[2024-01-24 13:43:26,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,820] [INFO] DQC Reference Directory: /var/lib/cwl/stge676d327-23b6-4405-85c0-30b8ddafeb19/dqc_reference
[2024-01-24 13:43:28,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,005] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d14e3e6-c406-484b-b58a-eb9a306296eb/GCF_001592005.1_ASM159200v1_genomic.fna.gz | prodigal -d GCF_001592005.1_ASM159200v1_genomic.fna/cds.fna -a GCF_001592005.1_ASM159200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:39,447] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:39,447] [INFO] Task started: HMMsearch
[2024-01-24 13:43:39,447] [INFO] Running command: hmmsearch --tblout GCF_001592005.1_ASM159200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge676d327-23b6-4405-85c0-30b8ddafeb19/dqc_reference/reference_markers.hmm GCF_001592005.1_ASM159200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:39,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:39,693] [INFO] Found 6/6 markers.
[2024-01-24 13:43:39,730] [INFO] Query marker FASTA was written to GCF_001592005.1_ASM159200v1_genomic.fna/markers.fasta
[2024-01-24 13:43:39,731] [INFO] Task started: Blastn
[2024-01-24 13:43:39,731] [INFO] Running command: blastn -query GCF_001592005.1_ASM159200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge676d327-23b6-4405-85c0-30b8ddafeb19/dqc_reference/reference_markers.fasta -out GCF_001592005.1_ASM159200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:40,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:40,308] [INFO] Selected 14 target genomes.
[2024-01-24 13:43:40,308] [INFO] Target genome list was writen to GCF_001592005.1_ASM159200v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:40,327] [INFO] Task started: fastANI
[2024-01-24 13:43:40,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d14e3e6-c406-484b-b58a-eb9a306296eb/GCF_001592005.1_ASM159200v1_genomic.fna.gz --refList GCF_001592005.1_ASM159200v1_genomic.fna/target_genomes.txt --output GCF_001592005.1_ASM159200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:50,862] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:50,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge676d327-23b6-4405-85c0-30b8ddafeb19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:50,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge676d327-23b6-4405-85c0-30b8ddafeb19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:50,871] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:43:50,871] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:43:50,871] [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 swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	83.6221	1092	1441	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	82.969	984	1441	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_000008425.1	1402	1402	type	True	82.9389	990	1441	95	below_threshold
Bacillus licheniformis	strain=ATCC 14580; DSM 13	GCA_000011645.1	1402	1402	type	True	82.9352	993	1441	95	below_threshold
Bacillus licheniformis	strain=ATCC 14580	GCA_006094335.1	1402	1402	type	True	82.9104	1001	1441	95	below_threshold
Bacillus velezensis	strain=KCTC 13012	GCA_001267695.1	492670	492670	type	True	78.4466	323	1441	95	below_threshold
Bacillus velezensis	strain=NRRL B-41580	GCA_001461825.1	492670	492670	type	True	78.3627	324	1441	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.1563	100	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:50,873] [INFO] DFAST Taxonomy check result was written to GCF_001592005.1_ASM159200v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:50,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:50,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:50,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge676d327-23b6-4405-85c0-30b8ddafeb19/dqc_reference/checkm_data
[2024-01-24 13:43:50,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:50,914] [INFO] Task started: CheckM
[2024-01-24 13:43:50,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001592005.1_ASM159200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001592005.1_ASM159200v1_genomic.fna/checkm_input GCF_001592005.1_ASM159200v1_genomic.fna/checkm_result
[2024-01-24 13:44:29,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:29,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:29,953] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:29,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:29,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001592005.1_ASM159200v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:29,954] [INFO] Task started: Blastn
[2024-01-24 13:44:29,954] [INFO] Running command: blastn -query GCF_001592005.1_ASM159200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge676d327-23b6-4405-85c0-30b8ddafeb19/dqc_reference/reference_markers_gtdb.fasta -out GCF_001592005.1_ASM159200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:30,728] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:30,730] [INFO] Selected 9 target genomes.
[2024-01-24 13:44:30,731] [INFO] Target genome list was writen to GCF_001592005.1_ASM159200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:30,752] [INFO] Task started: fastANI
[2024-01-24 13:44:30,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d14e3e6-c406-484b-b58a-eb9a306296eb/GCF_001592005.1_ASM159200v1_genomic.fna.gz --refList GCF_001592005.1_ASM159200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001592005.1_ASM159200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:39,234] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:39,242] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:39,242] [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_001592005.1	s__Bacillus sonorensis	100.0	1437	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.75	99.65	0.97	0.94	11	conclusive
GCF_001042475.2	s__Bacillus glycinifermentans	86.0246	1152	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.06	95.94	0.90	0.86	8	-
GCF_001969815.1	s__Bacillus swezeyi	83.6173	1093	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_900166645.1	s__Bacillus sonorensis_A	83.0072	1028	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.48	99.48	0.95	0.95	2	-
GCF_000011645.1	s__Bacillus licheniformis	82.945	992	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	-
GCF_001042485.2	s__Bacillus paralicheniformis	82.904	1034	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0745	98.70	96.39	0.96	0.84	103	-
GCF_001969855.1	s__Bacillus haynesii	82.7797	1019	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_001584325.1	s__Bacillus nakamurai	78.3728	328	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.07	99.07	0.94	0.94	2	-
GCF_001461825.1	s__Bacillus velezensis	78.3627	324	1441	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.12	97.33	0.94	0.90	498	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:39,244] [INFO] GTDB search result was written to GCF_001592005.1_ASM159200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:39,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:39,247] [INFO] DFAST_QC result json was written to GCF_001592005.1_ASM159200v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:39,247] [INFO] DFAST_QC completed!
[2024-01-24 13:44:39,247] [INFO] Total running time: 0h1m12s