[2024-01-24 13:21:42,611] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:42,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:42,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d3bd6ed-ef12-4e06-9436-1bcc775ec6d0/dqc_reference
[2024-01-24 13:21:43,911] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:43,912] [INFO] Task started: Prodigal
[2024-01-24 13:21:43,912] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaac18fd-57a6-4154-a123-35212c539fb6/GCF_001591985.1_ASM159198v1_genomic.fna.gz | prodigal -d GCF_001591985.1_ASM159198v1_genomic.fna/cds.fna -a GCF_001591985.1_ASM159198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:51,643] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:51,643] [INFO] Task started: HMMsearch
[2024-01-24 13:21:51,643] [INFO] Running command: hmmsearch --tblout GCF_001591985.1_ASM159198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d3bd6ed-ef12-4e06-9436-1bcc775ec6d0/dqc_reference/reference_markers.hmm GCF_001591985.1_ASM159198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:51,924] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:51,925] [INFO] Found 6/6 markers.
[2024-01-24 13:21:51,955] [INFO] Query marker FASTA was written to GCF_001591985.1_ASM159198v1_genomic.fna/markers.fasta
[2024-01-24 13:21:51,956] [INFO] Task started: Blastn
[2024-01-24 13:21:51,957] [INFO] Running command: blastn -query GCF_001591985.1_ASM159198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d3bd6ed-ef12-4e06-9436-1bcc775ec6d0/dqc_reference/reference_markers.fasta -out GCF_001591985.1_ASM159198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:52,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:52,609] [INFO] Selected 16 target genomes.
[2024-01-24 13:21:52,610] [INFO] Target genome list was writen to GCF_001591985.1_ASM159198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:52,621] [INFO] Task started: fastANI
[2024-01-24 13:21:52,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaac18fd-57a6-4154-a123-35212c539fb6/GCF_001591985.1_ASM159198v1_genomic.fna.gz --refList GCF_001591985.1_ASM159198v1_genomic.fna/target_genomes.txt --output GCF_001591985.1_ASM159198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:06,735] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:06,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d3bd6ed-ef12-4e06-9436-1bcc775ec6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:06,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d3bd6ed-ef12-4e06-9436-1bcc775ec6d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:06,745] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:06,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:06,745] [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 smithii	strain=NBRC 15311	GCA_001591985.1	1479	1479	type	True	100.0	1005	1015	95	conclusive
Bacillus smithii	strain=DSM 4216	GCA_001050115.1	1479	1479	type	True	99.9792	1000	1015	95	conclusive
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	77.438	90	1015	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	77.2855	53	1015	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	76.7902	67	1015	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	76.7627	63	1015	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.6922	52	1015	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	76.6339	60	1015	95	below_threshold
Bacillus ectoiniformans	strain=DSM 28970	GCA_016908875.1	1494429	1494429	type	True	76.3155	66	1015	95	below_threshold
Peribacillus loiseleuriae	strain=FJAT-27997	GCA_001183985.1	1679170	1679170	type	True	76.1852	53	1015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:06,747] [INFO] DFAST Taxonomy check result was written to GCF_001591985.1_ASM159198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:06,748] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:06,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:06,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d3bd6ed-ef12-4e06-9436-1bcc775ec6d0/dqc_reference/checkm_data
[2024-01-24 13:22:06,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:06,787] [INFO] Task started: CheckM
[2024-01-24 13:22:06,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591985.1_ASM159198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591985.1_ASM159198v1_genomic.fna/checkm_input GCF_001591985.1_ASM159198v1_genomic.fna/checkm_result
[2024-01-24 13:22:36,640] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:36,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:36,660] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:36,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:36,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591985.1_ASM159198v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:36,660] [INFO] Task started: Blastn
[2024-01-24 13:22:36,661] [INFO] Running command: blastn -query GCF_001591985.1_ASM159198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d3bd6ed-ef12-4e06-9436-1bcc775ec6d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591985.1_ASM159198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:37,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:37,484] [INFO] Selected 23 target genomes.
[2024-01-24 13:22:37,484] [INFO] Target genome list was writen to GCF_001591985.1_ASM159198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:37,525] [INFO] Task started: fastANI
[2024-01-24 13:22:37,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaac18fd-57a6-4154-a123-35212c539fb6/GCF_001591985.1_ASM159198v1_genomic.fna.gz --refList GCF_001591985.1_ASM159198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591985.1_ASM159198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:54,084] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:54,102] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:54,102] [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_001050115.1	s__Bacillus_O smithii	99.9792	1000	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Bacillus_O	95.0	98.56	97.85	0.91	0.87	4	conclusive
GCA_014896555.1	s__Bacillus_O sp014896555	90.4878	693	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Bacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000724485.1	s__Bacillus_Z methanolicus_A	77.496	99	1015	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_000262755.1	s__Bacillus_Z methanolicus	77.438	90	1015	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_002844575.1	s__Margalitia camelliae	76.7627	63	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.53	99.53	0.93	0.93	2	-
GCF_016772275.1	s__Heyndrickxia vini	76.7594	66	1015	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_001274725.1	s__Cytobacillus globisporus	76.7314	67	1015	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_018343695.1	s__FJAT-49711 sp018343695	76.6922	52	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166665.1	s__Cytobacillus gottheilii_A	76.6028	61	1015	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_017303275.1	s__Cytobacillus sp017303275	76.5637	61	1015	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_000620165.1	s__Anoxybacillus_A tepidamans_A	76.3903	61	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001510645.1	s__Peribacillus sp001510645	76.3525	56	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908875.1	s__Bacillus_BX ectoiniformans	76.3155	66	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Bacillus_BX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001183985.1	s__Peribacillus loiseleuriae	76.116	52	1015	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:54,104] [INFO] GTDB search result was written to GCF_001591985.1_ASM159198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:54,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:54,111] [INFO] DFAST_QC result json was written to GCF_001591985.1_ASM159198v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:54,111] [INFO] DFAST_QC completed!
[2024-01-24 13:22:54,111] [INFO] Total running time: 0h1m11s