[2024-01-24 11:05:49,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,405] [INFO] DQC Reference Directory: /var/lib/cwl/stge7f22ec5-0276-4399-8f2d-4a92db56ac60/dqc_reference
[2024-01-24 11:05:51,286] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,287] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,287] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ebbaa02-9bf6-4c97-8519-762d2e43594e/GCF_002237735.1_ASM223773v1_genomic.fna.gz | prodigal -d GCF_002237735.1_ASM223773v1_genomic.fna/cds.fna -a GCF_002237735.1_ASM223773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:01,246] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:01,246] [INFO] Task started: HMMsearch
[2024-01-24 11:06:01,246] [INFO] Running command: hmmsearch --tblout GCF_002237735.1_ASM223773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7f22ec5-0276-4399-8f2d-4a92db56ac60/dqc_reference/reference_markers.hmm GCF_002237735.1_ASM223773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:01,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:01,497] [INFO] Found 6/6 markers.
[2024-01-24 11:06:01,536] [INFO] Query marker FASTA was written to GCF_002237735.1_ASM223773v1_genomic.fna/markers.fasta
[2024-01-24 11:06:01,537] [INFO] Task started: Blastn
[2024-01-24 11:06:01,537] [INFO] Running command: blastn -query GCF_002237735.1_ASM223773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7f22ec5-0276-4399-8f2d-4a92db56ac60/dqc_reference/reference_markers.fasta -out GCF_002237735.1_ASM223773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:02,158] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:02,161] [INFO] Selected 20 target genomes.
[2024-01-24 11:06:02,162] [INFO] Target genome list was writen to GCF_002237735.1_ASM223773v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:02,171] [INFO] Task started: fastANI
[2024-01-24 11:06:02,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ebbaa02-9bf6-4c97-8519-762d2e43594e/GCF_002237735.1_ASM223773v1_genomic.fna.gz --refList GCF_002237735.1_ASM223773v1_genomic.fna/target_genomes.txt --output GCF_002237735.1_ASM223773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:16,311] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:16,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7f22ec5-0276-4399-8f2d-4a92db56ac60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:16,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7f22ec5-0276-4399-8f2d-4a92db56ac60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:16,325] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:16,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:16,325] [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
Priestia filamentosa	strain=SGD-14	GCA_900177535.1	1402861	1402861	type	True	100.0	1698	1699	95	conclusive
Priestia filamentosa	strain=DSM 27955	GCA_002237735.1	1402861	1402861	type	True	100.0	1698	1699	95	conclusive
Priestia endophytica	strain=DSM 13796	GCA_900115845.1	135735	135735	type	True	94.6041	1449	1699	95	below_threshold
Priestia koreensis	strain=DSM 16467	GCA_001274935.1	284581	284581	type	True	77.4849	148	1699	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	77.4691	59	1699	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	77.3594	143	1699	95	below_threshold
Bacillus licheniformis	strain=ATCC 14580; DSM 13	GCA_000011645.1	1402	1402	type	True	77.3299	61	1699	95	below_threshold
Bacillus altitudinis	strain=41KF2b	GCA_000691145.1	293387	293387	type	True	77.1967	77	1699	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	77.1834	133	1699	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	76.9674	67	1699	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.826	131	1699	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.803	100	1699	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	76.7818	61	1699	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.6666	89	1699	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	76.5679	130	1699	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.4617	65	1699	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.226	80	1699	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	76.2254	65	1699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:16,327] [INFO] DFAST Taxonomy check result was written to GCF_002237735.1_ASM223773v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:16,327] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:16,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:16,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7f22ec5-0276-4399-8f2d-4a92db56ac60/dqc_reference/checkm_data
[2024-01-24 11:06:16,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:16,375] [INFO] Task started: CheckM
[2024-01-24 11:06:16,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002237735.1_ASM223773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002237735.1_ASM223773v1_genomic.fna/checkm_input GCF_002237735.1_ASM223773v1_genomic.fna/checkm_result
[2024-01-24 11:06:49,546] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:49,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:49,570] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:49,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:49,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002237735.1_ASM223773v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:49,571] [INFO] Task started: Blastn
[2024-01-24 11:06:49,571] [INFO] Running command: blastn -query GCF_002237735.1_ASM223773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7f22ec5-0276-4399-8f2d-4a92db56ac60/dqc_reference/reference_markers_gtdb.fasta -out GCF_002237735.1_ASM223773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:50,563] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:50,566] [INFO] Selected 21 target genomes.
[2024-01-24 11:06:50,566] [INFO] Target genome list was writen to GCF_002237735.1_ASM223773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:50,580] [INFO] Task started: fastANI
[2024-01-24 11:06:50,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ebbaa02-9bf6-4c97-8519-762d2e43594e/GCF_002237735.1_ASM223773v1_genomic.fna.gz --refList GCF_002237735.1_ASM223773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002237735.1_ASM223773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:05,541] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:05,557] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:05,558] [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_900177535.1	s__Bacillus_I filamentosa	100.0	1698	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_I	95.0	99.55	98.90	0.95	0.92	6	conclusive
GCF_900115845.1	s__Bacillus_I endophytica	94.617	1448	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_I	95.0	98.63	96.70	0.92	0.89	9	-
GCF_001274935.1	s__Bacillus_AG koreensis	77.5058	147	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	77.4901	106	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909075.1	s__Priestia iocasae	77.3594	143	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011645.1	s__Bacillus licheniformis	77.3299	61	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	-
GCF_001969855.1	s__Bacillus haynesii	77.3027	64	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_003184905.1	s__Priestia sp003184905	77.3017	161	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691145.1	s__Bacillus altitudinis	77.2276	77	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.17	97.02	0.95	0.92	117	-
GCF_013314535.1	s__Bacillus_A sp013314535	77.1524	132	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001042485.2	s__Bacillus paralicheniformis	77.1188	67	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0745	98.70	96.39	0.96	0.84	103	-
GCF_003073175.1	s__Bacillus_BN acanthi	76.9674	67	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299035.1	s__Bacillus_A bingmayongensis	76.9163	139	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.40	97.40	0.86	0.86	2	-
GCF_002584535.1	s__Bacillus_A cereus_AW	76.9004	143	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.12	98.24	0.93	0.90	5	-
GCF_001455345.1	s__Bacillus_A thuringiensis_N	76.8766	132	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
GCF_016908395.1	s__Metabacillus crassostreae	76.5679	130	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588585.1	s__SM2101 sp018588585	76.4523	79	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SM2101;g__SM2101	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111345.1	s__Psychrobacillus sp900111345	76.3984	62	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207535.1	s__Bacillus_BD benzoevorans	76.2254	65	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001742425.1	s__Bacillus_AV solimangrovi	76.2221	79	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Bacillaceae_N;g__Bacillus_AV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007676755.1	s__Psychrobacillus sp007676755	76.2037	65	1699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:05,559] [INFO] GTDB search result was written to GCF_002237735.1_ASM223773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:05,560] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:05,564] [INFO] DFAST_QC result json was written to GCF_002237735.1_ASM223773v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:05,564] [INFO] DFAST_QC completed!
[2024-01-24 11:07:05,564] [INFO] Total running time: 0h1m16s