[2024-01-24 14:21:50,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a75fb57-2851-4ba8-aa96-840371c37975/dqc_reference
[2024-01-24 14:21:52,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,267] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg38ad3073-766a-46b2-8774-23ef4298b7d7/GCF_005870085.1_ASM587008v1_genomic.fna.gz | prodigal -d GCF_005870085.1_ASM587008v1_genomic.fna/cds.fna -a GCF_005870085.1_ASM587008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:01,532] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:01,532] [INFO] Task started: HMMsearch
[2024-01-24 14:22:01,532] [INFO] Running command: hmmsearch --tblout GCF_005870085.1_ASM587008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a75fb57-2851-4ba8-aa96-840371c37975/dqc_reference/reference_markers.hmm GCF_005870085.1_ASM587008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:01,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:01,876] [INFO] Found 6/6 markers.
[2024-01-24 14:22:01,910] [INFO] Query marker FASTA was written to GCF_005870085.1_ASM587008v1_genomic.fna/markers.fasta
[2024-01-24 14:22:01,910] [INFO] Task started: Blastn
[2024-01-24 14:22:01,910] [INFO] Running command: blastn -query GCF_005870085.1_ASM587008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a75fb57-2851-4ba8-aa96-840371c37975/dqc_reference/reference_markers.fasta -out GCF_005870085.1_ASM587008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:02,583] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:02,588] [INFO] Selected 32 target genomes.
[2024-01-24 14:22:02,588] [INFO] Target genome list was writen to GCF_005870085.1_ASM587008v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:02,618] [INFO] Task started: fastANI
[2024-01-24 14:22:02,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg38ad3073-766a-46b2-8774-23ef4298b7d7/GCF_005870085.1_ASM587008v1_genomic.fna.gz --refList GCF_005870085.1_ASM587008v1_genomic.fna/target_genomes.txt --output GCF_005870085.1_ASM587008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:23,491] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:23,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a75fb57-2851-4ba8-aa96-840371c37975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:23,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a75fb57-2851-4ba8-aa96-840371c37975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:23,515] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:23,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:23,516] [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
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	100.0	1425	1426	95	conclusive
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.7988	224	1426	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.5891	183	1426	95	below_threshold
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	77.5102	211	1426	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.389	142	1426	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	77.3462	227	1426	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.3199	135	1426	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.2115	128	1426	95	below_threshold
Thalassobacillus devorans	strain=CECT 7046	GCA_011761345.1	279813	279813	type	True	77.0939	61	1426	95	below_threshold
Thalassobacillus devorans	strain=CCM 7282	GCA_014635125.1	279813	279813	type	True	77.0482	59	1426	95	below_threshold
Gracilibacillus dipsosauri	strain=DD1	GCA_003176895.1	178340	178340	type	True	77.0142	91	1426	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.0102	129	1426	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	76.9953	58	1426	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	76.9595	64	1426	95	below_threshold
Gracilibacillus oryzae	strain=TD8	GCA_009498735.1	1672701	1672701	type	True	76.9264	106	1426	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	76.9231	118	1426	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	76.8544	81	1426	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	76.7697	113	1426	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.6234	119	1426	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.6203	60	1426	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	76.539	77	1426	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	76.466	75	1426	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.356	89	1426	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	76.1801	89	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:23,518] [INFO] DFAST Taxonomy check result was written to GCF_005870085.1_ASM587008v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:23,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:23,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:23,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a75fb57-2851-4ba8-aa96-840371c37975/dqc_reference/checkm_data
[2024-01-24 14:22:23,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:23,568] [INFO] Task started: CheckM
[2024-01-24 14:22:23,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005870085.1_ASM587008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005870085.1_ASM587008v1_genomic.fna/checkm_input GCF_005870085.1_ASM587008v1_genomic.fna/checkm_result
[2024-01-24 14:22:55,560] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:55,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:55,581] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:55,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:55,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005870085.1_ASM587008v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:55,582] [INFO] Task started: Blastn
[2024-01-24 14:22:55,582] [INFO] Running command: blastn -query GCF_005870085.1_ASM587008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a75fb57-2851-4ba8-aa96-840371c37975/dqc_reference/reference_markers_gtdb.fasta -out GCF_005870085.1_ASM587008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:56,395] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:56,400] [INFO] Selected 31 target genomes.
[2024-01-24 14:22:56,400] [INFO] Target genome list was writen to GCF_005870085.1_ASM587008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:56,677] [INFO] Task started: fastANI
[2024-01-24 14:22:56,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg38ad3073-766a-46b2-8774-23ef4298b7d7/GCF_005870085.1_ASM587008v1_genomic.fna.gz --refList GCF_005870085.1_ASM587008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005870085.1_ASM587008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:16,766] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:16,786] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:16,787] [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_005870085.1	s__BH258 sp005870085	100.0	1425	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016908325.1	s__Aquibacillus albus	77.858	220	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	77.5513	183	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649745.1	s__Aquibacillus_A halophilus	77.5095	209	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993965.1	s__Gracilibacillus sp010993965	77.4681	135	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	77.4005	146	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_000377765.1	s__Gracilibacillus lacisalsi	77.2875	136	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.1996	127	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761345.1	s__Thalassobacillus devorans	77.0557	62	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	100.00	100.00	1.00	1.00	4	-
GCF_001659985.1	s__Oceanobacillus sp001659985	77.0402	98	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	76.9946	128	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_000724085.1	s__Virgibacillus manasiensis	76.9759	76	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166625.1	s__Halobacillus_A massiliensis	76.9606	61	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337485.1	s__Saliterribacillus persicus	76.9258	119	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Saliterribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011245.1	s__Oceanobacillus iheyensis	76.9256	83	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018916875.1	s__Virgibacillus proomii_B	76.8883	62	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306965.1	s__Amphibacillus_C jilinensis	76.8603	83	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993955.1	s__YIM-98839 sp010993955	76.8324	109	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111445.1	s__Ornithinibacillus limi	76.7669	98	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	76.7586	116	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162615.1	s__Virgibacillus proomii_A	76.6561	80	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618145.1	s__Oceanobacillus damuensis	76.6437	74	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919165.1	s__Amphibacillus sp018919165	76.6415	62	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908155.1	s__Oceanobacillus caeni	76.5731	107	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_018075365.1	s__Virgibacillus pantothenticus	76.5574	91	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCF_001884045.1	s__Bacillus_A mobilis	75.6907	55	1426	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	96.91	95.80	0.85	0.81	33	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:16,788] [INFO] GTDB search result was written to GCF_005870085.1_ASM587008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:16,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:16,794] [INFO] DFAST_QC result json was written to GCF_005870085.1_ASM587008v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:16,795] [INFO] DFAST_QC completed!
[2024-01-24 14:23:16,795] [INFO] Total running time: 0h1m26s