[2024-01-24 12:42:09,578] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,581] [INFO] DQC Reference Directory: /var/lib/cwl/stgab3ffe00-3c13-441d-9676-8106d9d7ed40/dqc_reference
[2024-01-24 12:42:10,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,830] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg974e3346-7d0f-4687-afe8-8068d3555b6c/GCF_003966145.1_ASM396614v1_genomic.fna.gz | prodigal -d GCF_003966145.1_ASM396614v1_genomic.fna/cds.fna -a GCF_003966145.1_ASM396614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:18,465] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:18,466] [INFO] Task started: HMMsearch
[2024-01-24 12:42:18,466] [INFO] Running command: hmmsearch --tblout GCF_003966145.1_ASM396614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab3ffe00-3c13-441d-9676-8106d9d7ed40/dqc_reference/reference_markers.hmm GCF_003966145.1_ASM396614v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:18,773] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:18,775] [INFO] Found 6/6 markers.
[2024-01-24 12:42:18,817] [INFO] Query marker FASTA was written to GCF_003966145.1_ASM396614v1_genomic.fna/markers.fasta
[2024-01-24 12:42:18,818] [INFO] Task started: Blastn
[2024-01-24 12:42:18,818] [INFO] Running command: blastn -query GCF_003966145.1_ASM396614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab3ffe00-3c13-441d-9676-8106d9d7ed40/dqc_reference/reference_markers.fasta -out GCF_003966145.1_ASM396614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:19,429] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:19,432] [INFO] Selected 19 target genomes.
[2024-01-24 12:42:19,433] [INFO] Target genome list was writen to GCF_003966145.1_ASM396614v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:19,441] [INFO] Task started: fastANI
[2024-01-24 12:42:19,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg974e3346-7d0f-4687-afe8-8068d3555b6c/GCF_003966145.1_ASM396614v1_genomic.fna.gz --refList GCF_003966145.1_ASM396614v1_genomic.fna/target_genomes.txt --output GCF_003966145.1_ASM396614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:33,267] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:33,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab3ffe00-3c13-441d-9676-8106d9d7ed40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:33,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab3ffe00-3c13-441d-9676-8106d9d7ed40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:33,286] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:42:33,286] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:42:33,286] [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
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	79.6116	452	1369	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	79.5158	468	1369	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_000772955.1	561440	561440	type	True	79.1692	399	1369	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	79.169	413	1369	95	below_threshold
Ureibacillus sinduriensis	strain=JCM 15800	GCA_002200845.1	561440	561440	type	True	79.1678	400	1369	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	79.1304	425	1369	95	below_threshold
Ureibacillus massiliensis	strain=4400831	GCA_002200855.1	292806	292806	type	True	79.0499	395	1369	95	below_threshold
Ureibacillus manganicus	strain=DSM 26584	GCA_000772945.1	1266064	1266064	type	True	79.032	313	1369	95	below_threshold
Ureibacillus massiliensis	strain=CCUG 49529	GCA_000772965.1	292806	292806	type	True	79.0303	397	1369	95	below_threshold
Lysinibacillus xylanilyticus	strain=DSM 23493	GCA_001183605.1	582475	582475	type	True	78.3392	251	1369	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.165	71	1369	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.8387	86	1369	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.7479	72	1369	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.6815	58	1369	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.6629	65	1369	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	76.5715	63	1369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:33,289] [INFO] DFAST Taxonomy check result was written to GCF_003966145.1_ASM396614v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:33,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:33,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:33,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab3ffe00-3c13-441d-9676-8106d9d7ed40/dqc_reference/checkm_data
[2024-01-24 12:42:33,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:33,336] [INFO] Task started: CheckM
[2024-01-24 12:42:33,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003966145.1_ASM396614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003966145.1_ASM396614v1_genomic.fna/checkm_input GCF_003966145.1_ASM396614v1_genomic.fna/checkm_result
[2024-01-24 12:43:02,179] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:02,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:02,204] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:02,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:02,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003966145.1_ASM396614v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:02,205] [INFO] Task started: Blastn
[2024-01-24 12:43:02,206] [INFO] Running command: blastn -query GCF_003966145.1_ASM396614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab3ffe00-3c13-441d-9676-8106d9d7ed40/dqc_reference/reference_markers_gtdb.fasta -out GCF_003966145.1_ASM396614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:03,012] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:03,016] [INFO] Selected 12 target genomes.
[2024-01-24 12:43:03,017] [INFO] Target genome list was writen to GCF_003966145.1_ASM396614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:03,028] [INFO] Task started: fastANI
[2024-01-24 12:43:03,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg974e3346-7d0f-4687-afe8-8068d3555b6c/GCF_003966145.1_ASM396614v1_genomic.fna.gz --refList GCF_003966145.1_ASM396614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003966145.1_ASM396614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:11,868] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:11,878] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:11,878] [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_003966145.1	s__Ureibacillus telephonicus	100.0	1365	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003711845.1	s__Ureibacillus halotolerans	80.5879	509	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836845.1	s__Ureibacillus sp014836845	80.3275	554	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900217795.1	s__Ureibacillus xyleni	80.1404	482	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977595.1	s__Ureibacillus antri	79.7714	467	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	98.58	98.58	0.91	0.91	2	-
GCF_003628435.1	s__Ureibacillus endophyticus	79.661	482	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217295.1	s__Ureibacillus chungkukjangi	79.6002	453	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_005491425.1	s__Ureibacillus sp005491425	79.4183	482	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908465.1	s__Ureibacillus composti	79.1469	423	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002736105.1	s__Solibacillus sp002736105	77.7998	222	1369	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:11,880] [INFO] GTDB search result was written to GCF_003966145.1_ASM396614v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:11,881] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:11,885] [INFO] DFAST_QC result json was written to GCF_003966145.1_ASM396614v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:11,885] [INFO] DFAST_QC completed!
[2024-01-24 12:43:11,885] [INFO] Total running time: 0h1m2s