[2023-06-05 02:43:40,030] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:43:40,035] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:43:40,035] [INFO] DQC Reference Directory: /var/lib/cwl/stge7bdb3db-14a0-4428-b1c1-828dc26927c8/dqc_reference
[2023-06-05 02:43:41,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:43:41,340] [INFO] Task started: Prodigal
[2023-06-05 02:43:41,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ff225eb-8dbf-4d5d-b176-6fd9417a1e1c/GCA_001767455.1_ASM176745v1_genomic.fna.gz | prodigal -d GCA_001767455.1_ASM176745v1_genomic.fna/cds.fna -a GCA_001767455.1_ASM176745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:43:59,263] [INFO] Task succeeded: Prodigal
[2023-06-05 02:43:59,264] [INFO] Task started: HMMsearch
[2023-06-05 02:43:59,264] [INFO] Running command: hmmsearch --tblout GCA_001767455.1_ASM176745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7bdb3db-14a0-4428-b1c1-828dc26927c8/dqc_reference/reference_markers.hmm GCA_001767455.1_ASM176745v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:43:59,586] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:43:59,588] [INFO] Found 6/6 markers.
[2023-06-05 02:43:59,641] [INFO] Query marker FASTA was written to GCA_001767455.1_ASM176745v1_genomic.fna/markers.fasta
[2023-06-05 02:43:59,641] [INFO] Task started: Blastn
[2023-06-05 02:43:59,642] [INFO] Running command: blastn -query GCA_001767455.1_ASM176745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7bdb3db-14a0-4428-b1c1-828dc26927c8/dqc_reference/reference_markers.fasta -out GCA_001767455.1_ASM176745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:44:00,326] [INFO] Task succeeded: Blastn
[2023-06-05 02:44:00,332] [INFO] Selected 31 target genomes.
[2023-06-05 02:44:00,332] [INFO] Target genome list was writen to GCA_001767455.1_ASM176745v1_genomic.fna/target_genomes.txt
[2023-06-05 02:44:00,334] [INFO] Task started: fastANI
[2023-06-05 02:44:00,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff225eb-8dbf-4d5d-b176-6fd9417a1e1c/GCA_001767455.1_ASM176745v1_genomic.fna.gz --refList GCA_001767455.1_ASM176745v1_genomic.fna/target_genomes.txt --output GCA_001767455.1_ASM176745v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:44:28,823] [INFO] Task succeeded: fastANI
[2023-06-05 02:44:28,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7bdb3db-14a0-4428-b1c1-828dc26927c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:44:28,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7bdb3db-14a0-4428-b1c1-828dc26927c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:44:28,848] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:44:28,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:44:28,848] [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	76.9005	305	2109	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	75.3986	56	2109	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	75.3838	60	2109	95	below_threshold
Granulicella sibirica	strain=AF10	GCA_004115155.1	2479048	2479048	type	True	75.2743	52	2109	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1519	281	2109	95	below_threshold
Geomonas terrae	strain=Red111	GCA_004791675.1	2562681	2562681	type	True	75.1291	56	2109	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	75.103	109	2109	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	75.1029	86	2109	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	75.081	66	2109	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.0611	130	2109	95	below_threshold
Geomonas ferrireducens	strain=S62	GCA_004917065.1	2570227	2570227	type	True	75.0466	57	2109	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.0432	122	2109	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	74.9677	151	2109	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	74.9533	87	2109	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.9345	131	2109	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	74.9191	128	2109	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	74.8996	73	2109	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	74.861	113	2109	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	74.8587	113	2109	95	below_threshold
Paraburkholderia acidipaludis	strain=NBRC 101816	GCA_000684975.1	660537	660537	type	True	74.8515	148	2109	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8442	347	2109	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	74.7548	99	2109	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	74.7432	86	2109	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	74.7314	280	2109	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	74.7191	140	2109	95	below_threshold
