[2023-06-30 13:24:28,849] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:24:28,851] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:24:28,851] [INFO] DQC Reference Directory: /var/lib/cwl/stgb860b983-f10c-42e7-9a56-118e76936a95/dqc_reference
[2023-06-30 13:24:30,186] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:24:30,187] [INFO] Task started: Prodigal
[2023-06-30 13:24:30,187] [INFO] Running command: gunzip -c /var/lib/cwl/stgf59f56ba-d2d1-487d-9462-22770f17cf7b/GCA_016708825.1_ASM1670882v1_genomic.fna.gz | prodigal -d GCA_016708825.1_ASM1670882v1_genomic.fna/cds.fna -a GCA_016708825.1_ASM1670882v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:24:41,008] [INFO] Task succeeded: Prodigal
[2023-06-30 13:24:41,009] [INFO] Task started: HMMsearch
[2023-06-30 13:24:41,009] [INFO] Running command: hmmsearch --tblout GCA_016708825.1_ASM1670882v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb860b983-f10c-42e7-9a56-118e76936a95/dqc_reference/reference_markers.hmm GCA_016708825.1_ASM1670882v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:24:41,272] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:24:41,274] [INFO] Found 6/6 markers.
[2023-06-30 13:24:41,309] [INFO] Query marker FASTA was written to GCA_016708825.1_ASM1670882v1_genomic.fna/markers.fasta
[2023-06-30 13:24:41,310] [INFO] Task started: Blastn
[2023-06-30 13:24:41,310] [INFO] Running command: blastn -query GCA_016708825.1_ASM1670882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb860b983-f10c-42e7-9a56-118e76936a95/dqc_reference/reference_markers.fasta -out GCA_016708825.1_ASM1670882v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:42,162] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:42,167] [INFO] Selected 33 target genomes.
[2023-06-30 13:24:42,167] [INFO] Target genome list was writen to GCA_016708825.1_ASM1670882v1_genomic.fna/target_genomes.txt
[2023-06-30 13:24:42,171] [INFO] Task started: fastANI
[2023-06-30 13:24:42,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59f56ba-d2d1-487d-9462-22770f17cf7b/GCA_016708825.1_ASM1670882v1_genomic.fna.gz --refList GCA_016708825.1_ASM1670882v1_genomic.fna/target_genomes.txt --output GCA_016708825.1_ASM1670882v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:25:05,144] [INFO] Task succeeded: fastANI
[2023-06-30 13:25:05,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb860b983-f10c-42e7-9a56-118e76936a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:25:05,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb860b983-f10c-42e7-9a56-118e76936a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:25:05,173] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:25:05,173] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:25:05,174] [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
Usitatibacter rugosus	strain=0125_3	GCA_013003965.1	2732067	2732067	type	True	79.7327	580	1222	95	below_threshold
Usitatibacter palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	79.3247	573	1222	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.3999	174	1222	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.2771	168	1222	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.0703	260	1222	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.945	215	1222	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	76.865	185	1222	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	76.8587	192	1222	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	76.6475	194	1222	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	76.6378	167	1222	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	76.5897	227	1222	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	76.5435	230	1222	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	76.4802	184	1222	95	below_threshold
Lysobacter profundi	strain=CHu50b-3-2	GCA_009792795.1	2594501	2594501	type	True	76.4655	78	1222	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	76.4498	153	1222	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.4327	259	1222	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	76.417	201	1222	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.401	140	1222	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	76.3607	245	1222	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	76.316	201	1222	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	76.3017	122	1222	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.2737	204	1222	95	below_threshold
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	76.2586	233	1222	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	76.2564	148	1222	95	below_threshold
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	76.1935	201	1222	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.1561	138	1222	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.1134	115	1222	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.0866	89	1222	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	75.982	110	1222	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	75.9057	110	1222	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.8864	128	1222	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	75.8465	139	1222	95	below_threshold
Nocardioides agariphilus	strain=KCTC 19276	GCA_015352445.1	433664	433664	type	True	75.0674	66	1222	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:25:05,176] [INFO] DFAST Taxonomy check result was written to GCA_016708825.1_ASM1670882v1_genomic.fna/tc_result.tsv
[2023-06-30 13:25:05,176] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:25:05,177] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:25:05,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb860b983-f10c-42e7-9a56-118e76936a95/dqc_reference/checkm_data
[2023-06-30 13:25:05,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:25:05,222] [INFO] Task started: CheckM
[2023-06-30 13:25:05,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708825.1_ASM1670882v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708825.1_ASM1670882v1_genomic.fna/checkm_input GCA_016708825.1_ASM1670882v1_genomic.fna/checkm_result
[2023-06-30 13:25:42,386] [INFO] Task succeeded: CheckM
[2023-06-30 13:25:42,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:25:42,410] [INFO] ===== Completeness check finished =====
[2023-06-30 13:25:42,410] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:25:42,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708825.1_ASM1670882v1_genomic.fna/markers.fasta)
[2023-06-30 13:25:42,411] [INFO] Task started: Blastn
[2023-06-30 13:25:42,412] [INFO] Running command: blastn -query GCA_016708825.1_ASM1670882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb860b983-f10c-42e7-9a56-118e76936a95/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708825.1_ASM1670882v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:25:43,879] [INFO] Task succeeded: Blastn
[2023-06-30 13:25:43,883] [INFO] Selected 12 target genomes.
[2023-06-30 13:25:43,883] [INFO] Target genome list was writen to GCA_016708825.1_ASM1670882v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:25:43,888] [INFO] Task started: fastANI
[2023-06-30 13:25:43,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgf59f56ba-d2d1-487d-9462-22770f17cf7b/GCA_016708825.1_ASM1670882v1_genomic.fna.gz --refList GCA_016708825.1_ASM1670882v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708825.1_ASM1670882v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:25:52,903] [INFO] Task succeeded: fastANI
[2023-06-30 13:25:52,919] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:25:52,920] [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_016708825.1	s__FEB-7 sp016708825	100.0	1218	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003105245.1	s__FEB-7 sp003105245	83.6152	685	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	99.57	99.57	0.92	0.92	2	-
GCA_011391275.1	s__FEB-7 sp011391275	83.4061	650	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720855.1	s__FEB-7 sp016720855	82.7799	818	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709665.1	s__FEB-7 sp016709665	81.8257	791	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711875.1	s__FEB-7 sp016711875	81.6467	751	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012274175.1	s__Usitatibacter sp012274175	79.619	409	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880705.1	s__Usitatibacter sp017880705	79.2415	393	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853245.1	s__FEB-7 sp017853245	78.787	339	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711205.1	s__Polaromonas sp003711205	76.2717	127	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012515985.1	s__Luteimonas sp012515985	76.0947	68	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262975.1	s__JADFDG01 sp018262975	76.071	115	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__JADFDG01;g__JADFDG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:25:52,922] [INFO] GTDB search result was written to GCA_016708825.1_ASM1670882v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:25:52,923] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:25:52,927] [INFO] DFAST_QC result json was written to GCA_016708825.1_ASM1670882v1_genomic.fna/dqc_result.json
[2023-06-30 13:25:52,927] [INFO] DFAST_QC completed!
[2023-06-30 13:25:52,928] [INFO] Total running time: 0h1m24s