[2023-06-28 18:14:40,947] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:14:40,949] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:14:40,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg210475c3-3982-4ecd-b933-64afdbf496fe/dqc_reference
[2023-06-28 18:14:42,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:14:42,360] [INFO] Task started: Prodigal
[2023-06-28 18:14:42,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b53a84f-fb90-450f-a548-a04206338b1a/GCA_005879585.1_ASM587958v1_genomic.fna.gz | prodigal -d GCA_005879585.1_ASM587958v1_genomic.fna/cds.fna -a GCA_005879585.1_ASM587958v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:15:09,998] [INFO] Task succeeded: Prodigal
[2023-06-28 18:15:09,999] [INFO] Task started: HMMsearch
[2023-06-28 18:15:09,999] [INFO] Running command: hmmsearch --tblout GCA_005879585.1_ASM587958v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg210475c3-3982-4ecd-b933-64afdbf496fe/dqc_reference/reference_markers.hmm GCA_005879585.1_ASM587958v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:15:10,335] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:15:10,336] [INFO] Found 6/6 markers.
[2023-06-28 18:15:10,387] [INFO] Query marker FASTA was written to GCA_005879585.1_ASM587958v1_genomic.fna/markers.fasta
[2023-06-28 18:15:10,388] [INFO] Task started: Blastn
[2023-06-28 18:15:10,388] [INFO] Running command: blastn -query GCA_005879585.1_ASM587958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg210475c3-3982-4ecd-b933-64afdbf496fe/dqc_reference/reference_markers.fasta -out GCA_005879585.1_ASM587958v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:15:11,150] [INFO] Task succeeded: Blastn
[2023-06-28 18:15:11,155] [INFO] Selected 36 target genomes.
[2023-06-28 18:15:11,156] [INFO] Target genome list was writen to GCA_005879585.1_ASM587958v1_genomic.fna/target_genomes.txt
[2023-06-28 18:15:11,158] [INFO] Task started: fastANI
[2023-06-28 18:15:11,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b53a84f-fb90-450f-a548-a04206338b1a/GCA_005879585.1_ASM587958v1_genomic.fna.gz --refList GCA_005879585.1_ASM587958v1_genomic.fna/target_genomes.txt --output GCA_005879585.1_ASM587958v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:15:41,706] [INFO] Task succeeded: fastANI
[2023-06-28 18:15:41,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg210475c3-3982-4ecd-b933-64afdbf496fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:15:41,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg210475c3-3982-4ecd-b933-64afdbf496fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:15:41,735] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:15:41,735] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:15:41,735] [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
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	75.5549	50	1449	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.4479	131	1449	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.4402	139	1449	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.2978	56	1449	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.2586	312	1449	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	75.2336	196	1449	95	below_threshold
Lysobacter oculi	strain=83-4	GCA_003293695.1	2698682	2698682	type	True	75.2294	52	1449	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	75.1532	59	1449	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	75.0699	131	1449	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	75.069	137	1449	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.0336	121	1449	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	75.0228	72	1449	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.013	144	1449	95	below_threshold
Paraburkholderia mimosarum	strain=NBRC 106338	GCA_000739815.1	312026	312026	type	True	74.9496	124	1449	95	below_threshold
Paraburkholderia mimosarum	strain=LMG 23256	GCA_902833725.1	312026	312026	type	True	74.9432	125	1449	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.9414	185	1449	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	74.8925	277	1449	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	74.877	72	1449	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	74.8639	61	1449	95	below_threshold
Pandoraea captiosa	strain=LMG 31118	GCA_902459775.1	2508302	2508302	type	True	74.8521	59	1449	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	74.8461	279	1449	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	74.8253	195	1449	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	74.8208	174	1449	95	below_threshold
Mumia flava	strain=DSM 27763	GCA_002797495.1	1348852	1348852	type	True	74.8107	157	1449	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	74.7939	274	1449	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	74.7732	260	1449	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	74.7718	256	1449	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	74.7638	246	1449	95	below_threshold
Paraburkholderia guartelaensis	strain=CNPSo 3008	GCA_004353905.1	2546446	2546446	type	True	74.7634	147	1449	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	74.762	98	1449	95	below_threshold
Microbacterium halotolerans	strain=YIM 70130	GCA_003569805.1	246613	246613	type	True	74.7241	96	1449	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:15:41,737] [INFO] DFAST Taxonomy check result was written to GCA_005879585.1_ASM587958v1_genomic.fna/tc_result.tsv
[2023-06-28 18:15:41,738] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:15:41,738] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:15:41,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg210475c3-3982-4ecd-b933-64afdbf496fe/dqc_reference/checkm_data
[2023-06-28 18:15:41,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:15:41,788] [INFO] Task started: CheckM
[2023-06-28 18:15:41,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005879585.1_ASM587958v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005879585.1_ASM587958v1_genomic.fna/checkm_input GCA_005879585.1_ASM587958v1_genomic.fna/checkm_result
[2023-06-28 18:16:53,982] [INFO] Task succeeded: CheckM
[2023-06-28 18:16:53,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:16:54,011] [INFO] ===== Completeness check finished =====
[2023-06-28 18:16:54,012] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:16:54,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005879585.1_ASM587958v1_genomic.fna/markers.fasta)
[2023-06-28 18:16:54,012] [INFO] Task started: Blastn
[2023-06-28 18:16:54,012] [INFO] Running command: blastn -query GCA_005879585.1_ASM587958v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg210475c3-3982-4ecd-b933-64afdbf496fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_005879585.1_ASM587958v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:16:55,169] [INFO] Task succeeded: Blastn
[2023-06-28 18:16:55,174] [INFO] Selected 12 target genomes.
[2023-06-28 18:16:55,174] [INFO] Target genome list was writen to GCA_005879585.1_ASM587958v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:16:55,209] [INFO] Task started: fastANI
[2023-06-28 18:16:55,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b53a84f-fb90-450f-a548-a04206338b1a/GCA_005879585.1_ASM587958v1_genomic.fna.gz --refList GCA_005879585.1_ASM587958v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005879585.1_ASM587958v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:17:05,791] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:05,804] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:17:05,805] [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_005879585.1	s__DP-3 sp005879585	100.0	1436	1449	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005888095.1	s__DP-3 sp005888095	84.2197	1086	1449	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	98.46	98.46	0.92	0.92	2	-
GCA_005879205.1	s__DP-3 sp005879205	83.0957	810	1449	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879795.1	s__DP-6 sp005879795	79.8234	603	1449	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879245.1	s__DP-23 sp005879245	78.4569	374	1449	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-23	95.0	97.46	97.46	0.74	0.74	2	-
GCA_017853315.1	s__REEB422 sp017853315	76.2311	283	1449	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__REEB422	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874715.1	s__VGTK01 sp016874715	76.129	383	1449	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017505.1	s__Anaeromyxobacter sp000017505	75.2289	305	1449	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859305.1	s__Luteimonas wenzhouensis	75.0195	124	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_018129025.1	s__Roseomonas_B terrae	74.8151	137	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	74.7768	81	1449	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569805.1	s__Microbacterium halotolerans	74.7247	96	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:17:05,808] [INFO] GTDB search result was written to GCA_005879585.1_ASM587958v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:17:05,809] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:17:05,817] [INFO] DFAST_QC result json was written to GCA_005879585.1_ASM587958v1_genomic.fna/dqc_result.json
[2023-06-28 18:17:05,817] [INFO] DFAST_QC completed!
[2023-06-28 18:17:05,817] [INFO] Total running time: 0h2m25s