[2023-06-17 06:26:14,506] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:26:14,509] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:26:14,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgea6d4afc-6ebc-473a-a2d2-a1488f3921ea/dqc_reference
[2023-06-17 06:26:15,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:26:15,839] [INFO] Task started: Prodigal
[2023-06-17 06:26:15,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg290b6461-9b40-43b6-9b73-a1d95b3819ba/GCA_013349335.1_ASM1334933v1_genomic.fna.gz | prodigal -d GCA_013349335.1_ASM1334933v1_genomic.fna/cds.fna -a GCA_013349335.1_ASM1334933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:26:23,052] [INFO] Task succeeded: Prodigal
[2023-06-17 06:26:23,053] [INFO] Task started: HMMsearch
[2023-06-17 06:26:23,053] [INFO] Running command: hmmsearch --tblout GCA_013349335.1_ASM1334933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea6d4afc-6ebc-473a-a2d2-a1488f3921ea/dqc_reference/reference_markers.hmm GCA_013349335.1_ASM1334933v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:26:23,309] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:26:23,310] [INFO] Found 6/6 markers.
[2023-06-17 06:26:23,337] [INFO] Query marker FASTA was written to GCA_013349335.1_ASM1334933v1_genomic.fna/markers.fasta
[2023-06-17 06:26:23,338] [INFO] Task started: Blastn
[2023-06-17 06:26:23,338] [INFO] Running command: blastn -query GCA_013349335.1_ASM1334933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea6d4afc-6ebc-473a-a2d2-a1488f3921ea/dqc_reference/reference_markers.fasta -out GCA_013349335.1_ASM1334933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:26:24,156] [INFO] Task succeeded: Blastn
[2023-06-17 06:26:24,162] [INFO] Selected 36 target genomes.
[2023-06-17 06:26:24,162] [INFO] Target genome list was writen to GCA_013349335.1_ASM1334933v1_genomic.fna/target_genomes.txt
[2023-06-17 06:26:24,185] [INFO] Task started: fastANI
[2023-06-17 06:26:24,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg290b6461-9b40-43b6-9b73-a1d95b3819ba/GCA_013349335.1_ASM1334933v1_genomic.fna.gz --refList GCA_013349335.1_ASM1334933v1_genomic.fna/target_genomes.txt --output GCA_013349335.1_ASM1334933v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:26:55,518] [INFO] Task succeeded: fastANI
[2023-06-17 06:26:55,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea6d4afc-6ebc-473a-a2d2-a1488f3921ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:26:55,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea6d4afc-6ebc-473a-a2d2-a1488f3921ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:26:55,548] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:26:55,548] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 06:26:55,549] [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
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.7318	50	778	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.37	136	778	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.3263	103	778	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.3212	125	778	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.308	125	778	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.2793	114	778	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.2558	95	778	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.2096	96	778	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.1516	125	778	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.1301	110	778	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.1166	127	778	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1141	85	778	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0425	85	778	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.0415	117	778	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.04	117	778	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0051	89	778	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.9911	106	778	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	75.9558	58	778	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.9004	76	778	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.8992	62	778	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.8772	117	778	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	75.8755	107	778	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.8691	141	778	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	75.8222	58	778	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.7996	138	778	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.7687	114	778	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.7643	112	778	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	75.7024	50	778	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	75.6653	53	778	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.6176	88	778	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.5702	101	778	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	75.5493	80	778	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	75.2657	58	778	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:26:55,551] [INFO] DFAST Taxonomy check result was written to GCA_013349335.1_ASM1334933v1_genomic.fna/tc_result.tsv
[2023-06-17 06:26:55,551] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:26:55,552] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:26:55,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea6d4afc-6ebc-473a-a2d2-a1488f3921ea/dqc_reference/checkm_data
[2023-06-17 06:26:55,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:26:55,583] [INFO] Task started: CheckM
[2023-06-17 06:26:55,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013349335.1_ASM1334933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013349335.1_ASM1334933v1_genomic.fna/checkm_input GCA_013349335.1_ASM1334933v1_genomic.fna/checkm_result
[2023-06-17 06:27:21,109] [INFO] Task succeeded: CheckM
[2023-06-17 06:27:21,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 06:27:21,158] [INFO] ===== Completeness check finished =====
[2023-06-17 06:27:21,158] [INFO] ===== Start GTDB Search =====
[2023-06-17 06:27:21,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013349335.1_ASM1334933v1_genomic.fna/markers.fasta)
[2023-06-17 06:27:21,159] [INFO] Task started: Blastn
[2023-06-17 06:27:21,159] [INFO] Running command: blastn -query GCA_013349335.1_ASM1334933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea6d4afc-6ebc-473a-a2d2-a1488f3921ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_013349335.1_ASM1334933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:27:22,366] [INFO] Task succeeded: Blastn
[2023-06-17 06:27:22,371] [INFO] Selected 25 target genomes.
[2023-06-17 06:27:22,372] [INFO] Target genome list was writen to GCA_013349335.1_ASM1334933v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 06:27:22,391] [INFO] Task started: fastANI
[2023-06-17 06:27:22,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg290b6461-9b40-43b6-9b73-a1d95b3819ba/GCA_013349335.1_ASM1334933v1_genomic.fna.gz --refList GCA_013349335.1_ASM1334933v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013349335.1_ASM1334933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 06:27:35,385] [INFO] Task succeeded: fastANI
[2023-06-17 06:27:35,407] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 06:27:35,407] [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_013349695.1	s__GCA-2686765 sp013349695	99.6437	586	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765	95.0	98.27	95.45	0.83	0.65	4	conclusive
GCA_002725625.1	s__GCA-2725625 sp002725625	82.5685	65	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UBA2165;g__GCA-2725625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938315.1	s__Casp-alpha2 sp002938315	77.3546	107	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.2174	182	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	76.8848	135	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_009693905.1	s__2-12-FULL-67-15 sp009693905	76.7916	96	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.6756	121	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830425.1	s__2-02-FULL-58-16 sp001830425	76.6495	131	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.5094	84	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776525.1	s__JADHTD01 sp016776525	76.5021	100	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JADHTD01;g__JADHTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	76.4369	136	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_016763915.1	s__Casp-alpha2 sp016763915	76.383	79	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.3541	101	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_002706405.1	s__UBA1479 sp002706405	76.3324	113	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.3213	154	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.2629	120	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	76.231	105	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015231605.1	s__JADGBG01 sp015231605	76.1934	105	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetovibrionaceae;g__JADGBG01	95.0	99.19	99.19	0.87	0.87	2	-
GCA_016712595.1	s__SSA4 sp016712595	76.1528	60	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	76.1293	121	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776725.1	s__JABGRG01 sp016776725	76.1263	53	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JABGRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354135.1	s__GLO-3 sp003354135	76.122	99	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__GLO-3;g__GLO-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793875.1	s__SSA4 sp016793875	75.9998	87	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	75.6859	67	778	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 06:27:35,410] [INFO] GTDB search result was written to GCA_013349335.1_ASM1334933v1_genomic.fna/result_gtdb.tsv
[2023-06-17 06:27:35,410] [INFO] ===== GTDB Search completed =====
[2023-06-17 06:27:35,416] [INFO] DFAST_QC result json was written to GCA_013349335.1_ASM1334933v1_genomic.fna/dqc_result.json
[2023-06-17 06:27:35,416] [INFO] DFAST_QC completed!
[2023-06-17 06:27:35,416] [INFO] Total running time: 0h1m21s