[2024-01-24 11:43:53,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg632e1d6a-7b19-4b30-b899-9103dd297bbc/dqc_reference
[2024-01-24 11:43:54,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,494] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,494] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ebc2fb8-7f92-4a7b-8d1e-a60882ac747b/GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/cds.fna -a GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:15,091] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:15,091] [INFO] Task started: HMMsearch
[2024-01-24 11:44:15,091] [INFO] Running command: hmmsearch --tblout GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg632e1d6a-7b19-4b30-b899-9103dd297bbc/dqc_reference/reference_markers.hmm GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:15,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:15,361] [INFO] Found 6/6 markers.
[2024-01-24 11:44:15,404] [INFO] Query marker FASTA was written to GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:44:15,405] [INFO] Task started: Blastn
[2024-01-24 11:44:15,405] [INFO] Running command: blastn -query GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg632e1d6a-7b19-4b30-b899-9103dd297bbc/dqc_reference/reference_markers.fasta -out GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:16,008] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:16,011] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:16,012] [INFO] Target genome list was writen to GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:44:16,014] [INFO] Task started: fastANI
[2024-01-24 11:44:16,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebc2fb8-7f92-4a7b-8d1e-a60882ac747b/GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna.gz --refList GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:32,896] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:32,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg632e1d6a-7b19-4b30-b899-9103dd297bbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:32,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg632e1d6a-7b19-4b30-b899-9103dd297bbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:32,908] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:32,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:32,909] [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
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	100.0	1874	1887	95	conclusive
Pedobacter suwonensis	strain=DSM 18130	GCA_900111825.1	332999	332999	type	True	86.5679	1334	1887	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	85.9487	1305	1887	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	85.901	1319	1887	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	84.332	1039	1887	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	84.2302	1173	1887	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	84.0634	1164	1887	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	83.9985	1154	1887	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	82.6414	1075	1887	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	81.5525	932	1887	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	81.5136	960	1887	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	81.4494	945	1887	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	79.9738	668	1887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:32,910] [INFO] DFAST Taxonomy check result was written to GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:44:32,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:32,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:32,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg632e1d6a-7b19-4b30-b899-9103dd297bbc/dqc_reference/checkm_data
[2024-01-24 11:44:32,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:32,964] [INFO] Task started: CheckM
[2024-01-24 11:44:32,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/checkm_input GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:45:30,344] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:30,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:30,363] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:30,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:30,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:45:30,364] [INFO] Task started: Blastn
[2024-01-24 11:45:30,364] [INFO] Running command: blastn -query GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg632e1d6a-7b19-4b30-b899-9103dd297bbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:31,157] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:31,160] [INFO] Selected 12 target genomes.
[2024-01-24 11:45:31,160] [INFO] Target genome list was writen to GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:31,166] [INFO] Task started: fastANI
[2024-01-24 11:45:31,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebc2fb8-7f92-4a7b-8d1e-a60882ac747b/GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna.gz --refList GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:48,213] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:48,223] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:48,223] [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_900100705.1	s__Pedobacter terrae	100.0	1874	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016909215.1	s__Pedobacter terrae_B	87.743	1331	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111825.1	s__Pedobacter suwonensis	86.5737	1334	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.36	97.36	0.90	0.86	3	-
GCF_007994015.1	s__Pedobacter terrae_A	86.0151	1299	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664035.1	s__Pedobacter alluvionis	85.9443	1305	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004342125.1	s__Pedobacter sp004342125	85.7904	1325	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_005938645.2	s__Pedobacter sp005938645	85.7234	1327	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692875.1	s__Pedobacter sp011759615	84.6606	1196	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_014205835.1	s__Pedobacter sp014205835	84.5783	1191	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613605.1	s__Pedobacter sp018613605	84.1835	1139	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCA_002151545.1	s__Pedobacter sp002151545	83.9238	1144	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101435.1	s__Pedobacter soli	81.4945	964	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:48,225] [INFO] GTDB search result was written to GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:48,225] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:48,229] [INFO] DFAST_QC result json was written to GCF_900100705.1_IMG-taxon_2675903222_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:45:48,229] [INFO] DFAST_QC completed!
[2024-01-24 11:45:48,229] [INFO] Total running time: 0h1m55s