[2023-06-13 11:29:49,201] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:29:49,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:29:49,204] [INFO] DQC Reference Directory: /var/lib/cwl/stgabd794aa-2b9f-4f43-96a1-0a4705ee28a8/dqc_reference
[2023-06-13 11:29:50,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:29:50,774] [INFO] Task started: Prodigal
[2023-06-13 11:29:50,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg75c44fb4-2a2a-47fa-b6d1-de217a9452db/GCA_022820735.1_ASM2282073v1_genomic.fna.gz | prodigal -d GCA_022820735.1_ASM2282073v1_genomic.fna/cds.fna -a GCA_022820735.1_ASM2282073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:30:04,778] [INFO] Task succeeded: Prodigal
[2023-06-13 11:30:04,779] [INFO] Task started: HMMsearch
[2023-06-13 11:30:04,779] [INFO] Running command: hmmsearch --tblout GCA_022820735.1_ASM2282073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabd794aa-2b9f-4f43-96a1-0a4705ee28a8/dqc_reference/reference_markers.hmm GCA_022820735.1_ASM2282073v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:30:05,088] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:30:05,090] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg75c44fb4-2a2a-47fa-b6d1-de217a9452db/GCA_022820735.1_ASM2282073v1_genomic.fna.gz]
[2023-06-13 11:30:05,134] [INFO] Query marker FASTA was written to GCA_022820735.1_ASM2282073v1_genomic.fna/markers.fasta
[2023-06-13 11:30:05,135] [INFO] Task started: Blastn
[2023-06-13 11:30:05,135] [INFO] Running command: blastn -query GCA_022820735.1_ASM2282073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd794aa-2b9f-4f43-96a1-0a4705ee28a8/dqc_reference/reference_markers.fasta -out GCA_022820735.1_ASM2282073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:06,003] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:06,008] [INFO] Selected 29 target genomes.
[2023-06-13 11:30:06,008] [INFO] Target genome list was writen to GCA_022820735.1_ASM2282073v1_genomic.fna/target_genomes.txt
[2023-06-13 11:30:06,011] [INFO] Task started: fastANI
[2023-06-13 11:30:06,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c44fb4-2a2a-47fa-b6d1-de217a9452db/GCA_022820735.1_ASM2282073v1_genomic.fna.gz --refList GCA_022820735.1_ASM2282073v1_genomic.fna/target_genomes.txt --output GCA_022820735.1_ASM2282073v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:30:26,062] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:26,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabd794aa-2b9f-4f43-96a1-0a4705ee28a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:30:26,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabd794aa-2b9f-4f43-96a1-0a4705ee28a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:30:26,080] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:30:26,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:30:26,080] [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
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.1454	67	1454	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.9124	102	1454	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	75.838	60	1454	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.7957	58	1454	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.7303	50	1454	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.6938	62	1454	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	75.6047	65	1454	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.5528	52	1454	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.4374	118	1454	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	75.4112	72	1454	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.4105	120	1454	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	75.3595	60	1454	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.3159	77	1454	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.2948	127	1454	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	75.2241	78	1454	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.0223	106	1454	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.9731	80	1454	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.9376	76	1454	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	74.8217	74	1454	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	74.8187	75	1454	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7805	84	1454	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:30:26,083] [INFO] DFAST Taxonomy check result was written to GCA_022820735.1_ASM2282073v1_genomic.fna/tc_result.tsv
[2023-06-13 11:30:26,083] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:30:26,084] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:30:26,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabd794aa-2b9f-4f43-96a1-0a4705ee28a8/dqc_reference/checkm_data
[2023-06-13 11:30:26,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:30:26,136] [INFO] Task started: CheckM
[2023-06-13 11:30:26,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022820735.1_ASM2282073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022820735.1_ASM2282073v1_genomic.fna/checkm_input GCA_022820735.1_ASM2282073v1_genomic.fna/checkm_result
[2023-06-13 11:31:09,556] [INFO] Task succeeded: CheckM
[2023-06-13 11:31:09,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:31:09,581] [INFO] ===== Completeness check finished =====
[2023-06-13 11:31:09,581] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:31:09,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022820735.1_ASM2282073v1_genomic.fna/markers.fasta)
[2023-06-13 11:31:09,582] [INFO] Task started: Blastn
[2023-06-13 11:31:09,582] [INFO] Running command: blastn -query GCA_022820735.1_ASM2282073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd794aa-2b9f-4f43-96a1-0a4705ee28a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022820735.1_ASM2282073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:31:11,107] [INFO] Task succeeded: Blastn
[2023-06-13 11:31:11,115] [INFO] Selected 26 target genomes.
