[2023-06-29 19:13:40,374] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:40,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:40,376] [INFO] DQC Reference Directory: /var/lib/cwl/stgb873d18d-1a08-499c-8c27-d3afbb8b2c37/dqc_reference
[2023-06-29 19:13:41,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:41,839] [INFO] Task started: Prodigal
[2023-06-29 19:13:41,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg90b7baa3-20aa-4fd8-9452-d5c7d4fdf20e/GCA_021774515.1_ASM2177451v1_genomic.fna.gz | prodigal -d GCA_021774515.1_ASM2177451v1_genomic.fna/cds.fna -a GCA_021774515.1_ASM2177451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:54,526] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:54,526] [INFO] Task started: HMMsearch
[2023-06-29 19:13:54,527] [INFO] Running command: hmmsearch --tblout GCA_021774515.1_ASM2177451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb873d18d-1a08-499c-8c27-d3afbb8b2c37/dqc_reference/reference_markers.hmm GCA_021774515.1_ASM2177451v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:54,803] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:54,804] [INFO] Found 6/6 markers.
[2023-06-29 19:13:54,851] [INFO] Query marker FASTA was written to GCA_021774515.1_ASM2177451v1_genomic.fna/markers.fasta
[2023-06-29 19:13:54,852] [INFO] Task started: Blastn
[2023-06-29 19:13:54,852] [INFO] Running command: blastn -query GCA_021774515.1_ASM2177451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb873d18d-1a08-499c-8c27-d3afbb8b2c37/dqc_reference/reference_markers.fasta -out GCA_021774515.1_ASM2177451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:55,588] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:55,593] [INFO] Selected 27 target genomes.
[2023-06-29 19:13:55,593] [INFO] Target genome list was writen to GCA_021774515.1_ASM2177451v1_genomic.fna/target_genomes.txt
[2023-06-29 19:13:55,595] [INFO] Task started: fastANI
[2023-06-29 19:13:55,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b7baa3-20aa-4fd8-9452-d5c7d4fdf20e/GCA_021774515.1_ASM2177451v1_genomic.fna.gz --refList GCA_021774515.1_ASM2177451v1_genomic.fna/target_genomes.txt --output GCA_021774515.1_ASM2177451v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:14:19,777] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:19,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb873d18d-1a08-499c-8c27-d3afbb8b2c37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:14:19,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb873d18d-1a08-499c-8c27-d3afbb8b2c37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:14:19,796] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:14:19,796] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:14:19,796] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1842	145	1258	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.9058	150	1258	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.9042	150	1258	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	75.8642	70	1258	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.8565	86	1258	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.7476	61	1258	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.7441	112	1258	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.7242	73	1258	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	75.7009	83	1258	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	75.6778	70	1258	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	75.6778	70	1258	95	below_threshold
Ferruginivarius sediminum	strain=WD2A32	GCA_003344765.1	2661937	2661937	type	True	75.6149	55	1258	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.6136	141	1258	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	75.5524	98	1258	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	75.552	64	1258	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	75.3381	64	1258	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.3104	83	1258	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.2994	66	1258	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.2625	93	1258	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	75.1429	76	1258	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.1356	59	1258	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.0691	90	1258	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.0232	60	1258	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:14:19,798] [INFO] DFAST Taxonomy check result was written to GCA_021774515.1_ASM2177451v1_genomic.fna/tc_result.tsv
[2023-06-29 19:14:19,799] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:14:19,799] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:14:19,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb873d18d-1a08-499c-8c27-d3afbb8b2c37/dqc_reference/checkm_data
[2023-06-29 19:14:19,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:14:19,853] [INFO] Task started: CheckM
[2023-06-29 19:14:19,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021774515.1_ASM2177451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021774515.1_ASM2177451v1_genomic.fna/checkm_input GCA_021774515.1_ASM2177451v1_genomic.fna/checkm_result
[2023-06-29 19:14:59,620] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:59,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:59,650] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:59,650] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:59,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021774515.1_ASM2177451v1_genomic.fna/markers.fasta)
[2023-06-29 19:14:59,651] [INFO] Task started: Blastn
[2023-06-29 19:14:59,651] [INFO] Running command: blastn -query GCA_021774515.1_ASM2177451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb873d18d-1a08-499c-8c27-d3afbb8b2c37/dqc_reference/reference_markers_gtdb.fasta -out GCA_021774515.1_ASM2177451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:15:00,791] [INFO] Task succeeded: Blastn
[2023-06-29 19:15:00,797] [INFO] Selected 33 target genomes.
[2023-06-29 19:15:00,797] [INFO] Target genome list was writen to GCA_021774515.1_ASM2177451v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:15:00,849] [INFO] Task started: fastANI
[2023-06-29 19:15:00,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg90b7baa3-20aa-4fd8-9452-d5c7d4fdf20e/GCA_021774515.1_ASM2177451v1_genomic.fna.gz --refList GCA_021774515.1_ASM2177451v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021774515.1_ASM2177451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:15:24,769] [INFO] Task succeeded: fastANI
[2023-06-29 19:15:24,793] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:15:24,794] [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_003230015.1	s__SZUA-147 sp003230015	76.4353	115	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__SZUA-147	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.1846	145	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	76.1339	66	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721365.1	s__GCA-2721365 sp002721365	76.0684	63	1258	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	-
GCF_016583645.1	s__Rhodovibrio sodomensis	75.9309	94	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.8648	105	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.7994	80	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793925.1	s__JAEULH01 sp016793925	75.7564	63	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JAEULH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	75.7079	74	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCA_011523425.1	s__WTGU01 sp011523425	75.6907	65	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	75.6787	101	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	75.6647	57	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	75.631	81	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	75.6223	91	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	75.5973	143	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_016595245.1	s__Azospirillum sp016595245	75.574	122	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003285.1	s__JABDJY01 sp013003285	75.5494	65	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	75.5278	122	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	75.5267	74	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.5263	73	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377755.1	s__WHTM01 sp009377755	75.4978	54	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__WHTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305915.1	s__Reyranella sp017305915	75.4636	104	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	75.3905	73	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003336875.1	s__Oleisolibacter albus	75.3862	94	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	75.3325	92	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952505.1	s__Mesorhizobium sp003952505	75.2296	74	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCA_903927615.1	s__BOG-933 sp903927615	74.9183	55	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__BOG-933	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	74.6949	56	1258	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:15:24,796] [INFO] GTDB search result was written to GCA_021774515.1_ASM2177451v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:15:24,796] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:15:24,802] [INFO] DFAST_QC result json was written to GCA_021774515.1_ASM2177451v1_genomic.fna/dqc_result.json
[2023-06-29 19:15:24,802] [INFO] DFAST_QC completed!
[2023-06-29 19:15:24,802] [INFO] Total running time: 0h1m44s