[2024-01-24 12:30:33,759] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:33,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:33,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ec92fc0-6f9f-453b-be72-19e60acb3e93/dqc_reference
[2024-01-24 12:30:35,074] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:35,075] [INFO] Task started: Prodigal
[2024-01-24 12:30:35,075] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbdf9391-7e23-4f2f-8c3a-acd634a0f4a6/GCF_010894405.1_ASM1089440v1_genomic.fna.gz | prodigal -d GCF_010894405.1_ASM1089440v1_genomic.fna/cds.fna -a GCF_010894405.1_ASM1089440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:04,608] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:04,609] [INFO] Task started: HMMsearch
[2024-01-24 12:32:04,609] [INFO] Running command: hmmsearch --tblout GCF_010894405.1_ASM1089440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ec92fc0-6f9f-453b-be72-19e60acb3e93/dqc_reference/reference_markers.hmm GCF_010894405.1_ASM1089440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:05,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:05,221] [INFO] Found 6/6 markers.
[2024-01-24 12:32:05,317] [INFO] Query marker FASTA was written to GCF_010894405.1_ASM1089440v1_genomic.fna/markers.fasta
[2024-01-24 12:32:05,317] [INFO] Task started: Blastn
[2024-01-24 12:32:05,318] [INFO] Running command: blastn -query GCF_010894405.1_ASM1089440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec92fc0-6f9f-453b-be72-19e60acb3e93/dqc_reference/reference_markers.fasta -out GCF_010894405.1_ASM1089440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:06,047] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:06,052] [INFO] Selected 19 target genomes.
[2024-01-24 12:32:06,053] [INFO] Target genome list was writen to GCF_010894405.1_ASM1089440v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:06,062] [INFO] Task started: fastANI
[2024-01-24 12:32:06,062] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbdf9391-7e23-4f2f-8c3a-acd634a0f4a6/GCF_010894405.1_ASM1089440v1_genomic.fna.gz --refList GCF_010894405.1_ASM1089440v1_genomic.fna/target_genomes.txt --output GCF_010894405.1_ASM1089440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:53,777] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:53,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ec92fc0-6f9f-453b-be72-19e60acb3e93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:53,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ec92fc0-6f9f-453b-be72-19e60acb3e93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:53,804] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:53,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:53,804] [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
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	100.0	4410	4418	95	conclusive
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	89.2642	3249	4418	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	87.3072	2899	4418	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	84.8621	1880	4418	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	84.4773	2155	4418	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	84.3944	2176	4418	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	84.3351	2182	4418	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	83.8662	2478	4418	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	83.6787	2414	4418	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	83.2055	2229	4418	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.5898	2082	4418	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.3577	1990	4418	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.2883	458	4418	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	74.943	170	4418	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	74.9371	536	4418	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	74.9162	168	4418	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	74.9119	275	4418	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	74.8643	526	4418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:53,806] [INFO] DFAST Taxonomy check result was written to GCF_010894405.1_ASM1089440v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:53,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:53,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:53,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ec92fc0-6f9f-453b-be72-19e60acb3e93/dqc_reference/checkm_data
[2024-01-24 12:32:53,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:53,927] [INFO] Task started: CheckM
[2024-01-24 12:32:53,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010894405.1_ASM1089440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010894405.1_ASM1089440v1_genomic.fna/checkm_input GCF_010894405.1_ASM1089440v1_genomic.fna/checkm_result
[2024-01-24 12:38:14,882] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:14,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:14,918] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:14,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:14,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010894405.1_ASM1089440v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:14,921] [INFO] Task started: Blastn
[2024-01-24 12:38:14,921] [INFO] Running command: blastn -query GCF_010894405.1_ASM1089440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ec92fc0-6f9f-453b-be72-19e60acb3e93/dqc_reference/reference_markers_gtdb.fasta -out GCF_010894405.1_ASM1089440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:16,082] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:16,086] [INFO] Selected 11 target genomes.
[2024-01-24 12:38:16,086] [INFO] Target genome list was writen to GCF_010894405.1_ASM1089440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:16,106] [INFO] Task started: fastANI
[2024-01-24 12:38:16,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbdf9391-7e23-4f2f-8c3a-acd634a0f4a6/GCF_010894405.1_ASM1089440v1_genomic.fna.gz --refList GCF_010894405.1_ASM1089440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010894405.1_ASM1089440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:58,240] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:58,255] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:58,255] [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_010894405.1	s__Myxococcus caerfyrddinensis	100.0	4410	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017301735.1	s__Myxococcus sp017301735	89.6506	3356	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894435.1	s__Myxococcus trucidator	89.2711	3245	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	87.3131	2900	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305895.1	s__Myxococcus macrosporus	84.8346	2209	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_013372585.1	s__Myxococcus sp013372585	84.6629	2141	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.53	99.53	0.97	0.97	2	-
GCF_014656495.1	s__Myxococcus sp014656495	84.4672	2175	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101905.1	s__Myxococcus virescens	84.3905	2177	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	98.11	97.12	0.95	0.93	4	-
GCF_010894455.1	s__Myxococcus eversor	83.8792	2475	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	-
GCF_013336725.1	s__Myxococcus sp013336725	83.7594	2561	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.23	98.12	0.95	0.94	5	-
GCF_900111765.1	s__Myxococcus fulvus	83.7375	2419	4418	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:58,257] [INFO] GTDB search result was written to GCF_010894405.1_ASM1089440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:58,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:58,261] [INFO] DFAST_QC result json was written to GCF_010894405.1_ASM1089440v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:58,261] [INFO] DFAST_QC completed!
[2024-01-24 12:38:58,261] [INFO] Total running time: 0h8m25s