[2024-01-25 19:44:35,442] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:35,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:35,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgc03216a7-2bda-43d0-803b-4dd15cac2a09/dqc_reference
[2024-01-25 19:44:36,544] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:36,545] [INFO] Task started: Prodigal
[2024-01-25 19:44:36,545] [INFO] Running command: gunzip -c /var/lib/cwl/stgef5000a4-c2d1-4683-8fbb-9e4691be05b0/GCF_003989135.1_ASM398913v1_genomic.fna.gz | prodigal -d GCF_003989135.1_ASM398913v1_genomic.fna/cds.fna -a GCF_003989135.1_ASM398913v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:45,634] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:45,634] [INFO] Task started: HMMsearch
[2024-01-25 19:44:45,634] [INFO] Running command: hmmsearch --tblout GCF_003989135.1_ASM398913v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc03216a7-2bda-43d0-803b-4dd15cac2a09/dqc_reference/reference_markers.hmm GCF_003989135.1_ASM398913v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:45,897] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:45,899] [INFO] Found 6/6 markers.
[2024-01-25 19:44:45,937] [INFO] Query marker FASTA was written to GCF_003989135.1_ASM398913v1_genomic.fna/markers.fasta
[2024-01-25 19:44:45,937] [INFO] Task started: Blastn
[2024-01-25 19:44:45,937] [INFO] Running command: blastn -query GCF_003989135.1_ASM398913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc03216a7-2bda-43d0-803b-4dd15cac2a09/dqc_reference/reference_markers.fasta -out GCF_003989135.1_ASM398913v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:46,497] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:46,500] [INFO] Selected 32 target genomes.
[2024-01-25 19:44:46,500] [INFO] Target genome list was writen to GCF_003989135.1_ASM398913v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:46,528] [INFO] Task started: fastANI
[2024-01-25 19:44:46,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5000a4-c2d1-4683-8fbb-9e4691be05b0/GCF_003989135.1_ASM398913v1_genomic.fna.gz --refList GCF_003989135.1_ASM398913v1_genomic.fna/target_genomes.txt --output GCF_003989135.1_ASM398913v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:10,119] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:10,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc03216a7-2bda-43d0-803b-4dd15cac2a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:10,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc03216a7-2bda-43d0-803b-4dd15cac2a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:10,136] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:45:10,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:10,137] [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
Peribacillus cavernae	strain=L5	GCA_003989135.1	1674310	1674310	type	True	100.0	1482	1482	95	conclusive
Peribacillus glennii	strain=V44-8	GCA_003429105.1	2303991	2303991	type	True	78.6328	436	1482	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.9027	89	1482	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	77.8176	190	1482	95	below_threshold
Peribacillus simplex	strain=DSM 1321	GCA_002243645.1	1478	1478	suspected-type	True	77.7336	203	1482	95	below_threshold
Bacillus massiliglaciei	strain=Marseille-P2600	GCA_900098925.1	1816693	1816693	type	True	77.5984	145	1482	95	below_threshold
Peribacillus muralis	strain=DSM 16288	GCA_001439925.1	264697	264697	type	True	77.5983	183	1482	95	below_threshold
Peribacillus alkalitolerans	strain=KCTC 33631	GCA_010882125.1	1550385	1550385	type	True	77.5221	99	1482	95	below_threshold
Peribacillus simplex	strain=NBRC 15720	GCA_001591785.1	1478	1478	suspected-type	True	77.469	191	1482	95	below_threshold
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	77.4668	128	1482	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	77.1923	115	1482	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.1536	94	1482	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	77.0845	95	1482	95	below_threshold
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	77.0758	67	1482	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.0443	99	1482	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_006094495.1	1404	1404	type	True	76.9997	68	1482	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	76.8971	101	1482	95	below_threshold
Domibacillus iocasae	strain=DSM 29979	GCA_001750285.1	1714016	1714016	type	True	76.7817	56	1482	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	76.7308	89	1482	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.7196	62	1482	95	below_threshold
