[2024-01-25 17:44:21,041] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:21,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:21,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg7139bdd3-41ad-4b51-9f53-5854534e80ee/dqc_reference
[2024-01-25 17:44:22,184] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:22,185] [INFO] Task started: Prodigal
[2024-01-25 17:44:22,185] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5097eea-523d-411c-b0a9-09ac671aaa28/GCF_011008565.1_ASM1100856v1_genomic.fna.gz | prodigal -d GCF_011008565.1_ASM1100856v1_genomic.fna/cds.fna -a GCF_011008565.1_ASM1100856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:28,681] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:28,682] [INFO] Task started: HMMsearch
[2024-01-25 17:44:28,682] [INFO] Running command: hmmsearch --tblout GCF_011008565.1_ASM1100856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7139bdd3-41ad-4b51-9f53-5854534e80ee/dqc_reference/reference_markers.hmm GCF_011008565.1_ASM1100856v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:28,920] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:28,921] [INFO] Found 6/6 markers.
[2024-01-25 17:44:28,953] [INFO] Query marker FASTA was written to GCF_011008565.1_ASM1100856v1_genomic.fna/markers.fasta
[2024-01-25 17:44:28,953] [INFO] Task started: Blastn
[2024-01-25 17:44:28,953] [INFO] Running command: blastn -query GCF_011008565.1_ASM1100856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7139bdd3-41ad-4b51-9f53-5854534e80ee/dqc_reference/reference_markers.fasta -out GCF_011008565.1_ASM1100856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:29,515] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:29,518] [INFO] Selected 30 target genomes.
[2024-01-25 17:44:29,518] [INFO] Target genome list was writen to GCF_011008565.1_ASM1100856v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:29,556] [INFO] Task started: fastANI
[2024-01-25 17:44:29,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5097eea-523d-411c-b0a9-09ac671aaa28/GCF_011008565.1_ASM1100856v1_genomic.fna.gz --refList GCF_011008565.1_ASM1100856v1_genomic.fna/target_genomes.txt --output GCF_011008565.1_ASM1100856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:46,496] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:46,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7139bdd3-41ad-4b51-9f53-5854534e80ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:46,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7139bdd3-41ad-4b51-9f53-5854534e80ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:46,508] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:46,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:46,509] [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
Weizmannia ginsengihumi	strain=Gsoil 114	GCA_011008565.1	363870	363870	type	True	100.0	1214	1215	95	conclusive
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	77.3465	157	1215	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	77.1554	148	1215	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	77.1384	161	1215	95	below_threshold
Bacillus coahuilensis	strain=m4-4	GCA_000171615.1	408580	408580	type	True	77.0877	64	1215	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.9092	97	1215	95	below_threshold
Bacillus mycoides	strain=ATCC 6462	GCA_000832605.1	1405	1405	type	True	76.7724	74	1215	95	below_threshold
Lederbergia panacisoli	strain=KACC 17503	GCA_024626525.1	1255251	1255251	type	True	76.7374	72	1215	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_000003925.1	1405	1405	type	True	76.694	73	1215	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	76.598	86	1215	95	below_threshold
Anoxybacillus rupiensis	strain=DSM 17127	GCA_014196195.1	311460	311460	type	True	76.5482	56	1215	95	below_threshold
Lederbergia lenta	strain=NCTC4824	GCA_900478165.1	1467	1467	type	True	76.5052	84	1215	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	76.4856	67	1215	95	below_threshold
Anoxybacillus calidus	strain=DSM 25220	GCA_013760845.1	575178	575178	type	True	76.4643	71	1215	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.4378	91	1215	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	76.4188	55	1215	95	below_threshold
Gottfriedia luciferensis	strain=DSM 18845	GCA_002156865.1	178774	178774	type	True	76.4061	86	1215	95	below_threshold
Anaerobacillus isosaccharinicus	strain=NB2006	GCA_001866075.3	1532552	1532552	type	True	76.3504	60	1215	95	below_threshold
Lederbergia lenta	strain=NBRC 16444	GCA_001591545.1	1467	1467	type	True	76.1812	80	1215	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.141	80	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:46,510] [INFO] DFAST Taxonomy check result was written to GCF_011008565.1_ASM1100856v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:46,510] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:46,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:46,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7139bdd3-41ad-4b51-9f53-5854534e80ee/dqc_reference/checkm_data
[2024-01-25 17:44:46,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:46,550] [INFO] Task started: CheckM
[2024-01-25 17:44:46,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011008565.1_ASM1100856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011008565.1_ASM1100856v1_genomic.fna/checkm_input GCF_011008565.1_ASM1100856v1_genomic.fna/checkm_result
[2024-01-25 17:45:10,873] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:10,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:10,899] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:10,899] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:10,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011008565.1_ASM1100856v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:10,900] [INFO] Task started: Blastn
[2024-01-25 17:45:10,900] [INFO] Running command: blastn -query GCF_011008565.1_ASM1100856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7139bdd3-41ad-4b51-9f53-5854534e80ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_011008565.1_ASM1100856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:11,738] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:11,740] [INFO] Selected 29 target genomes.
