[2024-01-24 13:36:42,793] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:42,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:42,795] [INFO] DQC Reference Directory: /var/lib/cwl/stgc50fcf04-51c0-45a9-9617-2ccfebbe5a08/dqc_reference
[2024-01-24 13:36:43,997] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:43,998] [INFO] Task started: Prodigal
[2024-01-24 13:36:43,998] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6da5359-ff70-496b-b151-35c4ac89b365/GCF_013423485.1_ASM1342348v1_genomic.fna.gz | prodigal -d GCF_013423485.1_ASM1342348v1_genomic.fna/cds.fna -a GCF_013423485.1_ASM1342348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:08,197] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:08,197] [INFO] Task started: HMMsearch
[2024-01-24 13:37:08,197] [INFO] Running command: hmmsearch --tblout GCF_013423485.1_ASM1342348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc50fcf04-51c0-45a9-9617-2ccfebbe5a08/dqc_reference/reference_markers.hmm GCF_013423485.1_ASM1342348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:08,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:08,581] [INFO] Found 6/6 markers.
[2024-01-24 13:37:08,645] [INFO] Query marker FASTA was written to GCF_013423485.1_ASM1342348v1_genomic.fna/markers.fasta
[2024-01-24 13:37:08,646] [INFO] Task started: Blastn
[2024-01-24 13:37:08,646] [INFO] Running command: blastn -query GCF_013423485.1_ASM1342348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc50fcf04-51c0-45a9-9617-2ccfebbe5a08/dqc_reference/reference_markers.fasta -out GCF_013423485.1_ASM1342348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:09,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:09,701] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:09,701] [INFO] Target genome list was writen to GCF_013423485.1_ASM1342348v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:09,725] [INFO] Task started: fastANI
[2024-01-24 13:37:09,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6da5359-ff70-496b-b151-35c4ac89b365/GCF_013423485.1_ASM1342348v1_genomic.fna.gz --refList GCF_013423485.1_ASM1342348v1_genomic.fna/target_genomes.txt --output GCF_013423485.1_ASM1342348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:41,144] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:41,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc50fcf04-51c0-45a9-9617-2ccfebbe5a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:41,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc50fcf04-51c0-45a9-9617-2ccfebbe5a08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:41,163] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:41,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:41,163] [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
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	100.0	2544	2547	95	conclusive
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	81.2941	1067	2547	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	81.2155	1097	2547	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	81.2117	1220	2547	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	81.1823	1122	2547	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	81.1384	1155	2547	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	81.1317	1145	2547	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	81.0865	1106	2547	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	81.0181	1150	2547	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	80.9339	1132	2547	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	80.8904	1080	2547	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	80.7394	1110	2547	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	80.5678	1104	2547	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	80.5591	1056	2547	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	80.4585	1138	2547	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	80.2632	1032	2547	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	79.1095	868	2547	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.1551	702	2547	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.4635	576	2547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:41,165] [INFO] DFAST Taxonomy check result was written to GCF_013423485.1_ASM1342348v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:41,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:41,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:41,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc50fcf04-51c0-45a9-9617-2ccfebbe5a08/dqc_reference/checkm_data
[2024-01-24 13:37:41,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:41,243] [INFO] Task started: CheckM
[2024-01-24 13:37:41,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013423485.1_ASM1342348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013423485.1_ASM1342348v1_genomic.fna/checkm_input GCF_013423485.1_ASM1342348v1_genomic.fna/checkm_result
[2024-01-24 13:39:16,287] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:16,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:16,316] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:16,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:16,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013423485.1_ASM1342348v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:16,317] [INFO] Task started: Blastn
[2024-01-24 13:39:16,317] [INFO] Running command: blastn -query GCF_013423485.1_ASM1342348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc50fcf04-51c0-45a9-9617-2ccfebbe5a08/dqc_reference/reference_markers_gtdb.fasta -out GCF_013423485.1_ASM1342348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:18,301] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:18,305] [INFO] Selected 21 target genomes.
[2024-01-24 13:39:18,305] [INFO] Target genome list was writen to GCF_013423485.1_ASM1342348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:18,334] [INFO] Task started: fastANI
[2024-01-24 13:39:18,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6da5359-ff70-496b-b151-35c4ac89b365/GCF_013423485.1_ASM1342348v1_genomic.fna.gz --refList GCF_013423485.1_ASM1342348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013423485.1_ASM1342348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:52,913] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:52,930] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:52,930] [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
GCF_013423485.1	s__Azospirillum oleiclasticum	100.0	2544	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003119115.1	s__Azospirillum sp003119115	81.3565	1180	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_014192915.1	s__Azospirillum sp014192915	81.2781	1141	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827815.1	s__Azospirillum brasilense_C	81.2561	1157	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_008365405.1	s__Azospirillum brasilense_D	81.2279	1142	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827795.1	s__Azospirillum brasilense_E	81.2239	1077	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_017876155.1	s__Azospirillum rugosum	81.1868	1224	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	81.1829	1136	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_008365375.1	s__Azospirillum sp008365375	81.1641	1085	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001315015.1	s__Azospirillum brasilense	81.1244	1100	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_017876095.1	s__Azospirillum agricola	80.9943	1154	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_003130795.1	s__Azospirillum thermophilum	80.9266	1136	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	80.9239	1077	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	80.7389	1191	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	80.5567	1118	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	80.5516	1056	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364955.1	s__Azospirillum lipoferum	80.5458	1121	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356015.1	s__Azospirillum sp017356015	80.4748	1018	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	80.2888	1150	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	80.2276	1039	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966125.1	s__Azospirillum griseum	79.3707	814	2547	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:52,932] [INFO] GTDB search result was written to GCF_013423485.1_ASM1342348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:52,932] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:52,937] [INFO] DFAST_QC result json was written to GCF_013423485.1_ASM1342348v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:52,937] [INFO] DFAST_QC completed!
[2024-01-24 13:39:52,937] [INFO] Total running time: 0h3m10s