[2024-01-24 11:42:20,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,310] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg57700abd-ccc6-493f-9692-ff9ec5884127/dqc_reference
[2024-01-24 11:42:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stgca4a36d8-3873-4812-b7d1-5c8fbaa72be4/GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/cds.fna -a GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:40,835] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:40,835] [INFO] Task started: HMMsearch
[2024-01-24 11:42:40,835] [INFO] Running command: hmmsearch --tblout GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57700abd-ccc6-493f-9692-ff9ec5884127/dqc_reference/reference_markers.hmm GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:41,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:41,155] [INFO] Found 6/6 markers.
[2024-01-24 11:42:41,209] [INFO] Query marker FASTA was written to GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:42:41,209] [INFO] Task started: Blastn
[2024-01-24 11:42:41,210] [INFO] Running command: blastn -query GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg57700abd-ccc6-493f-9692-ff9ec5884127/dqc_reference/reference_markers.fasta -out GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:41,895] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:41,899] [INFO] Selected 16 target genomes.
[2024-01-24 11:42:41,899] [INFO] Target genome list was writen to GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:42:41,906] [INFO] Task started: fastANI
[2024-01-24 11:42:41,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4a36d8-3873-4812-b7d1-5c8fbaa72be4/GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna.gz --refList GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:03,524] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:03,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57700abd-ccc6-493f-9692-ff9ec5884127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:03,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57700abd-ccc6-493f-9692-ff9ec5884127/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:03,539] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:03,539] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:03,539] [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
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	100.0	2196	2201	95	conclusive
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	82.9316	1301	2201	95	below_threshold
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	82.7002	1353	2201	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	80.6305	766	2201	95	below_threshold
Paenibacillus riograndensis		GCA_000981585.1	483937	483937	type	True	80.6146	1019	2201	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	80.5644	1017	2201	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	80.5554	1158	2201	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	80.5519	1174	2201	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	80.3714	1027	2201	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	80.347	971	2201	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	80.259	1042	2201	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	80.2055	1016	2201	95	below_threshold
Paenibacillus tepidiphilus	strain=SYSU G01001	GCA_008635795.1	2608683	2608683	type	True	80.1668	952	2201	95	below_threshold
Paenibacillus tengchongensis	strain=SYSU G01003	GCA_008973665.1	2608684	2608684	type	True	79.7693	944	2201	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.2185	584	2201	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.2882	474	2201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:03,541] [INFO] DFAST Taxonomy check result was written to GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:43:03,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:03,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:03,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57700abd-ccc6-493f-9692-ff9ec5884127/dqc_reference/checkm_data
[2024-01-24 11:43:03,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:03,610] [INFO] Task started: CheckM
[2024-01-24 11:43:03,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/checkm_input GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:43:53,113] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:53,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:53,139] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:53,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:53,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:43:53,140] [INFO] Task started: Blastn
[2024-01-24 11:43:53,140] [INFO] Running command: blastn -query GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg57700abd-ccc6-493f-9692-ff9ec5884127/dqc_reference/reference_markers_gtdb.fasta -out GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:53,972] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:53,976] [INFO] Selected 7 target genomes.
[2024-01-24 11:43:53,976] [INFO] Target genome list was writen to GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:43:53,991] [INFO] Task started: fastANI
[2024-01-24 11:43:53,991] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4a36d8-3873-4812-b7d1-5c8fbaa72be4/GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna.gz --refList GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:06,647] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:06,660] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:06,660] [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_900099765.1	s__Paenibacillus typhae	100.0	2196	2201	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	conclusive
GCF_001517085.1	s__Paenibacillus sp001517085	94.0248	1907	2201	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758625.1	s__Paenibacillus sp000758625	87.4815	1790	2201	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000723885.1	s__Paenibacillus camerounensis	86.6331	1679	2201	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.67	95.67	0.88	0.88	2	-
GCF_017086365.1	s__Paenibacillus sp017086365	82.9316	1301	2201	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368795.1	s__Paenibacillus ihuae	82.6985	1353	2201	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001955925.1	s__Paenibacillus sp001955925	80.1665	1035	2201	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.91	98.91	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:06,661] [INFO] GTDB search result was written to GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:06,662] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:06,665] [INFO] DFAST_QC result json was written to GCF_900099765.1_IMG-taxon_2667527451_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:44:06,665] [INFO] DFAST_QC completed!
[2024-01-24 11:44:06,666] [INFO] Total running time: 0h1m46s