[2024-01-25 18:54:50,878] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:50,879] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:50,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f44315f-b728-4709-a5fd-a1bd2e85784d/dqc_reference
[2024-01-25 18:54:52,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:52,042] [INFO] Task started: Prodigal
[2024-01-25 18:54:52,043] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ffd727e-027b-4553-abf5-b8fdf3e9e74e/GCF_022809095.1_ASM2280909v1_genomic.fna.gz | prodigal -d GCF_022809095.1_ASM2280909v1_genomic.fna/cds.fna -a GCF_022809095.1_ASM2280909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:58,188] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:58,189] [INFO] Task started: HMMsearch
[2024-01-25 18:54:58,189] [INFO] Running command: hmmsearch --tblout GCF_022809095.1_ASM2280909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f44315f-b728-4709-a5fd-a1bd2e85784d/dqc_reference/reference_markers.hmm GCF_022809095.1_ASM2280909v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:58,432] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:58,433] [INFO] Found 6/6 markers.
[2024-01-25 18:54:58,461] [INFO] Query marker FASTA was written to GCF_022809095.1_ASM2280909v1_genomic.fna/markers.fasta
[2024-01-25 18:54:58,461] [INFO] Task started: Blastn
[2024-01-25 18:54:58,461] [INFO] Running command: blastn -query GCF_022809095.1_ASM2280909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f44315f-b728-4709-a5fd-a1bd2e85784d/dqc_reference/reference_markers.fasta -out GCF_022809095.1_ASM2280909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:59,019] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:59,023] [INFO] Selected 24 target genomes.
[2024-01-25 18:54:59,024] [INFO] Target genome list was writen to GCF_022809095.1_ASM2280909v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:59,036] [INFO] Task started: fastANI
[2024-01-25 18:54:59,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ffd727e-027b-4553-abf5-b8fdf3e9e74e/GCF_022809095.1_ASM2280909v1_genomic.fna.gz --refList GCF_022809095.1_ASM2280909v1_genomic.fna/target_genomes.txt --output GCF_022809095.1_ASM2280909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:17,719] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:17,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f44315f-b728-4709-a5fd-a1bd2e85784d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:17,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f44315f-b728-4709-a5fd-a1bd2e85784d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:17,733] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:17,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:17,733] [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
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	100.0	1096	1097	95	conclusive
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	77.4904	129	1097	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.4479	91	1097	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	77.4152	126	1097	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	77.3179	86	1097	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	77.2316	70	1097	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	77.2113	99	1097	95	below_threshold
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	77.1544	103	1097	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	77.1434	104	1097	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	77.1332	69	1097	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	77.0033	130	1097	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.9756	113	1097	95	below_threshold
Bacillus altitudinis	strain=41KF2b	GCA_000691145.1	293387	293387	type	True	76.9713	70	1097	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.9161	77	1097	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.9106	115	1097	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	76.8404	119	1097	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.819	77	1097	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	76.6783	92	1097	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.6749	76	1097	95	below_threshold
Jeotgalibacillus soli	strain=P9	GCA_000829435.1	889306	889306	type	True	76.5967	59	1097	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.4782	92	1097	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	76.4434	51	1097	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:17,735] [INFO] DFAST Taxonomy check result was written to GCF_022809095.1_ASM2280909v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:17,735] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:17,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:17,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f44315f-b728-4709-a5fd-a1bd2e85784d/dqc_reference/checkm_data
[2024-01-25 18:55:17,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:17,772] [INFO] Task started: CheckM
[2024-01-25 18:55:17,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022809095.1_ASM2280909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022809095.1_ASM2280909v1_genomic.fna/checkm_input GCF_022809095.1_ASM2280909v1_genomic.fna/checkm_result
[2024-01-25 18:55:41,323] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:41,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:41,346] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:41,346] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:41,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022809095.1_ASM2280909v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:41,347] [INFO] Task started: Blastn
[2024-01-25 18:55:41,347] [INFO] Running command: blastn -query GCF_022809095.1_ASM2280909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f44315f-b728-4709-a5fd-a1bd2e85784d/dqc_reference/reference_markers_gtdb.fasta -out GCF_022809095.1_ASM2280909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:42,171] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:42,175] [INFO] Selected 31 target genomes.
[2024-01-25 18:55:42,175] [INFO] Target genome list was writen to GCF_022809095.1_ASM2280909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:42,199] [INFO] Task started: fastANI
[2024-01-25 18:55:42,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ffd727e-027b-4553-abf5-b8fdf3e9e74e/GCF_022809095.1_ASM2280909v1_genomic.fna.gz --refList GCF_022809095.1_ASM2280909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022809095.1_ASM2280909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:05,783] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:05,802] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:56:05,803] [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
GCA_017656295.1	s__JACDOC01 sp017656295	77.36	120	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__JACDOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104555.1	s__Litchfieldia salsa	77.318	86	1097	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_003259415.1	s__Metabacillus sp003259415	77.2864	109	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128405.1	s__Gottfriedia solisilvae	77.2316	70	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	98.14	96.28	0.93	0.87	3	-
GCF_008180335.1	s__Priestia megaterium_B	77.1937	109	1097	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_002250055.1	s__Sutcliffiella cohnii	77.1833	100	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
GCF_000262755.1	s__Bacillus_Z methanolicus	77.1735	74	1097	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_002871465.1	s__Metabacillus sp002871465	77.1614	128	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_003259935.1	s__Anoxybacillus_B vitaminiphilus	77.1544	103	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591625.1	s__Metabacillus fastidiosus	77.1434	104	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307105.1	s__Bacillus australimaris	77.1387	67	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014217835.1	s__Metabacillus litoralis_A	77.0799	119	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	77.0697	76	1097	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_014960805.1	s__Bacillus_BV sp014960805	77.0695	83	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	77.0033	130	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_017497975.1	s__Metabacillus sp017497975	76.9756	113	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691145.1	s__Bacillus altitudinis	76.9713	70	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.17	97.02	0.95	0.92	117	-
GCF_016909075.1	s__Priestia iocasae	76.9474	115	1097	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_007994985.1	s__Metabacillus litoralis	76.8406	120	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551815.1	s__Bacillus_A sp002551815	76.8371	84	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
GCF_002156865.1	s__Gottfriedia luciferensis	76.819	77	1097	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_000518865.1	s__Metabacillus sp000518865	76.7928	121	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003431975.1	s__Bacillus pumilus_N	76.7787	74	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.39	99.09	0.95	0.93	4	-
GCF_001884135.1	s__Bacillus_A nitratireducens	76.7146	77	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.14	95.62	0.90	0.85	78	-
GCF_003586445.1	s__Robertmurraya sp003586445	76.6615	98	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116295.1	s__Bacillus_A sp900116295	76.6051	102	1097	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:05,804] [INFO] GTDB search result was written to GCF_022809095.1_ASM2280909v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:05,805] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:05,811] [INFO] DFAST_QC result json was written to GCF_022809095.1_ASM2280909v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:05,812] [INFO] DFAST_QC completed!
[2024-01-25 18:56:05,812] [INFO] Total running time: 0h1m15s