[2024-01-24 12:34:20,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bd3e4d9-3352-426f-9b40-fe9320a6ce9d/dqc_reference
[2024-01-24 12:34:21,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,523] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg70012cdf-7df0-47a2-8e62-513ea673febf/GCF_007994985.1_ASM799498v1_genomic.fna.gz | prodigal -d GCF_007994985.1_ASM799498v1_genomic.fna/cds.fna -a GCF_007994985.1_ASM799498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:30,227] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:30,227] [INFO] Task started: HMMsearch
[2024-01-24 12:34:30,228] [INFO] Running command: hmmsearch --tblout GCF_007994985.1_ASM799498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bd3e4d9-3352-426f-9b40-fe9320a6ce9d/dqc_reference/reference_markers.hmm GCF_007994985.1_ASM799498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:30,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:30,526] [INFO] Found 6/6 markers.
[2024-01-24 12:34:30,567] [INFO] Query marker FASTA was written to GCF_007994985.1_ASM799498v1_genomic.fna/markers.fasta
[2024-01-24 12:34:30,567] [INFO] Task started: Blastn
[2024-01-24 12:34:30,567] [INFO] Running command: blastn -query GCF_007994985.1_ASM799498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bd3e4d9-3352-426f-9b40-fe9320a6ce9d/dqc_reference/reference_markers.fasta -out GCF_007994985.1_ASM799498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:31,174] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:31,178] [INFO] Selected 15 target genomes.
[2024-01-24 12:34:31,178] [INFO] Target genome list was writen to GCF_007994985.1_ASM799498v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:31,185] [INFO] Task started: fastANI
[2024-01-24 12:34:31,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg70012cdf-7df0-47a2-8e62-513ea673febf/GCF_007994985.1_ASM799498v1_genomic.fna.gz --refList GCF_007994985.1_ASM799498v1_genomic.fna/target_genomes.txt --output GCF_007994985.1_ASM799498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:47,410] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:47,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bd3e4d9-3352-426f-9b40-fe9320a6ce9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:47,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bd3e4d9-3352-426f-9b40-fe9320a6ce9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:47,431] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:34:47,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:47,432] [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
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	100.0	1600	1602	95	conclusive
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	94.1277	1369	1602	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	79.6318	619	1602	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	79.4762	526	1602	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	79.2978	537	1602	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	79.2023	517	1602	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	79.1838	584	1602	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	78.9927	454	1602	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	78.931	462	1602	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	77.3161	221	1602	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.792	121	1602	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.6674	102	1602	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.6355	123	1602	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.4544	126	1602	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	76.415	128	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:47,437] [INFO] DFAST Taxonomy check result was written to GCF_007994985.1_ASM799498v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:47,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:47,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:47,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bd3e4d9-3352-426f-9b40-fe9320a6ce9d/dqc_reference/checkm_data
[2024-01-24 12:34:47,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:47,489] [INFO] Task started: CheckM
[2024-01-24 12:34:47,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007994985.1_ASM799498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007994985.1_ASM799498v1_genomic.fna/checkm_input GCF_007994985.1_ASM799498v1_genomic.fna/checkm_result
[2024-01-24 12:35:18,657] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:18,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:18,679] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:18,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:18,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007994985.1_ASM799498v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:18,680] [INFO] Task started: Blastn
[2024-01-24 12:35:18,680] [INFO] Running command: blastn -query GCF_007994985.1_ASM799498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bd3e4d9-3352-426f-9b40-fe9320a6ce9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007994985.1_ASM799498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:19,479] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:19,482] [INFO] Selected 15 target genomes.
[2024-01-24 12:35:19,483] [INFO] Target genome list was writen to GCF_007994985.1_ASM799498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:19,494] [INFO] Task started: fastANI
[2024-01-24 12:35:19,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg70012cdf-7df0-47a2-8e62-513ea673febf/GCF_007994985.1_ASM799498v1_genomic.fna.gz --refList GCF_007994985.1_ASM799498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007994985.1_ASM799498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:38,655] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:38,671] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:38,671] [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_007994985.1	s__Metabacillus litoralis	100.0	1600	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016908395.1	s__Metabacillus crassostreae	94.1249	1369	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002577655.1	s__Metabacillus sp002577655	79.4734	563	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667825.1	s__Metabacillus litoralis_B	79.3878	607	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_014217835.1	s__Metabacillus litoralis_A	79.3211	556	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	79.2977	537	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_000518865.1	s__Metabacillus sp000518865	79.2893	511	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871465.1	s__Metabacillus sp002871465	79.2599	540	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_017497975.1	s__Metabacillus sp017497975	79.1645	586	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720625.1	s__Metabacillus sp004801455	78.8933	466	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259415.1	s__Metabacillus sp003259415	78.7315	400	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981385.1	s__Metabacillus sp000981385	78.6355	418	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409995.1	s__Neobacillus niacini_B	76.6963	114	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380245.2	s__Bacillus_AD massiliogorillae	76.6202	124	1602	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_002272245.1	s__Neobacillus sp002272245	76.5543	113	1602	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.06	97.06	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:35:38,672] [INFO] GTDB search result was written to GCF_007994985.1_ASM799498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:38,673] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:38,676] [INFO] DFAST_QC result json was written to GCF_007994985.1_ASM799498v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:38,677] [INFO] DFAST_QC completed!
[2024-01-24 12:35:38,677] [INFO] Total running time: 0h1m18s