Caballeronia novacaledonica	strain=LMG 28615	GCA_900258035.1	1544861	1544861	type	True	74.6985	147	2109	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	74.688	63	2109	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:44:28,850] [INFO] DFAST Taxonomy check result was written to GCA_001767455.1_ASM176745v1_genomic.fna/tc_result.tsv
[2023-06-05 02:44:28,851] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:44:28,851] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:44:28,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7bdb3db-14a0-4428-b1c1-828dc26927c8/dqc_reference/checkm_data
[2023-06-05 02:44:28,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:44:28,910] [INFO] Task started: CheckM
[2023-06-05 02:44:28,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001767455.1_ASM176745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001767455.1_ASM176745v1_genomic.fna/checkm_input GCA_001767455.1_ASM176745v1_genomic.fna/checkm_result
[2023-06-05 02:45:23,986] [INFO] Task succeeded: CheckM
[2023-06-05 02:45:23,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:45:24,022] [INFO] ===== Completeness check finished =====
[2023-06-05 02:45:24,022] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:45:24,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001767455.1_ASM176745v1_genomic.fna/markers.fasta)
[2023-06-05 02:45:24,023] [INFO] Task started: Blastn
[2023-06-05 02:45:24,023] [INFO] Running command: blastn -query GCA_001767455.1_ASM176745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7bdb3db-14a0-4428-b1c1-828dc26927c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_001767455.1_ASM176745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:45:25,048] [INFO] Task succeeded: Blastn
[2023-06-05 02:45:25,053] [INFO] Selected 17 target genomes.
[2023-06-05 02:45:25,053] [INFO] Target genome list was writen to GCA_001767455.1_ASM176745v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:45:25,054] [INFO] Task started: fastANI
[2023-06-05 02:45:25,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ff225eb-8dbf-4d5d-b176-6fd9417a1e1c/GCA_001767455.1_ASM176745v1_genomic.fna.gz --refList GCA_001767455.1_ASM176745v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001767455.1_ASM176745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:45:41,019] [INFO] Task succeeded: fastANI
[2023-06-05 02:45:41,034] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:45:41,034] [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_001767455.1	s__2-12-FULL-66-21 sp001767455	100.0	2103	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__2-12-FULL-66-21	95.0	99.91	99.91	0.96	0.96	2	conclusive
GCA_013813355.1	s__JACCRT01 sp013813355	78.3137	151	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACCRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223835.1	s__Gp6-AA38 sp003223835	78.2008	575	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__Gp6-AA38	95.0	98.48	98.48	0.89	0.89	2	-
GCA_013694635.1	s__JACDCA01 sp013694635	78.0932	266	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222675.1	s__QHWT01 sp003222675	77.957	554	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817065.1	s__JACDCA01 sp013817065	77.8647	314	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362195.1	s__QHWT01 sp013362195	77.7769	422	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__QHWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697225.1	s__JACCXG01 sp013697225	77.7171	220	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACCXG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694845.1	s__JACDCA01 sp013694845	77.3843	349	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACDCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	77.1461	419	2109	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_003222395.1	s__Gp6-AA45 sp003222395	76.876	472	2109	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_012271165.1	s__JAAXGX01 sp012271165	76.1114	176	2109	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016193045.1	s__CSP1-6 sp016193045	75.3242	72	2109	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__CSP1-6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	74.9524	69	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110275.1	s__Duganella sp900110275	74.743	169	2109	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:45:41,036] [INFO] GTDB search result was written to GCA_001767455.1_ASM176745v1_genomic.fna/result_gtdb.tsv
[2023-06-05 02:45:41,036] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:45:41,041] [INFO] DFAST_QC result json was written to GCA_001767455.1_ASM176745v1_genomic.fna/dqc_result.json
[2023-06-05 02:45:41,042] [INFO] DFAST_QC completed!
[2023-06-05 02:45:41,042] [INFO] Total running time: 0h2m1s