[2024-01-24 12:14:35,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg4235181f-d8ff-4096-924f-823faddc8079/dqc_reference
[2024-01-24 12:14:37,018] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,019] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,020] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4a80c72-50e8-4968-b6c2-a7196222ef54/GCF_017497975.1_ASM1749797v1_genomic.fna.gz | prodigal -d GCF_017497975.1_ASM1749797v1_genomic.fna/cds.fna -a GCF_017497975.1_ASM1749797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:48,614] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:48,615] [INFO] Task started: HMMsearch
[2024-01-24 12:14:48,615] [INFO] Running command: hmmsearch --tblout GCF_017497975.1_ASM1749797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4235181f-d8ff-4096-924f-823faddc8079/dqc_reference/reference_markers.hmm GCF_017497975.1_ASM1749797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:48,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:48,959] [INFO] Found 6/6 markers.
[2024-01-24 12:14:49,025] [INFO] Query marker FASTA was written to GCF_017497975.1_ASM1749797v1_genomic.fna/markers.fasta
[2024-01-24 12:14:49,026] [INFO] Task started: Blastn
[2024-01-24 12:14:49,026] [INFO] Running command: blastn -query GCF_017497975.1_ASM1749797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4235181f-d8ff-4096-924f-823faddc8079/dqc_reference/reference_markers.fasta -out GCF_017497975.1_ASM1749797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,669] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,676] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:49,676] [INFO] Target genome list was writen to GCF_017497975.1_ASM1749797v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:49,681] [INFO] Task started: fastANI
[2024-01-24 12:14:49,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a80c72-50e8-4968-b6c2-a7196222ef54/GCF_017497975.1_ASM1749797v1_genomic.fna.gz --refList GCF_017497975.1_ASM1749797v1_genomic.fna/target_genomes.txt --output GCF_017497975.1_ASM1749797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:06,325] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:06,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4235181f-d8ff-4096-924f-823faddc8079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:06,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4235181f-d8ff-4096-924f-823faddc8079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:06,339] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:06,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:06,339] [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
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	100.0	2052	2053	95	conclusive
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	80.9175	864	2053	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	80.8298	851	2053	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	79.4823	597	2053	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	79.4339	573	2053	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	79.41	591	2053	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	79.3282	566	2053	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	79.2376	611	2053	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.4844	95	2053	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.3936	139	2053	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.3553	118	2053	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.966	119	2053	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	76.8345	94	2053	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.5927	91	2053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,341] [INFO] DFAST Taxonomy check result was written to GCF_017497975.1_ASM1749797v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:06,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:06,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:06,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4235181f-d8ff-4096-924f-823faddc8079/dqc_reference/checkm_data
[2024-01-24 12:15:06,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:06,404] [INFO] Task started: CheckM
[2024-01-24 12:15:06,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017497975.1_ASM1749797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017497975.1_ASM1749797v1_genomic.fna/checkm_input GCF_017497975.1_ASM1749797v1_genomic.fna/checkm_result
[2024-01-24 12:15:45,491] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:45,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:45,519] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:45,519] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:45,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017497975.1_ASM1749797v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:45,520] [INFO] Task started: Blastn
[2024-01-24 12:15:45,520] [INFO] Running command: blastn -query GCF_017497975.1_ASM1749797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4235181f-d8ff-4096-924f-823faddc8079/dqc_reference/reference_markers_gtdb.fasta -out GCF_017497975.1_ASM1749797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:46,305] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:46,309] [INFO] Selected 10 target genomes.
[2024-01-24 12:15:46,309] [INFO] Target genome list was writen to GCF_017497975.1_ASM1749797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:46,315] [INFO] Task started: fastANI
[2024-01-24 12:15:46,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a80c72-50e8-4968-b6c2-a7196222ef54/GCF_017497975.1_ASM1749797v1_genomic.fna.gz --refList GCF_017497975.1_ASM1749797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017497975.1_ASM1749797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:00,232] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:00,241] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:00,242] [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_017497975.1	s__Metabacillus sp017497975	100.0	2052	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014217835.1	s__Metabacillus litoralis_A	92.8429	1516	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_009720625.1	s__Metabacillus sp004801455	80.9366	861	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259415.1	s__Metabacillus sp003259415	80.5574	764	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981385.1	s__Metabacillus sp000981385	80.4262	959	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994985.1	s__Metabacillus litoralis	79.4229	569	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871465.1	s__Metabacillus sp002871465	79.2708	600	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCA_019219025.1	s__Neobacillus sp019219025	78.4029	174	2053	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_000482325.1	s__Neobacillus sp000482325	77.3247	152	2053	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_011008855.1	s__Bacillus_BT aquiflavi	76.5927	91	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BT	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:00,243] [INFO] GTDB search result was written to GCF_017497975.1_ASM1749797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:00,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:00,247] [INFO] DFAST_QC result json was written to GCF_017497975.1_ASM1749797v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:00,247] [INFO] DFAST_QC completed!
[2024-01-24 12:16:00,248] [INFO] Total running time: 0h1m25s