[2024-01-25 20:19:20,722] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:20,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:20,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgabdb995d-26aa-4d3a-acd0-3c0edc54a728/dqc_reference
[2024-01-25 20:19:21,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:21,873] [INFO] Task started: Prodigal
[2024-01-25 20:19:21,873] [INFO] Running command: gunzip -c /var/lib/cwl/stg6176c5eb-e7ae-48ad-b213-7810d9c56039/GCF_001278705.1_ASM127870v1_genomic.fna.gz | prodigal -d GCF_001278705.1_ASM127870v1_genomic.fna/cds.fna -a GCF_001278705.1_ASM127870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:31,189] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:31,190] [INFO] Task started: HMMsearch
[2024-01-25 20:19:31,190] [INFO] Running command: hmmsearch --tblout GCF_001278705.1_ASM127870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabdb995d-26aa-4d3a-acd0-3c0edc54a728/dqc_reference/reference_markers.hmm GCF_001278705.1_ASM127870v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:31,454] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:31,455] [INFO] Found 6/6 markers.
[2024-01-25 20:19:31,495] [INFO] Query marker FASTA was written to GCF_001278705.1_ASM127870v1_genomic.fna/markers.fasta
[2024-01-25 20:19:31,495] [INFO] Task started: Blastn
[2024-01-25 20:19:31,495] [INFO] Running command: blastn -query GCF_001278705.1_ASM127870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabdb995d-26aa-4d3a-acd0-3c0edc54a728/dqc_reference/reference_markers.fasta -out GCF_001278705.1_ASM127870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:32,045] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:32,048] [INFO] Selected 32 target genomes.
[2024-01-25 20:19:32,048] [INFO] Target genome list was writen to GCF_001278705.1_ASM127870v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:32,086] [INFO] Task started: fastANI
[2024-01-25 20:19:32,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg6176c5eb-e7ae-48ad-b213-7810d9c56039/GCF_001278705.1_ASM127870v1_genomic.fna.gz --refList GCF_001278705.1_ASM127870v1_genomic.fna/target_genomes.txt --output GCF_001278705.1_ASM127870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:52,162] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:52,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabdb995d-26aa-4d3a-acd0-3c0edc54a728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:52,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabdb995d-26aa-4d3a-acd0-3c0edc54a728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:52,176] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:19:52,176] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:19:52,177] [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
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	79.1646	55	1532	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	79.0477	143	1532	95	below_threshold
Bacillus vallismortis	strain=DSM 11031	GCA_004116955.1	72361	72361	type	True	79.0323	162	1532	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	78.545	82	1532	95	below_threshold
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	78.5435	154	1532	95	below_threshold
Bacillus spizizenii	strain=TU-B-10	GCA_000227465.1	96241	96241	type	True	78.4955	162	1532	95	below_threshold
Bacillus mojavensis	strain=RO-H-1	GCA_000245335.1	72360	72360	type	True	78.4326	164	1532	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	78.163	128	1532	95	below_threshold
Bacillus swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	77.9849	162	1532	95	below_threshold
Bacillus halotolerans	strain=ATCC 25096	GCA_001517105.1	260554	260554	type	True	77.868	151	1532	95	below_threshold
Bacillus mojavensis	strain=RO-H-1	GCA_014499005.1	72360	72360	type	True	77.7922	160	1532	95	below_threshold
Bacillus atrophaeus	strain=NRRL NRS 213	GCA_001584335.1	1452	1452	type	True	77.7531	156	1532	95	below_threshold
Bacillus atrophaeus	strain=NBRC 15539	GCA_001591925.1	1452	1452	type	True	77.7381	162	1532	95	below_threshold
Bacillus mojavensis	strain=RO-H-1 = KCTC 3706	GCA_000507105.1	72360	72360	type	True	77.7009	160	1532	95	below_threshold
Bacillus safensis subsp. osmophilus	strain=BC09	GCA_003254445.1	1982610	561879	type	True	77.5472	132	1532	95	below_threshold
Bacillus aerolatus	strain=CX253	GCA_009183655.1	2653354	2653354	type	True	77.5234	64	1532	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	77.4792	147	1532	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.2128	74	1532	95	below_threshold
Bacillus zhangzhouensis	strain=DW5-4	GCA_000715205.1	1178540	1178540	type	True	77.1902	123	1532	95	below_threshold
Bacillus australimaris	strain=NH7I_1	GCA_001307105.1	1326968	1326968	type	True	77.1391	130	1532	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	76.887	76	1532	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	76.7448	78	1532	95	below_threshold
Domibacillus robiginosus	strain=WS 4628	GCA_000966195.1	1071054	1071054	type	True	76.6941	52	1532	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	76.4516	56	1532	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	76.4447	50	1532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:52,178] [INFO] DFAST Taxonomy check result was written to GCF_001278705.1_ASM127870v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:52,179] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:52,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:52,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabdb995d-26aa-4d3a-acd0-3c0edc54a728/dqc_reference/checkm_data
[2024-01-25 20:19:52,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:52,239] [INFO] Task started: CheckM
[2024-01-25 20:19:52,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001278705.1_ASM127870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001278705.1_ASM127870v1_genomic.fna/checkm_input GCF_001278705.1_ASM127870v1_genomic.fna/checkm_result
[2024-01-25 20:20:23,787] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:23,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:23,816] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:23,816] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:23,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001278705.1_ASM127870v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:23,817] [INFO] Task started: Blastn
[2024-01-25 20:20:23,817] [INFO] Running command: blastn -query GCF_001278705.1_ASM127870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabdb995d-26aa-4d3a-acd0-3c0edc54a728/dqc_reference/reference_markers_gtdb.fasta -out GCF_001278705.1_ASM127870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:24,590] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:24,593] [INFO] Selected 28 target genomes.
