[2024-01-24 12:06:22,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:22,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:22,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3868eb0-7b4a-43c2-8035-e554026786e6/dqc_reference
[2024-01-24 12:06:24,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:24,096] [INFO] Task started: Prodigal
[2024-01-24 12:06:24,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c745a55-fb1d-4e4b-a63b-1d508d10d50e/GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/cds.fna -a GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:40,312] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:40,312] [INFO] Task started: HMMsearch
[2024-01-24 12:06:40,312] [INFO] Running command: hmmsearch --tblout GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3868eb0-7b4a-43c2-8035-e554026786e6/dqc_reference/reference_markers.hmm GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:40,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:40,582] [INFO] Found 6/6 markers.
[2024-01-24 12:06:40,624] [INFO] Query marker FASTA was written to GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:06:40,625] [INFO] Task started: Blastn
[2024-01-24 12:06:40,625] [INFO] Running command: blastn -query GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3868eb0-7b4a-43c2-8035-e554026786e6/dqc_reference/reference_markers.fasta -out GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:41,265] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:41,269] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:41,269] [INFO] Target genome list was writen to GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:06:41,292] [INFO] Task started: fastANI
[2024-01-24 12:06:41,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c745a55-fb1d-4e4b-a63b-1d508d10d50e/GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna.gz --refList GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:54,185] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:54,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3868eb0-7b4a-43c2-8035-e554026786e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:54,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3868eb0-7b4a-43c2-8035-e554026786e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:54,198] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:54,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:54,198] [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
Daejeonella rubra	strain=DSM 24536	GCA_900103545.1	990371	990371	type	True	100.0	1383	1387	95	conclusive
Daejeonella lutea	strain=DSM 22385	GCA_900168015.1	572036	572036	type	True	77.949	231	1387	95	below_threshold
Flavihumibacter soli	strain=R14	GCA_010692725.1	2705549	2705549	type	True	77.7262	100	1387	95	below_threshold
Daejeonella oryzae	strain=DSM 19973	GCA_000422945.1	1122943	1122943	type	True	77.2693	168	1387	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	76.8985	71	1387	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	76.8394	52	1387	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	76.736	66	1387	95	below_threshold
Arcticibacter pallidicorallinus	strain=CGMCC 1.9313	GCA_003002875.1	1259464	1259464	type	True	76.7241	56	1387	95	below_threshold
Pedobacter antarcticus	strain=4BY	GCA_000722885.1	34086	34086	type	True	76.5523	66	1387	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	76.4984	75	1387	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	76.3188	72	1387	95	below_threshold
Pedobacter antarcticus	strain=ATCC 51969	GCA_900112985.1	34086	34086	type	True	76.2748	64	1387	95	below_threshold
Pedobacter duraquae	strain=DSM 19034	GCA_004362245.1	425511	425511	type	True	76.2613	72	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:54,201] [INFO] DFAST Taxonomy check result was written to GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:06:54,202] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:54,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:54,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3868eb0-7b4a-43c2-8035-e554026786e6/dqc_reference/checkm_data
[2024-01-24 12:06:54,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:54,245] [INFO] Task started: CheckM
[2024-01-24 12:06:54,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/checkm_input GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:07:41,875] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:41,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:41,893] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:41,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:41,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:07:41,894] [INFO] Task started: Blastn
[2024-01-24 12:07:41,894] [INFO] Running command: blastn -query GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3868eb0-7b4a-43c2-8035-e554026786e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:42,708] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:42,711] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:42,712] [INFO] Target genome list was writen to GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:42,724] [INFO] Task started: fastANI
[2024-01-24 12:07:42,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c745a55-fb1d-4e4b-a63b-1d508d10d50e/GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna.gz --refList GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:52,460] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:52,470] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:52,471] [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_900103545.1	s__Daejeonella rubra	100.0	1383	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903821625.1	s__Daejeonella sp903821625	83.4866	563	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257025.1	s__Daejeonella sp002257025	79.591	547	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_017495225.1	s__Daejeonella sp017495225	79.203	446	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168015.1	s__Daejeonella lutea	77.949	231	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010692725.1	s__Daejeonella soli	77.7262	100	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868395.1	s__Daejeonella sp016868395	77.4982	232	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377665.1	s__Pedobacter sp014377665	76.7805	51	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	76.7099	63	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197755.1	s__Pedobacter sp002197755	76.5434	70	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378705.1	s__Daejeonella sp014378705	76.3281	92	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799115.1	s__Pelobium glucosidilyticum_A	76.1626	76	1387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	97.72	97.72	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:52,472] [INFO] GTDB search result was written to GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:52,473] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:52,476] [INFO] DFAST_QC result json was written to GCF_900103545.1_IMG-taxon_2675903227_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:07:52,476] [INFO] DFAST_QC completed!
[2024-01-24 12:07:52,476] [INFO] Total running time: 0h1m30s