[2024-01-24 13:40:00,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:00,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:00,212] [INFO] DQC Reference Directory: /var/lib/cwl/stgba27f044-ce2f-40a5-8ea9-c32781ac1179/dqc_reference
[2024-01-24 13:40:01,498] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:01,498] [INFO] Task started: Prodigal
[2024-01-24 13:40:01,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg8002f988-79f5-4c95-8fb0-05f9ed37f558/GCF_000307855.1_BAZO1.0_genomic.fna.gz | prodigal -d GCF_000307855.1_BAZO1.0_genomic.fna/cds.fna -a GCF_000307855.1_BAZO1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:09,789] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:09,789] [INFO] Task started: HMMsearch
[2024-01-24 13:40:09,789] [INFO] Running command: hmmsearch --tblout GCF_000307855.1_BAZO1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba27f044-ce2f-40a5-8ea9-c32781ac1179/dqc_reference/reference_markers.hmm GCF_000307855.1_BAZO1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:10,103] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:10,105] [INFO] Found 6/6 markers.
[2024-01-24 13:40:10,146] [INFO] Query marker FASTA was written to GCF_000307855.1_BAZO1.0_genomic.fna/markers.fasta
[2024-01-24 13:40:10,147] [INFO] Task started: Blastn
[2024-01-24 13:40:10,147] [INFO] Running command: blastn -query GCF_000307855.1_BAZO1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgba27f044-ce2f-40a5-8ea9-c32781ac1179/dqc_reference/reference_markers.fasta -out GCF_000307855.1_BAZO1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:10,736] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:10,739] [INFO] Selected 30 target genomes.
[2024-01-24 13:40:10,739] [INFO] Target genome list was writen to GCF_000307855.1_BAZO1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:40:10,787] [INFO] Task started: fastANI
[2024-01-24 13:40:10,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg8002f988-79f5-4c95-8fb0-05f9ed37f558/GCF_000307855.1_BAZO1.0_genomic.fna.gz --refList GCF_000307855.1_BAZO1.0_genomic.fna/target_genomes.txt --output GCF_000307855.1_BAZO1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:27,771] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:27,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba27f044-ce2f-40a5-8ea9-c32781ac1179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:27,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba27f044-ce2f-40a5-8ea9-c32781ac1179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:27,789] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:27,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:27,790] [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
Schinkia azotoformans	strain=LMG 9581	GCA_000307855.1	1454	1454	type	True	100.0	1340	1342	95	conclusive
Calidifontibacillus oryziterrae	strain=ZYK	GCA_000331575.1	1191699	1191699	type	True	77.7401	243	1342	95	below_threshold
Calidifontibacillus erzurumensis	strain=P2	GCA_013303125.1	2741433	2741433	type	True	77.6224	327	1342	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	76.8324	91	1342	95	below_threshold
Peribacillus loiseleuriae	strain=FJAT-27997	GCA_001183985.1	1679170	1679170	type	True	76.338	70	1342	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	76.2691	69	1342	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	76.2579	87	1342	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.2547	81	1342	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	76.2208	61	1342	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.2187	65	1342	95	below_threshold
Cytobacillus stercorigallinarum	strain=Sa5YUA1	GCA_014836495.1	2762240	2762240	type	True	76.2167	72	1342	95	below_threshold
Niallia nealsonii	strain=FO-92	GCA_002835805.1	115979	115979	type	True	76.1945	73	1342	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.1831	77	1342	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	76.1261	67	1342	95	below_threshold
Gottfriedia endophyticus	strain=RG28	GCA_017814275.1	2820819	2820819	type	True	76.0737	66	1342	95	below_threshold
Lederbergia lenta	strain=NCTC4824	GCA_900478165.1	1467	1467	type	True	75.4114	56	1342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:27,792] [INFO] DFAST Taxonomy check result was written to GCF_000307855.1_BAZO1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:40:27,792] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:27,792] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:27,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba27f044-ce2f-40a5-8ea9-c32781ac1179/dqc_reference/checkm_data
[2024-01-24 13:40:27,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:27,842] [INFO] Task started: CheckM
[2024-01-24 13:40:27,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000307855.1_BAZO1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000307855.1_BAZO1.0_genomic.fna/checkm_input GCF_000307855.1_BAZO1.0_genomic.fna/checkm_result
[2024-01-24 13:40:59,868] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:59,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.91%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2024-01-24 13:40:59,899] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:59,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:59,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000307855.1_BAZO1.0_genomic.fna/markers.fasta)
[2024-01-24 13:40:59,901] [INFO] Task started: Blastn
[2024-01-24 13:40:59,901] [INFO] Running command: blastn -query GCF_000307855.1_BAZO1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgba27f044-ce2f-40a5-8ea9-c32781ac1179/dqc_reference/reference_markers_gtdb.fasta -out GCF_000307855.1_BAZO1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:00,748] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:00,751] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:00,752] [INFO] Target genome list was writen to GCF_000307855.1_BAZO1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:00,762] [INFO] Task started: fastANI
[2024-01-24 13:41:00,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg8002f988-79f5-4c95-8fb0-05f9ed37f558/GCF_000307855.1_BAZO1.0_genomic.fna.gz --refList GCF_000307855.1_BAZO1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000307855.1_BAZO1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:11,190] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:11,200] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:11,200] [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_000307855.1	s__Calidifontibacillus azotoformans	100.0	1338	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	97.05	97.05	0.89	0.89	2	conclusive
GCA_012840465.1	s__Calidifontibacillus sp012840465	88.9437	863	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841285.1	s__Calidifontibacillus sp016841285	86.7036	774	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842745.1	s__Calidifontibacillus sp012842745	79.2612	507	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331575.1	s__Calidifontibacillus oryziterrae	77.7401	243	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013303125.1	s__Calidifontibacillus erzurumensis	77.6109	329	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240995.1	s__OESV01 sp900240995	77.4444	218	1342	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	-
GCF_002734215.1	s__Fredinandcohnia onubensis	76.8051	93	1342	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_001866655.1	s__Neobacillus sp001866655	76.2969	82	1342	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_003570725.1	s__Peribacillus asahii	76.2691	69	1342	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_003184905.1	s__Priestia sp003184905	76.2622	70	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,201] [INFO] GTDB search result was written to GCF_000307855.1_BAZO1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:11,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:11,207] [INFO] DFAST_QC result json was written to GCF_000307855.1_BAZO1.0_genomic.fna/dqc_result.json
[2024-01-24 13:41:11,207] [INFO] DFAST_QC completed!
[2024-01-24 13:41:11,207] [INFO] Total running time: 0h1m11s