[2023-06-13 11:31:11,115] [INFO] Target genome list was writen to GCA_022820735.1_ASM2282073v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:31:11,124] [INFO] Task started: fastANI
[2023-06-13 11:31:11,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c44fb4-2a2a-47fa-b6d1-de217a9452db/GCA_022820735.1_ASM2282073v1_genomic.fna.gz --refList GCA_022820735.1_ASM2282073v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022820735.1_ASM2282073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:31:28,849] [INFO] Task succeeded: fastANI
[2023-06-13 11:31:28,872] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 11:31:28,872] [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_009843625.1	s__BD2-11 sp009843625	82.75	95	1454	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840525.1	s__BD2-11 sp009840525	81.8903	99	1454	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	96.09	95.11	0.90	0.85	6	-
GCA_002238605.1	s__BD2-11 sp002238605	80.8394	115	1454	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001798595.1	s__2-12-FULL-60-19 sp001798595	76.5557	121	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA9968;f__UBA9968;g__2-12-FULL-60-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184235.1	s__UBA9968 sp016184235	76.3144	87	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA9968;f__UBA9968;g__UBA9968	95.0	98.24	98.21	0.77	0.76	3	-
GCF_008632335.1	s__Thiohalocapsa marina	76.1454	67	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879405.1	s__DP-19 sp005879405	76.0639	73	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__DP-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016193385.1	s__2-12-FULL-57-22 sp016193385	76.0042	64	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA9968;f__UBA9968;g__2-12-FULL-57-22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	75.9411	100	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200545.1	s__DP-19 sp016200545	75.8271	77	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__DP-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016180805.1	s__2-12-FULL-57-22 sp016180805	75.7842	81	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA9968;f__UBA9968;g__2-12-FULL-57-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822105.1	s__Humidesulfovibrio sp018822105	75.761	58	1454	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCA_014762505.1	s__SpSt-1174 sp014762505	75.6987	55	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050235.1	s__UTPRO1 sp002050235	75.644	76	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__UTPRO1;g__UTPRO1	95.0	99.98	99.98	0.96	0.96	2	-
GCF_013019105.1	s__Fundidesulfovibrio sp013019105	75.6213	64	1454	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Fundidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874795.1	s__VGTG01 sp016874795	75.5844	73	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874715.1	s__VGTK01 sp016874715	75.5195	114	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853315.1	s__REEB422 sp017853315	75.4882	72	1454	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__REEB422	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003069545.1	s__Rhodanobacter thiooxydans_A	75.4553	63	1454	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.26	98.26	0.94	0.94	2	-
GCA_016218825.1	s__JACRCV01 sp016218825	75.1725	89	1454	d__Bacteria;p__Myxococcota;c__XYA12-FULL-58-9;o__XYA12-FULL-58-9;f__XYA12-FULL-58-9;g__JACRCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871255.1	s__VFZH01 sp016871255	74.9888	50	1454	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__VFZH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:31:28,874] [INFO] GTDB search result was written to GCA_022820735.1_ASM2282073v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:31:28,875] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:31:28,880] [INFO] DFAST_QC result json was written to GCA_022820735.1_ASM2282073v1_genomic.fna/dqc_result.json
[2023-06-13 11:31:28,880] [INFO] DFAST_QC completed!
[2023-06-13 11:31:28,880] [INFO] Total running time: 0h1m40s