Bacillus benzoevorans	strain=DSM 5391	GCA_014207535.1	1456	1456	type	True	76.5807	83	1482	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.5329	97	1482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:10,138] [INFO] DFAST Taxonomy check result was written to GCF_003989135.1_ASM398913v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:10,139] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:10,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:10,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc03216a7-2bda-43d0-803b-4dd15cac2a09/dqc_reference/checkm_data
[2024-01-25 19:45:10,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:10,195] [INFO] Task started: CheckM
[2024-01-25 19:45:10,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003989135.1_ASM398913v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003989135.1_ASM398913v1_genomic.fna/checkm_input GCF_003989135.1_ASM398913v1_genomic.fna/checkm_result
[2024-01-25 19:45:40,497] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:40,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:40,518] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:40,518] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:40,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003989135.1_ASM398913v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:40,518] [INFO] Task started: Blastn
[2024-01-25 19:45:40,518] [INFO] Running command: blastn -query GCF_003989135.1_ASM398913v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc03216a7-2bda-43d0-803b-4dd15cac2a09/dqc_reference/reference_markers_gtdb.fasta -out GCF_003989135.1_ASM398913v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:41,288] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:41,291] [INFO] Selected 18 target genomes.
[2024-01-25 19:45:41,291] [INFO] Target genome list was writen to GCF_003989135.1_ASM398913v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:41,309] [INFO] Task started: fastANI
[2024-01-25 19:45:41,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgef5000a4-c2d1-4683-8fbb-9e4691be05b0/GCF_003989135.1_ASM398913v1_genomic.fna.gz --refList GCF_003989135.1_ASM398913v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003989135.1_ASM398913v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:00,521] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:00,532] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:00,532] [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_003989135.1	s__Peribacillus cavernae	100.0	1482	1482	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	conclusive
GCF_003429085.1	s__Peribacillus sp003429085	79.5126	556	1482	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	-
GCF_003429105.1	s__Peribacillus glennii	78.6328	436	1482	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	-
GCF_002863565.1	s__Peribacillus sp002863565	78.3017	376	1482	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	-
GCF_001273755.1	s__Peribacillus butanolivorans	78.1433	202	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.70	97.35	0.87	0.86	10	-
GCF_004006295.1	s__Peribacillus asahii_A	77.9451	148	1482	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	-
GCF_002243645.1	s__Peribacillus simplex	77.719	204	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	99.44	98.94	0.96	0.92	4	-
GCF_018613325.1	s__Peribacillus sp018613325	77.6525	177	1482	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	-
GCF_900098925.1	s__Peribacillus massiliglaciei	77.6148	145	1482	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	-
GCF_002835675.1	s__Peribacillus sp002835675	77.5739	197	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	96.47	96.35	0.90	0.87	3	-
GCF_001542915.1	s__Peribacillus simplex_B	77.2598	170	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	97.35	97.35	0.89	0.89	2	-
GCF_004366035.1	s__Cytobacillus oceanisediminis_C	77.0434	114	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011393025.1	s__URHB0009 sp011393025	77.0209	87	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180415.1	s__Bacillus_BM vietnamensis_B	76.8918	62	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969855.1	s__Bacillus haynesii	76.8532	56	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_010975035.1	s__Neobacillus thermocopriae	76.7581	72	1482	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_001591665.1	s__Neobacillus soli	76.7308	89	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014207535.1	s__Bacillus_BD benzoevorans	76.5807	83	1482	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:00,534] [INFO] GTDB search result was written to GCF_003989135.1_ASM398913v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:00,534] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:00,538] [INFO] DFAST_QC result json was written to GCF_003989135.1_ASM398913v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:00,538] [INFO] DFAST_QC completed!
[2024-01-25 19:46:00,538] [INFO] Total running time: 0h1m25s