[2024-01-24 13:28:29,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg8614bcaa-5bbb-4fbc-89ab-551f89a03ef5/dqc_reference
[2024-01-24 13:28:30,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,363] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgf13ef990-4c0a-4810-a4bc-d6573ecfde15/GCF_903166545.1_P9898_genomic.fna.gz | prodigal -d GCF_903166545.1_P9898_genomic.fna/cds.fna -a GCF_903166545.1_P9898_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,371] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,372] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,372] [INFO] Running command: hmmsearch --tblout GCF_903166545.1_P9898_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8614bcaa-5bbb-4fbc-89ab-551f89a03ef5/dqc_reference/reference_markers.hmm GCF_903166545.1_P9898_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,705] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,751] [INFO] Query marker FASTA was written to GCF_903166545.1_P9898_genomic.fna/markers.fasta
[2024-01-24 13:28:41,752] [INFO] Task started: Blastn
[2024-01-24 13:28:41,752] [INFO] Running command: blastn -query GCF_903166545.1_P9898_genomic.fna/markers.fasta -db /var/lib/cwl/stg8614bcaa-5bbb-4fbc-89ab-551f89a03ef5/dqc_reference/reference_markers.fasta -out GCF_903166545.1_P9898_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,369] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,372] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:42,372] [INFO] Target genome list was writen to GCF_903166545.1_P9898_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,380] [INFO] Task started: fastANI
[2024-01-24 13:28:42,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgf13ef990-4c0a-4810-a4bc-d6573ecfde15/GCF_903166545.1_P9898_genomic.fna.gz --refList GCF_903166545.1_P9898_genomic.fna/target_genomes.txt --output GCF_903166545.1_P9898_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:00,803] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:00,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8614bcaa-5bbb-4fbc-89ab-551f89a03ef5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:00,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8614bcaa-5bbb-4fbc-89ab-551f89a03ef5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:00,816] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:00,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:00,817] [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 schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	100.0	1831	1832	95	conclusive
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	85.7366	1261	1832	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	80.6446	682	1832	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	79.7602	429	1832	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	79.4118	560	1832	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	79.3676	618	1832	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	79.2063	541	1832	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	79.1871	526	1832	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	78.8049	92	1832	95	below_threshold
Priestia megaterium	strain=NCTC10342	GCA_900445485.1	1404	1404	type	True	78.4067	140	1832	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	78.2484	124	1832	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	77.5321	92	1832	95	below_threshold
Metabacillus fastidiosus	strain=NBRC 101226	GCA_001591625.1	1458	1458	type	True	77.4904	210	1832	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.3389	146	1832	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	77.0376	131	1832	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.6909	77	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:00,818] [INFO] DFAST Taxonomy check result was written to GCF_903166545.1_P9898_genomic.fna/tc_result.tsv
[2024-01-24 13:29:00,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:00,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:00,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8614bcaa-5bbb-4fbc-89ab-551f89a03ef5/dqc_reference/checkm_data
[2024-01-24 13:29:00,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:00,879] [INFO] Task started: CheckM
[2024-01-24 13:29:00,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903166545.1_P9898_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903166545.1_P9898_genomic.fna/checkm_input GCF_903166545.1_P9898_genomic.fna/checkm_result
[2024-01-24 13:29:38,451] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:38,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:38,478] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:38,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:38,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903166545.1_P9898_genomic.fna/markers.fasta)
[2024-01-24 13:29:38,480] [INFO] Task started: Blastn
[2024-01-24 13:29:38,480] [INFO] Running command: blastn -query GCF_903166545.1_P9898_genomic.fna/markers.fasta -db /var/lib/cwl/stg8614bcaa-5bbb-4fbc-89ab-551f89a03ef5/dqc_reference/reference_markers_gtdb.fasta -out GCF_903166545.1_P9898_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:39,317] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:39,322] [INFO] Selected 14 target genomes.
[2024-01-24 13:29:39,322] [INFO] Target genome list was writen to GCF_903166545.1_P9898_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:39,334] [INFO] Task started: fastANI
[2024-01-24 13:29:39,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgf13ef990-4c0a-4810-a4bc-d6573ecfde15/GCF_903166545.1_P9898_genomic.fna.gz --refList GCF_903166545.1_P9898_genomic.fna/target_genomes_gtdb.txt --output GCF_903166545.1_P9898_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:55,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:55,575] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:55,576] [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_002871465.1	s__Metabacillus sp002871465	98.7356	1670	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	conclusive
GCF_002019635.1	s__Metabacillus halosaccharovorans	85.7149	1260	1832	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	85.3102	1222	1832	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	80.6954	683	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_002577655.1	s__Metabacillus sp002577655	80.3644	657	1832	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	79.9208	646	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_001889165.1	s__Metabacillus weihaiensis	79.7344	428	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	97.24	97.24	0.88	0.88	2	-
GCF_007994985.1	s__Metabacillus litoralis	79.382	563	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017497975.1	s__Metabacillus sp017497975	79.3774	615	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908395.1	s__Metabacillus crassostreae	79.1788	525	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832985.1	s__Priestia megaterium	78.4281	141	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.5311	96.82	95.69	0.88	0.73	151	-
GCF_014837155.1	s__Litchfieldia sp014837155	77.6057	193	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591625.1	s__Metabacillus fastidiosus	77.5193	208	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866655.1	s__Neobacillus sp001866655	77.4008	138	1832	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:55,581] [INFO] GTDB search result was written to GCF_903166545.1_P9898_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:55,582] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:55,586] [INFO] DFAST_QC result json was written to GCF_903166545.1_P9898_genomic.fna/dqc_result.json
[2024-01-24 13:29:55,586] [INFO] DFAST_QC completed!
[2024-01-24 13:29:55,587] [INFO] Total running time: 0h1m26s