[2024-01-24 12:31:03,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f7198d2-daba-40e8-a5da-725d8169cc89/dqc_reference
[2024-01-24 12:31:04,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,874] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg67a5350e-338b-4d50-a7e2-282fa7440140/GCF_003055085.1_ASM305508v1_genomic.fna.gz | prodigal -d GCF_003055085.1_ASM305508v1_genomic.fna/cds.fna -a GCF_003055085.1_ASM305508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:11,490] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:11,490] [INFO] Task started: HMMsearch
[2024-01-24 12:31:11,490] [INFO] Running command: hmmsearch --tblout GCF_003055085.1_ASM305508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f7198d2-daba-40e8-a5da-725d8169cc89/dqc_reference/reference_markers.hmm GCF_003055085.1_ASM305508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:11,801] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:11,803] [INFO] Found 6/6 markers.
[2024-01-24 12:31:11,834] [INFO] Query marker FASTA was written to GCF_003055085.1_ASM305508v1_genomic.fna/markers.fasta
[2024-01-24 12:31:11,835] [INFO] Task started: Blastn
[2024-01-24 12:31:11,835] [INFO] Running command: blastn -query GCF_003055085.1_ASM305508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f7198d2-daba-40e8-a5da-725d8169cc89/dqc_reference/reference_markers.fasta -out GCF_003055085.1_ASM305508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:12,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:12,490] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:12,491] [INFO] Target genome list was writen to GCF_003055085.1_ASM305508v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:12,495] [INFO] Task started: fastANI
[2024-01-24 12:31:12,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a5350e-338b-4d50-a7e2-282fa7440140/GCF_003055085.1_ASM305508v1_genomic.fna.gz --refList GCF_003055085.1_ASM305508v1_genomic.fna/target_genomes.txt --output GCF_003055085.1_ASM305508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:23,355] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:23,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f7198d2-daba-40e8-a5da-725d8169cc89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:23,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f7198d2-daba-40e8-a5da-725d8169cc89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:23,375] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:23,375] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:23,375] [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
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	100.0	1002	1018	95	conclusive
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	99.9494	999	1018	95	conclusive
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	89.6345	856	1018	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	79.3502	398	1018	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	79.296	408	1018	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	79.1848	121	1018	95	below_threshold
Peribacillus frigoritolerans	strain=DSM 8801	GCA_024169475.1	450367	450367	type	True	77.5083	70	1018	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.1758	102	1018	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.0236	91	1018	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	77.022	102	1018	95	below_threshold
Lederbergia lenta	strain=NCTC4824	GCA_900478165.1	1467	1467	type	True	76.8375	79	1018	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.6251	85	1018	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.5074	75	1018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:23,377] [INFO] DFAST Taxonomy check result was written to GCF_003055085.1_ASM305508v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:23,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:23,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:23,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f7198d2-daba-40e8-a5da-725d8169cc89/dqc_reference/checkm_data
[2024-01-24 12:31:23,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:23,422] [INFO] Task started: CheckM
[2024-01-24 12:31:23,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003055085.1_ASM305508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003055085.1_ASM305508v1_genomic.fna/checkm_input GCF_003055085.1_ASM305508v1_genomic.fna/checkm_result
[2024-01-24 12:31:49,799] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:49,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:49,825] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:49,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:49,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003055085.1_ASM305508v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:49,826] [INFO] Task started: Blastn
[2024-01-24 12:31:49,826] [INFO] Running command: blastn -query GCF_003055085.1_ASM305508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f7198d2-daba-40e8-a5da-725d8169cc89/dqc_reference/reference_markers_gtdb.fasta -out GCF_003055085.1_ASM305508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:50,886] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:50,890] [INFO] Selected 18 target genomes.
[2024-01-24 12:31:50,890] [INFO] Target genome list was writen to GCF_003055085.1_ASM305508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:50,918] [INFO] Task started: fastANI
[2024-01-24 12:31:50,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a5350e-338b-4d50-a7e2-282fa7440140/GCF_003055085.1_ASM305508v1_genomic.fna.gz --refList GCF_003055085.1_ASM305508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003055085.1_ASM305508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:04,895] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:04,909] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:04,909] [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_016756695.1	s__Heyndrickxia sporothermodurans	99.9349	1010	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	conclusive
GCF_016772275.1	s__Heyndrickxia vini	89.6345	856	1018	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	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	79.6474	447	1018	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_017809215.1	s__Heyndrickxia oleronia	79.2893	407	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	98.68	97.33	0.92	0.89	7	-
GCF_001420715.1	s__Margalitia shackletonii	78.2477	238	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	99.16	98.74	0.93	0.89	4	-
GCF_002844575.1	s__Margalitia camelliae	78.0332	222	1018	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_002577655.1	s__Metabacillus sp002577655	77.9597	105	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166665.1	s__Cytobacillus gottheilii_A	77.853	96	1018	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_018343615.1	s__Margalitia sp018343615	77.8096	205	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900199695.1	s__Niallia sp900199695	77.2911	106	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia	95.0	98.49	98.15	0.84	0.82	5	-
GCF_010975035.1	s__Neobacillus thermocopriae	77.2142	86	1018	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_017497975.1	s__Metabacillus sp017497975	77.1918	103	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668575.1	s__Falsibacillus albus	77.1756	81	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002585305.1	s__Neobacillus sp002585305	76.8603	108	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_000242895.2	s__Bacillus_BU sp000242895	76.7327	94	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015071065.1	s__Bacillus_A cereus_BA	76.6559	73	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.35	97.35	0.87	0.87	2	-
GCF_001591545.1	s__Bacillus_AH lentus	76.6318	76	1018	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:04,911] [INFO] GTDB search result was written to GCF_003055085.1_ASM305508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:04,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:04,918] [INFO] DFAST_QC result json was written to GCF_003055085.1_ASM305508v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:04,918] [INFO] DFAST_QC completed!
[2024-01-24 12:32:04,918] [INFO] Total running time: 0h1m1s