[2023-06-19 02:24:59,111] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:24:59,114] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:24:59,114] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4c4bab8-20f9-4a83-a4cf-ebce4bf4d183/dqc_reference
[2023-06-19 02:25:00,350] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:00,351] [INFO] Task started: Prodigal
[2023-06-19 02:25:00,351] [INFO] Running command: gunzip -c /var/lib/cwl/stg418bcf42-56b1-442d-8b8c-f5d6948477e9/GCA_018660475.1_ASM1866047v1_genomic.fna.gz | prodigal -d GCA_018660475.1_ASM1866047v1_genomic.fna/cds.fna -a GCA_018660475.1_ASM1866047v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:10,395] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:10,396] [INFO] Task started: HMMsearch
[2023-06-19 02:25:10,396] [INFO] Running command: hmmsearch --tblout GCA_018660475.1_ASM1866047v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4c4bab8-20f9-4a83-a4cf-ebce4bf4d183/dqc_reference/reference_markers.hmm GCA_018660475.1_ASM1866047v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:10,665] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:10,667] [INFO] Found 6/6 markers.
[2023-06-19 02:25:10,710] [INFO] Query marker FASTA was written to GCA_018660475.1_ASM1866047v1_genomic.fna/markers.fasta
[2023-06-19 02:25:10,710] [INFO] Task started: Blastn
[2023-06-19 02:25:10,711] [INFO] Running command: blastn -query GCA_018660475.1_ASM1866047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c4bab8-20f9-4a83-a4cf-ebce4bf4d183/dqc_reference/reference_markers.fasta -out GCA_018660475.1_ASM1866047v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:11,459] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:11,464] [INFO] Selected 38 target genomes.
[2023-06-19 02:25:11,464] [INFO] Target genome list was writen to GCA_018660475.1_ASM1866047v1_genomic.fna/target_genomes.txt
[2023-06-19 02:25:11,467] [INFO] Task started: fastANI
[2023-06-19 02:25:11,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg418bcf42-56b1-442d-8b8c-f5d6948477e9/GCA_018660475.1_ASM1866047v1_genomic.fna.gz --refList GCA_018660475.1_ASM1866047v1_genomic.fna/target_genomes.txt --output GCA_018660475.1_ASM1866047v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:42,046] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:42,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4c4bab8-20f9-4a83-a4cf-ebce4bf4d183/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:42,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4c4bab8-20f9-4a83-a4cf-ebce4bf4d183/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:42,073] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:25:42,074] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:25:42,074] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.2473	113	1060	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.0034	121	1060	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8888	106	1060	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.7934	81	1060	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.779	55	1060	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.7388	75	1060	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	75.7102	87	1060	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.7076	58	1060	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.6595	84	1060	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.6499	58	1060	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.5921	72	1060	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.5748	79	1060	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.5556	123	1060	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.5471	65	1060	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.5212	93	1060	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.5077	72	1060	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.499	70	1060	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	75.4963	104	1060	95	below_threshold
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	75.4951	54	1060	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.4899	109	1060	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	75.4768	73	1060	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	75.4767	73	1060	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	75.4645	61	1060	95	below_threshold
Tistrella bauzanensis	strain=CGMCC 1.10188	GCA_014636235.1	657419	657419	type	True	75.4549	68	1060	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	75.4526	78	1060	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.4383	89	1060	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	75.4367	78	1060	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.4161	108	1060	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	75.4009	94	1060	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.3407	97	1060	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.3147	88	1060	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	75.2856	65	1060	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	75.0631	56	1060	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:25:42,076] [INFO] DFAST Taxonomy check result was written to GCA_018660475.1_ASM1866047v1_genomic.fna/tc_result.tsv
[2023-06-19 02:25:42,077] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:42,077] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:42,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4c4bab8-20f9-4a83-a4cf-ebce4bf4d183/dqc_reference/checkm_data
[2023-06-19 02:25:42,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:42,120] [INFO] Task started: CheckM
[2023-06-19 02:25:42,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018660475.1_ASM1866047v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018660475.1_ASM1866047v1_genomic.fna/checkm_input GCA_018660475.1_ASM1866047v1_genomic.fna/checkm_result
[2023-06-19 02:26:15,550] [INFO] Task succeeded: CheckM
[2023-06-19 02:26:15,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:26:15,576] [INFO] ===== Completeness check finished =====
[2023-06-19 02:26:15,576] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:26:15,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018660475.1_ASM1866047v1_genomic.fna/markers.fasta)
[2023-06-19 02:26:15,577] [INFO] Task started: Blastn
[2023-06-19 02:26:15,577] [INFO] Running command: blastn -query GCA_018660475.1_ASM1866047v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c4bab8-20f9-4a83-a4cf-ebce4bf4d183/dqc_reference/reference_markers_gtdb.fasta -out GCA_018660475.1_ASM1866047v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:16,873] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:16,894] [INFO] Selected 25 target genomes.
[2023-06-19 02:26:16,894] [INFO] Target genome list was writen to GCA_018660475.1_ASM1866047v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:26:16,904] [INFO] Task started: fastANI
[2023-06-19 02:26:16,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg418bcf42-56b1-442d-8b8c-f5d6948477e9/GCA_018660475.1_ASM1866047v1_genomic.fna.gz --refList GCA_018660475.1_ASM1866047v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018660475.1_ASM1866047v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:33,364] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:33,386] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:26:33,387] [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_018666805.1	s__PTKB01 sp018666805	99.2558	937	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	conclusive
GCA_002937555.1	s__PTKB01 sp002937555	80.1276	410	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869195.1	s__SHWC01 sp016869195	76.8829	154	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__SHWC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523425.1	s__WTGU01 sp011523425	76.7228	191	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717225.1	s__PTKB01 sp002717225	76.7157	154	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214125.1	s__JACRPC01 sp016214125	76.1694	93	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__WMHbin7;g__JACRPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.1273	145	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.0472	87	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.0037	106	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	75.9921	122	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721365.1	s__GCA-2721365 sp002721365	75.9354	66	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794165.1	s__Dongia sp016794165	75.8602	74	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201015.1	s__JACQDQ01 sp016201015	75.7945	88	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQDQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011022235.1	s__Magnetospirillum aberrantis	75.7541	56	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	75.5784	51	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCA_015232025.1	s__JADFZP01 sp015232025	75.5481	59	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	75.4596	70	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCF_004341885.1	s__Shinella granuli	75.4231	79	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_900230255.1	s__Caenispirillum bisanense	75.4005	100	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900079695.1	s__Alpha-05 sp900079695	75.36	85	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240295.1	s__Aquamicrobium_A sediminum	75.2659	67	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:33,389] [INFO] GTDB search result was written to GCA_018660475.1_ASM1866047v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:33,389] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:33,395] [INFO] DFAST_QC result json was written to GCA_018660475.1_ASM1866047v1_genomic.fna/dqc_result.json
[2023-06-19 02:26:33,396] [INFO] DFAST_QC completed!
[2023-06-19 02:26:33,396] [INFO] Total running time: 0h1m34s