[2024-01-25 18:57:35,833] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:35,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:35,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg03884a68-fe32-492b-9e89-ebc043ea8e02/dqc_reference
[2024-01-25 18:57:36,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:36,955] [INFO] Task started: Prodigal
[2024-01-25 18:57:36,955] [INFO] Running command: gunzip -c /var/lib/cwl/stga3d281c6-ae91-4253-b036-1ad8a390eea2/GCF_003073175.1_ASM307317v1_genomic.fna.gz | prodigal -d GCF_003073175.1_ASM307317v1_genomic.fna/cds.fna -a GCF_003073175.1_ASM307317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:44,244] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:44,245] [INFO] Task started: HMMsearch
[2024-01-25 18:57:44,245] [INFO] Running command: hmmsearch --tblout GCF_003073175.1_ASM307317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03884a68-fe32-492b-9e89-ebc043ea8e02/dqc_reference/reference_markers.hmm GCF_003073175.1_ASM307317v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:44,488] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:44,489] [INFO] Found 6/6 markers.
[2024-01-25 18:57:44,523] [INFO] Query marker FASTA was written to GCF_003073175.1_ASM307317v1_genomic.fna/markers.fasta
[2024-01-25 18:57:44,523] [INFO] Task started: Blastn
[2024-01-25 18:57:44,523] [INFO] Running command: blastn -query GCF_003073175.1_ASM307317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03884a68-fe32-492b-9e89-ebc043ea8e02/dqc_reference/reference_markers.fasta -out GCF_003073175.1_ASM307317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:45,078] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:45,084] [INFO] Selected 17 target genomes.
[2024-01-25 18:57:45,084] [INFO] Target genome list was writen to GCF_003073175.1_ASM307317v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:45,097] [INFO] Task started: fastANI
[2024-01-25 18:57:45,097] [INFO] Running command: fastANI --query /var/lib/cwl/stga3d281c6-ae91-4253-b036-1ad8a390eea2/GCF_003073175.1_ASM307317v1_genomic.fna.gz --refList GCF_003073175.1_ASM307317v1_genomic.fna/target_genomes.txt --output GCF_003073175.1_ASM307317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:58,412] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:58,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03884a68-fe32-492b-9e89-ebc043ea8e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:58,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03884a68-fe32-492b-9e89-ebc043ea8e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:58,422] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:58,422] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:58,423] [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 acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	100.0	1324	1325	95	conclusive
Peribacillus alkalitolerans	strain=KCTC 33631	GCA_010882125.1	1550385	1550385	type	True	83.7516	918	1325	95	below_threshold
Bacillus tepidiphilus	strain=SYSU G01002	GCA_009466385.1	2652445	2652445	type	True	78.1094	214	1325	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	77.9899	153	1325	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.7894	121	1325	95	below_threshold
Peribacillus faecalis	strain=AGMB 02131	GCA_014712675.1	2772559	2772559	type	True	77.6921	113	1325	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	77.6889	115	1325	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.6889	115	1325	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.4004	116	1325	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	77.4	94	1325	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.3757	101	1325	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.1755	100	1325	95	below_threshold
Priestia taiwanensis	strain=CGMCC 1.12698	GCA_014638355.1	1347902	1347902	type	True	76.8652	69	1325	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	76.7261	64	1325	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.6573	85	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:58,424] [INFO] DFAST Taxonomy check result was written to GCF_003073175.1_ASM307317v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:58,424] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:58,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:58,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03884a68-fe32-492b-9e89-ebc043ea8e02/dqc_reference/checkm_data
[2024-01-25 18:57:58,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:58,467] [INFO] Task started: CheckM
[2024-01-25 18:57:58,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003073175.1_ASM307317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003073175.1_ASM307317v1_genomic.fna/checkm_input GCF_003073175.1_ASM307317v1_genomic.fna/checkm_result
[2024-01-25 18:58:24,588] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:24,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:24,610] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:24,610] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:24,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003073175.1_ASM307317v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:24,611] [INFO] Task started: Blastn
[2024-01-25 18:58:24,612] [INFO] Running command: blastn -query GCF_003073175.1_ASM307317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03884a68-fe32-492b-9e89-ebc043ea8e02/dqc_reference/reference_markers_gtdb.fasta -out GCF_003073175.1_ASM307317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:25,443] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:25,446] [INFO] Selected 24 target genomes.
[2024-01-25 18:58:25,446] [INFO] Target genome list was writen to GCF_003073175.1_ASM307317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:25,471] [INFO] Task started: fastANI
[2024-01-25 18:58:25,472] [INFO] Running command: fastANI --query /var/lib/cwl/stga3d281c6-ae91-4253-b036-1ad8a390eea2/GCF_003073175.1_ASM307317v1_genomic.fna.gz --refList GCF_003073175.1_ASM307317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003073175.1_ASM307317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:43,813] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:43,826] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:43,826] [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_003073175.1	s__Bacillus_BN acanthi	100.0	1324	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010882125.1	s__Bacillus_BN alkalitolerans	83.7516	918	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380245.2	s__Bacillus_AD massiliogorillae	77.9899	153	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908835.1	s__Bacillus_AD endoradicis	77.9114	149	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006295.1	s__Peribacillus asahii_A	77.7649	145	1325	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_005116465.1	s__Robertmurraya kyonggiensis	77.7605	105	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280205.1	s__Robertmurraya yapensis	77.6801	116	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014712675.1	s__Bacillus_AD faecalis	77.6291	114	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551815.1	s__Bacillus_A sp002551815	77.6219	74	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
GCF_014138605.1	s__Peribacillus huizhouensis	77.6036	116	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	98.72	98.72	0.94	0.94	2	-
GCF_002734215.1	s__Fredinandcohnia onubensis	77.385	93	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002585305.1	s__Neobacillus sp002585305	77.2635	85	1325	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_018343665.1	s__Cytobacillus sp018343665	77.194	121	1325	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_000504165.1	s__Bacillus_BA sp000504165	77.1742	101	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Bacillus_BA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014960805.1	s__Bacillus_BV sp014960805	77.1418	105	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Bacillus_BV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	77.1129	95	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017497975.1	s__Metabacillus sp017497975	77.1089	100	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217835.1	s__Metabacillus litoralis_A	76.8516	108	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_018343615.1	s__Margalitia sp018343615	76.8201	82	1325	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	-
GCF_003667865.1	s__Bacillus_BQ marisflavi_A	76.7669	107	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Bacillus_BQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	76.3088	78	1325	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__OESV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:43,827] [INFO] GTDB search result was written to GCF_003073175.1_ASM307317v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:43,828] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:43,831] [INFO] DFAST_QC result json was written to GCF_003073175.1_ASM307317v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:43,831] [INFO] DFAST_QC completed!
[2024-01-25 18:58:43,831] [INFO] Total running time: 0h1m8s