[2024-01-24 13:36:42,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:42,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:42,199] [INFO] DQC Reference Directory: /var/lib/cwl/stga9303df2-7927-49d8-bcb2-3263a772fed7/dqc_reference
[2024-01-24 13:36:43,435] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:43,436] [INFO] Task started: Prodigal
[2024-01-24 13:36:43,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f2d4af6-3e08-4266-a288-a60d650ec7ec/GCF_014280935.1_ASM1428093v1_genomic.fna.gz | prodigal -d GCF_014280935.1_ASM1428093v1_genomic.fna/cds.fna -a GCF_014280935.1_ASM1428093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:51,185] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:51,186] [INFO] Task started: HMMsearch
[2024-01-24 13:36:51,186] [INFO] Running command: hmmsearch --tblout GCF_014280935.1_ASM1428093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9303df2-7927-49d8-bcb2-3263a772fed7/dqc_reference/reference_markers.hmm GCF_014280935.1_ASM1428093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:51,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:51,455] [INFO] Found 6/6 markers.
[2024-01-24 13:36:51,494] [INFO] Query marker FASTA was written to GCF_014280935.1_ASM1428093v1_genomic.fna/markers.fasta
[2024-01-24 13:36:51,495] [INFO] Task started: Blastn
[2024-01-24 13:36:51,495] [INFO] Running command: blastn -query GCF_014280935.1_ASM1428093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9303df2-7927-49d8-bcb2-3263a772fed7/dqc_reference/reference_markers.fasta -out GCF_014280935.1_ASM1428093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:52,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:52,148] [INFO] Selected 25 target genomes.
[2024-01-24 13:36:52,148] [INFO] Target genome list was writen to GCF_014280935.1_ASM1428093v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:52,181] [INFO] Task started: fastANI
[2024-01-24 13:36:52,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f2d4af6-3e08-4266-a288-a60d650ec7ec/GCF_014280935.1_ASM1428093v1_genomic.fna.gz --refList GCF_014280935.1_ASM1428093v1_genomic.fna/target_genomes.txt --output GCF_014280935.1_ASM1428093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:11,273] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:11,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9303df2-7927-49d8-bcb2-3263a772fed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:11,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9303df2-7927-49d8-bcb2-3263a772fed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:11,287] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:11,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:11,288] [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 kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	100.0	1388	1390	95	conclusive
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.8811	248	1390	95	below_threshold
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	77.6535	197	1390	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	77.5793	193	1390	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.5481	128	1390	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	77.4251	130	1390	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.4146	110	1390	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.3272	196	1390	95	below_threshold
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	77.2551	147	1390	95	below_threshold
Gracilibacillus oryzae	strain=TD8	GCA_009498735.1	1672701	1672701	type	True	77.1214	102	1390	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.0573	155	1390	95	below_threshold
Amphibacillus jilinensis	strain=Y1	GCA_000306965.1	1216008	1216008	type	True	76.9768	64	1390	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	76.9429	119	1390	95	below_threshold
Terribacillus aidingensis	strain=CGMCC 1.8913	GCA_900215625.1	586416	586416	type	True	76.7604	58	1390	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.6975	56	1390	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	76.6725	58	1390	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_018075365.1	1473	1473	type	True	76.5827	59	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:11,289] [INFO] DFAST Taxonomy check result was written to GCF_014280935.1_ASM1428093v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:11,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:11,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:11,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9303df2-7927-49d8-bcb2-3263a772fed7/dqc_reference/checkm_data
[2024-01-24 13:37:11,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:11,334] [INFO] Task started: CheckM
[2024-01-24 13:37:11,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014280935.1_ASM1428093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014280935.1_ASM1428093v1_genomic.fna/checkm_input GCF_014280935.1_ASM1428093v1_genomic.fna/checkm_result
[2024-01-24 13:37:41,879] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:41,880] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:41,901] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:41,902] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:41,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014280935.1_ASM1428093v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:41,903] [INFO] Task started: Blastn
[2024-01-24 13:37:41,903] [INFO] Running command: blastn -query GCF_014280935.1_ASM1428093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9303df2-7927-49d8-bcb2-3263a772fed7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014280935.1_ASM1428093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:42,990] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:42,994] [INFO] Selected 26 target genomes.
[2024-01-24 13:37:42,995] [INFO] Target genome list was writen to GCF_014280935.1_ASM1428093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:43,027] [INFO] Task started: fastANI
[2024-01-24 13:37:43,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f2d4af6-3e08-4266-a288-a60d650ec7ec/GCF_014280935.1_ASM1428093v1_genomic.fna.gz --refList GCF_014280935.1_ASM1428093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014280935.1_ASM1428093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:00,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:00,307] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:00,308] [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_014280935.1	s__HU2P27 sp014280935	100.0	1388	1390	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009649745.1	s__Aquibacillus_A halophilus	77.6385	197	1390	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_003315295.1	s__Paraliobacillus ryukyuensis	77.4146	110	1390	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_016908325.1	s__Aquibacillus albus	77.3231	197	1390	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_000377765.1	s__Gracilibacillus lacisalsi	77.3184	115	1390	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_000482485.1	s__Ornithinibacillus globulus	77.2643	101	1390	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_007301515.1	s__Radiobacillus deserti	77.2524	148	1390	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038425.2	s__Ornithinibacillus contaminans	77.2002	78	1390	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_009498735.1	s__Gracilibacillus sp009498735	77.1359	103	1390	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_001368815.1	s__Paraliobacillus sp001368815	77.0878	125	1390	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_003268595.1	s__Paraliobacillus_A zengyii	77.0447	156	1390	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_016919725.1	s__Virgibacillus sp016919725	76.986	74	1390	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_014083865.1	s__Paraliobacillus salinarum	76.9429	119	1390	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_000306965.1	s__Amphibacillus_C jilinensis	76.871	67	1390	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_000724085.1	s__Virgibacillus manasiensis	76.7559	70	1390	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_019056395.1	s__Terribacillus aidingensis_A	76.7192	54	1390	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Terribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018075365.1	s__Virgibacillus pantothenticus	76.5827	59	1390	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_900184735.1	s__Ornithinibacillus globulus_B	76.3792	92	1390	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_016908235.1	s__Halobacillus_A seohaensis	76.3467	65	1390	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_000284515.1	s__Halobacillus halophilus	76.2073	51	1390	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017745675.1	s__Bacillus_BH sp017745675	75.5904	51	1390	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:00,311] [INFO] GTDB search result was written to GCF_014280935.1_ASM1428093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:00,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:00,316] [INFO] DFAST_QC result json was written to GCF_014280935.1_ASM1428093v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:00,316] [INFO] DFAST_QC completed!
[2024-01-24 13:38:00,316] [INFO] Total running time: 0h1m18s