[2024-01-25 17:45:11,741] [INFO] Target genome list was writen to GCF_011008565.1_ASM1100856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:11,769] [INFO] Task started: fastANI
[2024-01-25 17:45:11,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5097eea-523d-411c-b0a9-09ac671aaa28/GCF_011008565.1_ASM1100856v1_genomic.fna.gz --refList GCF_011008565.1_ASM1100856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011008565.1_ASM1100856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:34,358] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:34,373] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:34,374] [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_011008565.1	s__Weizmannia ginsengihum	100.0	1214	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	99.62	99.53	0.95	0.92	4	conclusive
GCF_000724485.1	s__Bacillus_Z methanolicus_A	77.4409	64	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_Z	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018343615.1	s__Margalitia sp018343615	77.4031	126	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	77.3971	156	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772275.1	s__Heyndrickxia vini	77.3282	158	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756695.1	s__Heyndrickxia sporothermodurans	77.1209	166	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	-
GCF_000171615.1	s__Bacillus_T coahuilensis	77.0877	64	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_K;g__Bacillus_T	95.0	98.94	98.61	0.92	0.90	3	-
GCF_005154805.1	s__Neobacillus sp005154805	77.083	89	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003726095.1	s__Niallia circulans_A	76.9924	114	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.27	98.85	0.92	0.89	8	-
GCF_008180335.1	s__Priestia megaterium_B	76.9147	83	1215	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_001591585.1	s__Niallia circulans	76.9092	97	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	99.18	98.58	0.93	0.91	9	-
GCA_017656295.1	s__JACDOC01 sp017656295	76.8562	68	1215	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_002276165.1	s__Cytobacillus kochii	76.7754	91	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272245.1	s__Neobacillus sp002272245	76.7116	71	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.06	97.06	0.86	0.86	2	-
GCF_019039215.1	s__Cytobacillus sp019039215	76.6832	69	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679095.1	s__DE0126 sp007679095	76.6644	79	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712755.1	s__Gottfriedia luciferensis_B	76.5918	81	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	99.30	99.28	0.95	0.93	3	-
GCF_001278755.1	s__Psychrobacillus sp001278755	76.5853	62	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.52	97.52	0.91	0.91	2	-
GCF_010975035.1	s__Neobacillus thermocopriae	76.546	84	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	-
GCF_013760845.1	s__Anoxybacillus_B calidus	76.4643	71	1215	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_002571225.1	s__Bacillus_A sp002571225	76.4606	79	1215	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_014836495.1	s__Cytobacillus sp014836495	76.4378	91	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073175.1	s__Bacillus_BN acanthi	76.4247	69	1215	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_001866005.1	s__Anaerobacillus alkalilacustris	76.4188	55	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014932895.1	s__Bacillus_A thuringiensis_AA	76.394	77	1215	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_004138285.1	s__Gottfriedia acidiceleris_A	76.3666	77	1215	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_001866075.3	s__Anaerobacillus isosaccharinicus	76.3532	61	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994985.1	s__Metabacillus litoralis	76.1167	79	1215	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:34,376] [INFO] GTDB search result was written to GCF_011008565.1_ASM1100856v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:34,376] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:34,380] [INFO] DFAST_QC result json was written to GCF_011008565.1_ASM1100856v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:34,381] [INFO] DFAST_QC completed!
[2024-01-25 17:45:34,381] [INFO] Total running time: 0h1m13s