:29,788] [INFO] Running command: blastn -query GCA_018819845.1_ASM1881984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2a66bb4-a4ab-4e54-9847-8fa8ae5425b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018819845.1_ASM1881984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:06:31,812] [INFO] Task succeeded: Blastn
[2023-06-19 10:06:31,817] [INFO] Selected 16 target genomes.
[2023-06-19 10:06:31,818] [INFO] Target genome list was writen to GCA_018819845.1_ASM1881984v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:06:31,821] [INFO] Task started: fastANI
[2023-06-19 10:06:31,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg464f90d4-ecef-498f-a6d4-64fa2f27edfd/GCA_018819845.1_ASM1881984v1_genomic.fna.gz --refList GCA_018819845.1_ASM1881984v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018819845.1_ASM1881984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:06:42,257] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:42,276] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:06:42,276] [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_002256995.1	s__Thiobacillus sp002256995	97.9346	862	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	98.94	97.93	0.93	0.88	3	conclusive
GCA_018820745.1	s__Thiobacillus sp018820745	90.882	469	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001530125.1	s__Thiobacillus denitrificans_C	90.3114	765	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820765.1	s__Thiobacillus sp018820765	86.9059	746	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.99	99.99	0.98	0.97	3	-
GCA_011391285.1	s__Thiobacillus sp011391285	86.2385	567	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262815.1	s__Thiobacillus sp018262815	85.8597	548	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003510325.1	s__Thiobacillus sp003510325	85.5629	526	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.33	99.33	0.73	0.73	2	-
GCA_016195805.1	s__Thiobacillus sp016195805	85.2179	633	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376425.1	s__Thiobacillus denitrificans	85.0876	657	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	84.9971	623	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002424845.1	s__Thiobacillus denitrificans_F	84.2901	419	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124745.1	s__Thiobacillus sp016124745	83.5282	585	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802655.1	s__Thiobacillus sp001802655	82.6756	605	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	95.00	95.00	0.84	0.84	2	-
GCA_002279795.1	s__Thiobacillus sp002279795	82.5091	563	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.62	99.62	0.89	0.89	2	-
GCA_010365175.1	s__Thiobacillus sp010365175	80.186	362	977	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:06:42,278] [INFO] GTDB search result was written to GCA_018819845.1_ASM1881984v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:06:42,278] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:06:42,283] [INFO] DFAST_QC result json was written to GCA_018819845.1_ASM1881984v1_genomic.fna/dqc_result.json
[2023-06-19 10:06:42,283] [INFO] DFAST_QC completed!
[2023-06-19 10:06:42,283] [INFO] Total running time: 0h1m12s