[2024-01-25 20:20:24,593] [INFO] Target genome list was writen to GCF_001278705.1_ASM127870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:24,634] [INFO] Task started: fastANI
[2024-01-25 20:20:24,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg6176c5eb-e7ae-48ad-b213-7810d9c56039/GCF_001278705.1_ASM127870v1_genomic.fna.gz --refList GCF_001278705.1_ASM127870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001278705.1_ASM127870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:44,432] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:44,447] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:44,448] [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_001278705.1	s__Bacillus gobiensis	100.0	1531	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.94	99.94	0.99	0.99	2	conclusive
GCF_004116955.1	s__Bacillus vallismortis	78.8629	161	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	-
GCF_000227465.1	s__Bacillus spizizenii	78.7738	165	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCF_000262755.1	s__Bacillus_Z methanolicus	78.749	80	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000245335.1	s__Bacillus mojavensis	78.4417	163	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4726	99.54	98.69	0.98	0.95	4	-
GCF_001969815.1	s__Bacillus swezeyi	77.9943	161	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_000504165.1	s__Bacillus_BA sp000504165	77.984	88	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_BA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517105.1	s__Bacillus halotolerans	77.8514	151	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4726	98.36	97.72	0.93	0.91	37	-
GCF_010093085.1	s__Bacillus sp010093085	77.8326	136	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042475.2	s__Bacillus glycinifermentans	77.7616	155	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.06	95.94	0.90	0.86	8	-
GCF_001584335.1	s__Bacillus atrophaeus	77.7531	156	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.59	97.38	0.93	0.89	38	-
GCF_000507145.1	s__Bacillus tequilensis	77.7451	150	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_004124315.1	s__Bacillus cabrialesii	77.7064	149	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_014764715.1	s__Bacillus sp014764715	77.6713	118	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262045.1	s__Bacillus siamensis	77.4909	142	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.73	0.95	0.92	11	-
GCF_009183655.1	s__Pseudobacillus aerolatus	77.4706	63	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592005.1	s__Bacillus sonorensis	77.4657	172	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.75	99.65	0.97	0.94	11	-
GCF_003053645.1	s__Gottfriedia sp003053645	77.2761	52	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674805.1	s__Metabacillus_C lacus	77.2506	70	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715205.1	s__Bacillus zhangzhouensis	77.2133	122	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.04	95.33	0.94	0.92	3	-
GCF_002153395.1	s__Bacillus subtilis_G	77.1892	159	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_001307105.1	s__Bacillus australimaris	77.1084	129	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000708755.2	s__Bacillus_P indicus	76.887	76	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	97.93	97.85	0.93	0.91	3	-
GCF_007994985.1	s__Metabacillus litoralis	76.6964	78	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000966195.1	s__Domibacillus robiginosus	76.6296	51	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502275.1	s__Robertmurraya siralis	76.5471	58	1532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	99.13	99.00	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:44,449] [INFO] GTDB search result was written to GCF_001278705.1_ASM127870v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:44,449] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:44,453] [INFO] DFAST_QC result json was written to GCF_001278705.1_ASM127870v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:44,454] [INFO] DFAST_QC completed!
[2024-01-25 20:20:44,454] [INFO] Total running time: 0h1m24s