[2024-01-24 13:01:49,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:49,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:49,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bcbfadc-001b-4c62-8808-dd6a2273ae3d/dqc_reference
[2024-01-24 13:01:51,307] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:51,308] [INFO] Task started: Prodigal
[2024-01-24 13:01:51,308] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f7ba22c-087c-4b17-a597-fca4853af113/GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/cds.fna -a GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:29,718] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:29,719] [INFO] Task started: HMMsearch
[2024-01-24 13:02:29,720] [INFO] Running command: hmmsearch --tblout GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bcbfadc-001b-4c62-8808-dd6a2273ae3d/dqc_reference/reference_markers.hmm GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:30,121] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:30,123] [INFO] Found 6/6 markers.
[2024-01-24 13:02:30,189] [INFO] Query marker FASTA was written to GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:02:30,189] [INFO] Task started: Blastn
[2024-01-24 13:02:30,190] [INFO] Running command: blastn -query GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bcbfadc-001b-4c62-8808-dd6a2273ae3d/dqc_reference/reference_markers.fasta -out GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:30,855] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:30,859] [INFO] Selected 11 target genomes.
[2024-01-24 13:02:30,859] [INFO] Target genome list was writen to GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:02:30,865] [INFO] Task started: fastANI
[2024-01-24 13:02:30,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7ba22c-087c-4b17-a597-fca4853af113/GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna.gz --refList GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:43,940] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:43,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bcbfadc-001b-4c62-8808-dd6a2273ae3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:43,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bcbfadc-001b-4c62-8808-dd6a2273ae3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:43,955] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:43,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:43,956] [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
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	100.0	2563	2566	95	conclusive
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	99.9986	2565	2566	95	conclusive
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	79.7274	937	2566	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	77.2131	295	2566	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	77.2033	300	2566	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	76.8576	78	2566	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	76.375	156	2566	95	below_threshold
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	76.1966	55	2566	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.1699	70	2566	95	below_threshold
Niabella yanshanensis	strain=HAMBI_3031	GCA_003349965.1	577386	577386	type	True	76.0341	75	2566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:43,957] [INFO] DFAST Taxonomy check result was written to GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:02:43,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:43,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:43,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bcbfadc-001b-4c62-8808-dd6a2273ae3d/dqc_reference/checkm_data
[2024-01-24 13:02:43,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:44,042] [INFO] Task started: CheckM
[2024-01-24 13:02:44,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/checkm_input GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:04:22,772] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:22,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:22,800] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:22,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:22,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:04:22,802] [INFO] Task started: Blastn
[2024-01-24 13:04:22,802] [INFO] Running command: blastn -query GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bcbfadc-001b-4c62-8808-dd6a2273ae3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:23,557] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:23,561] [INFO] Selected 10 target genomes.
[2024-01-24 13:04:23,561] [INFO] Target genome list was writen to GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:23,569] [INFO] Task started: fastANI
[2024-01-24 13:04:23,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7ba22c-087c-4b17-a597-fca4853af113/GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna.gz --refList GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:35,563] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:35,580] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:35,580] [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_002355595.1	s__Filimonas lacunae	99.9986	2565	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003097095.1	s__Filimonas sp003097095	79.8971	1004	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641615.1	s__Filimonas zeae	79.7363	936	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994055.1	s__Filimonas endophytica	79.6296	853	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412455.1	s__Deminuibacter soli	77.2131	295	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118675.1	s__Filimonas effusa	77.185	302	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	77.1083	195	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349965.1	s__Niabella yanshanensis	76.0564	74	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744515.1	s__Paraflavitalea sp017744515	76.0264	102	2566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:35,582] [INFO] GTDB search result was written to GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:35,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:35,588] [INFO] DFAST_QC result json was written to GCF_900156765.1_IMG-taxon_2681813554_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:04:35,588] [INFO] DFAST_QC completed!
[2024-01-24 13:04:35,588] [INFO] Total running time: 0h2m46s