[2024-01-24 13:12:55,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,872] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg89c6fed7-35e4-45b9-a487-3d7f0789016f/dqc_reference
[2024-01-24 13:12:57,294] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,295] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg7522d03e-7cb1-4dc0-acd1-95100d67a532/GCF_003668875.1_ASM366887v1_genomic.fna.gz | prodigal -d GCF_003668875.1_ASM366887v1_genomic.fna/cds.fna -a GCF_003668875.1_ASM366887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:40,564] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:40,564] [INFO] Task started: HMMsearch
[2024-01-24 13:13:40,565] [INFO] Running command: hmmsearch --tblout GCF_003668875.1_ASM366887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89c6fed7-35e4-45b9-a487-3d7f0789016f/dqc_reference/reference_markers.hmm GCF_003668875.1_ASM366887v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:40,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:40,985] [INFO] Found 6/6 markers.
[2024-01-24 13:13:41,055] [INFO] Query marker FASTA was written to GCF_003668875.1_ASM366887v1_genomic.fna/markers.fasta
[2024-01-24 13:13:41,055] [INFO] Task started: Blastn
[2024-01-24 13:13:41,055] [INFO] Running command: blastn -query GCF_003668875.1_ASM366887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c6fed7-35e4-45b9-a487-3d7f0789016f/dqc_reference/reference_markers.fasta -out GCF_003668875.1_ASM366887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:41,855] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:41,858] [INFO] Selected 19 target genomes.
[2024-01-24 13:13:41,859] [INFO] Target genome list was writen to GCF_003668875.1_ASM366887v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:41,881] [INFO] Task started: fastANI
[2024-01-24 13:13:41,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg7522d03e-7cb1-4dc0-acd1-95100d67a532/GCF_003668875.1_ASM366887v1_genomic.fna.gz --refList GCF_003668875.1_ASM366887v1_genomic.fna/target_genomes.txt --output GCF_003668875.1_ASM366887v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:22,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:22,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89c6fed7-35e4-45b9-a487-3d7f0789016f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:22,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89c6fed7-35e4-45b9-a487-3d7f0789016f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:22,695] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:22,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:22,696] [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
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	100.0	2981	2993	95	conclusive
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	93.1235	2677	2993	95	below_threshold
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	92.7048	2612	2993	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	92.3446	2349	2993	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	92.2969	2410	2993	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	92.2292	2476	2993	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	89.7349	2304	2993	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	88.5592	2339	2993	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	82.5135	1864	2993	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	79.9876	1461	2993	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.8962	508	2993	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.2221	367	2993	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	75.2116	90	2993	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.21	376	2993	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	75.0869	142	2993	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	74.9525	125	2993	95	below_threshold
Bradyrhizobium arachidis	strain=CCBAU 051107	GCA_015291705.1	858423	858423	type	True	74.8933	155	2993	95	below_threshold
Bradyrhizobium arachidis	strain=LMG 26795	GCA_900116675.1	858423	858423	type	True	74.8906	155	2993	95	below_threshold
Bradyrhizobium huanghuaihaiense	strain=CGMCC 1.10948	GCA_007830635.1	990078	990078	type	True	74.8499	162	2993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:22,698] [INFO] DFAST Taxonomy check result was written to GCF_003668875.1_ASM366887v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:22,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:22,699] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:22,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89c6fed7-35e4-45b9-a487-3d7f0789016f/dqc_reference/checkm_data
[2024-01-24 13:14:22,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:22,783] [INFO] Task started: CheckM
[2024-01-24 13:14:22,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003668875.1_ASM366887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003668875.1_ASM366887v1_genomic.fna/checkm_input GCF_003668875.1_ASM366887v1_genomic.fna/checkm_result
[2024-01-24 13:17:24,288] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:24,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:24,314] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:24,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:24,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003668875.1_ASM366887v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:24,315] [INFO] Task started: Blastn
[2024-01-24 13:17:24,316] [INFO] Running command: blastn -query GCF_003668875.1_ASM366887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c6fed7-35e4-45b9-a487-3d7f0789016f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003668875.1_ASM366887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:25,732] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:25,735] [INFO] Selected 12 target genomes.
[2024-01-24 13:17:25,736] [INFO] Target genome list was writen to GCF_003668875.1_ASM366887v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:25,782] [INFO] Task started: fastANI
[2024-01-24 13:17:25,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg7522d03e-7cb1-4dc0-acd1-95100d67a532/GCF_003668875.1_ASM366887v1_genomic.fna.gz --refList GCF_003668875.1_ASM366887v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003668875.1_ASM366887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:55,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:55,311] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:17:55,311] [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_003668875.1	s__Corallococcus interemptor	100.0	2981	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.20	99.20	0.95	0.95	2	conclusive
GCF_000255295.1	s__Corallococcus coralloides	93.1289	2678	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	95.87	95.41	0.89	0.88	6	-
GCF_017309135.1	s__Corallococcus sp017309135	93.0199	2596	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909105.1	s__Corallococcus exiguus	92.6939	2614	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	97.29	96.40	0.91	0.89	16	-
GCF_017302985.1	s__Corallococcus macrosporus_A	92.4022	2607	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611585.1	s__Corallococcus exercitus	92.377	2345	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	96.95	95.08	0.87	0.82	3	-
GCF_003612165.1	s__Corallococcus aberystwythensis	92.2994	2409	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611695.1	s__Corallococcus carmarthensis	92.2259	2477	2993	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216735.1	s__Bradyrhizobium sp004216735	74.9974	150	2993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013240495.1	s__Bradyrhizobium sp013240495	74.9484	134	2993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.36	98.36	0.89	0.89	2	-
GCF_011602485.1	s__Bradyrhizobium sp011602485	74.9108	151	2993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.68	97.67	0.91	0.90	3	-
GCF_003837805.1	s__Bradyrhizobium sp003837805	74.8047	125	2993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:55,313] [INFO] GTDB search result was written to GCF_003668875.1_ASM366887v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:55,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:55,319] [INFO] DFAST_QC result json was written to GCF_003668875.1_ASM366887v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:55,320] [INFO] DFAST_QC completed!
[2024-01-24 13:17:55,320] [INFO] Total running time: 0h4m59s