[2024-01-25 19:09:20,572] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg07416bd5-7e06-493a-b86b-e82eeb3bf72d/dqc_reference
[2024-01-25 19:09:21,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,773] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,774] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b9dac07-d1c3-42d8-8b14-6ab8043892fc/GCF_025154055.1_ASM2515405v1_genomic.fna.gz | prodigal -d GCF_025154055.1_ASM2515405v1_genomic.fna/cds.fna -a GCF_025154055.1_ASM2515405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:29,301] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:29,301] [INFO] Task started: HMMsearch
[2024-01-25 19:09:29,302] [INFO] Running command: hmmsearch --tblout GCF_025154055.1_ASM2515405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07416bd5-7e06-493a-b86b-e82eeb3bf72d/dqc_reference/reference_markers.hmm GCF_025154055.1_ASM2515405v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:29,552] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:29,553] [INFO] Found 6/6 markers.
[2024-01-25 19:09:29,590] [INFO] Query marker FASTA was written to GCF_025154055.1_ASM2515405v1_genomic.fna/markers.fasta
[2024-01-25 19:09:29,590] [INFO] Task started: Blastn
[2024-01-25 19:09:29,590] [INFO] Running command: blastn -query GCF_025154055.1_ASM2515405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07416bd5-7e06-493a-b86b-e82eeb3bf72d/dqc_reference/reference_markers.fasta -out GCF_025154055.1_ASM2515405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:30,149] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:30,152] [INFO] Selected 25 target genomes.
[2024-01-25 19:09:30,152] [INFO] Target genome list was writen to GCF_025154055.1_ASM2515405v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:30,153] [INFO] Task started: fastANI
[2024-01-25 19:09:30,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b9dac07-d1c3-42d8-8b14-6ab8043892fc/GCF_025154055.1_ASM2515405v1_genomic.fna.gz --refList GCF_025154055.1_ASM2515405v1_genomic.fna/target_genomes.txt --output GCF_025154055.1_ASM2515405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:46,388] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:46,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07416bd5-7e06-493a-b86b-e82eeb3bf72d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:46,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07416bd5-7e06-493a-b86b-e82eeb3bf72d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:46,400] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:46,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:46,400] [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 koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	100.0	1412	1415	95	conclusive
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	78.1049	242	1415	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	77.702	235	1415	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.7013	118	1415	95	below_threshold
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	77.4835	136	1415	95	below_threshold
Paraliobacillus zengyii	strain=X-1125	GCA_003268595.1	2213194	2213194	type	True	77.4613	157	1415	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.421	204	1415	95	below_threshold
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	77.3757	235	1415	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	77.3022	143	1415	95	below_threshold
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	77.2286	113	1415	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.0741	80	1415	95	below_threshold
Pontibacillus marinus	strain=DSM 16465	GCA_000425225.1	273164	273164	type	True	76.8213	77	1415	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.7208	70	1415	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	76.6901	82	1415	95	below_threshold
Virgibacillus alimentarius	strain=J18	GCA_000709085.1	698769	698769	type	True	76.5488	55	1415	95	below_threshold
Salirhabdus euzebyi	strain=DSM 19612	GCA_014207435.1	394506	394506	type	True	76.447	90	1415	95	below_threshold
Pseudogracilibacillus auburnensis	strain=DSM 28556	GCA_003201975.1	1494959	1494959	type	True	76.2027	54	1415	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:46,407] [INFO] DFAST Taxonomy check result was written to GCF_025154055.1_ASM2515405v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:46,408] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:46,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:46,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07416bd5-7e06-493a-b86b-e82eeb3bf72d/dqc_reference/checkm_data
[2024-01-25 19:09:46,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:46,452] [INFO] Task started: CheckM
[2024-01-25 19:09:46,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025154055.1_ASM2515405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025154055.1_ASM2515405v1_genomic.fna/checkm_input GCF_025154055.1_ASM2515405v1_genomic.fna/checkm_result
[2024-01-25 19:10:13,264] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:13,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:13,284] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:13,284] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:13,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025154055.1_ASM2515405v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:13,285] [INFO] Task started: Blastn
[2024-01-25 19:10:13,285] [INFO] Running command: blastn -query GCF_025154055.1_ASM2515405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07416bd5-7e06-493a-b86b-e82eeb3bf72d/dqc_reference/reference_markers_gtdb.fasta -out GCF_025154055.1_ASM2515405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:14,038] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:14,040] [INFO] Selected 30 target genomes.
[2024-01-25 19:10:14,041] [INFO] Target genome list was writen to GCF_025154055.1_ASM2515405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:14,042] [INFO] Task started: fastANI
[2024-01-25 19:10:14,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b9dac07-d1c3-42d8-8b14-6ab8043892fc/GCF_025154055.1_ASM2515405v1_genomic.fna.gz --refList GCF_025154055.1_ASM2515405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025154055.1_ASM2515405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:35,103] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:35,117] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:10:35,118] [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	78.039	248	1415	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_003315295.1	s__Paraliobacillus ryukyuensis	77.7079	119	1415	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_007301515.1	s__Radiobacillus deserti	77.4835	136	1415	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_003268595.1	s__Paraliobacillus_A zengyii	77.4127	158	1415	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_016908325.1	s__Aquibacillus albus	77.3875	202	1415	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_009649745.1	s__Aquibacillus_A halophilus	77.3777	237	1415	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_003337485.1	s__Saliterribacillus persicus	77.3013	143	1415	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_001368815.1	s__Paraliobacillus sp001368815	77.3008	130	1415	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_000482485.1	s__Ornithinibacillus globulus	77.1921	93	1415	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_900258515.1	s__Virgibacillus_E sp900258515	77.1467	82	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821245.2	s__Sediminibacillus senegalensis	77.0951	102	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.0916	89	1415	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_018916875.1	s__Virgibacillus proomii_B	77.0758	55	1415	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_016908235.1	s__Halobacillus_A seohaensis	76.8899	69	1415	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_900104555.1	s__Litchfieldia salsa	76.7712	70	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	76.7242	79	1415	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_014637405.1	s__Ornithinibacillus halotolerans	76.6901	82	1415	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_003667865.1	s__Bacillus_BQ marisflavi_A	76.6782	69	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628505.1	s__Oceanobacillus halophilus	76.636	87	1415	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_902829255.1	s__Metabacillus niabensis	76.5663	59	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.58	98.41	0.91	0.90	3	-
GCF_900111445.1	s__Ornithinibacillus limi	76.5485	86	1415	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_009183415.1	s__Niallia sp009183415	76.4534	64	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207435.1	s__Salirhabdus euzebyi	76.4446	90	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Alkalibacillaceae;g__Salirhabdus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002224365.1	s__Virgibacillus_F necropolis	76.3316	88	1415	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:35,120] [INFO] GTDB search result was written to GCF_025154055.1_ASM2515405v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:35,121] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:35,128] [INFO] DFAST_QC result json was written to GCF_025154055.1_ASM2515405v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:35,128] [INFO] DFAST_QC completed!
[2024-01-25 19:10:35,128] [INFO] Total running time: 0h1m15s