[2024-01-25 18:54:51,092] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:51,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:51,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg09f5f4c9-4708-494a-8cd9-f8a92484fa10/dqc_reference
[2024-01-25 18:54:52,269] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:52,269] [INFO] Task started: Prodigal
[2024-01-25 18:54:52,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9944dc0-675b-4eca-bb31-1a9f03450d19/GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/cds.fna -a GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:09,831] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:09,831] [INFO] Task started: HMMsearch
[2024-01-25 18:55:09,832] [INFO] Running command: hmmsearch --tblout GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09f5f4c9-4708-494a-8cd9-f8a92484fa10/dqc_reference/reference_markers.hmm GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:10,116] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:10,117] [INFO] Found 6/6 markers.
[2024-01-25 18:55:10,162] [INFO] Query marker FASTA was written to GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:55:10,162] [INFO] Task started: Blastn
[2024-01-25 18:55:10,162] [INFO] Running command: blastn -query GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg09f5f4c9-4708-494a-8cd9-f8a92484fa10/dqc_reference/reference_markers.fasta -out GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:10,759] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:10,762] [INFO] Selected 20 target genomes.
[2024-01-25 18:55:10,762] [INFO] Target genome list was writen to GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:55:10,773] [INFO] Task started: fastANI
[2024-01-25 18:55:10,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9944dc0-675b-4eca-bb31-1a9f03450d19/GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna.gz --refList GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:31,302] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:31,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09f5f4c9-4708-494a-8cd9-f8a92484fa10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:31,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09f5f4c9-4708-494a-8cd9-f8a92484fa10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:31,314] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:55:31,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:31,314] [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 rhizosphaerae	strain=DSM 18610	GCA_900111155.1	390241	390241	type	True	100.0	1878	1887	95	conclusive
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	79.4264	640	1887	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	79.3711	579	1887	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	79.2787	696	1887	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	79.2632	620	1887	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	79.2396	636	1887	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	79.2368	518	1887	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	79.2361	717	1887	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	79.2227	634	1887	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	79.1956	671	1887	95	below_threshold
Pedobacter nototheniae	strain=36B243	GCA_004335085.1	2488994	2488994	type	True	79.1827	541	1887	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	79.0916	576	1887	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	78.948	683	1887	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	78.9258	541	1887	95	below_threshold
Pedobacter psychrotolerans	strain=DSM 103236	GCA_004340665.1	1843235	1843235	type	True	78.8837	544	1887	95	below_threshold
Pedobacter suwonensis	strain=DSM 18130	GCA_900111825.1	332999	332999	type	True	78.8811	601	1887	95	below_threshold
Pedobacter petrophilus	strain=LMG 29686	GCA_009674725.1	1908241	1908241	type	True	78.7725	569	1887	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	76.8046	54	1887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:31,315] [INFO] DFAST Taxonomy check result was written to GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:55:31,317] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:31,317] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:31,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09f5f4c9-4708-494a-8cd9-f8a92484fa10/dqc_reference/checkm_data
[2024-01-25 18:55:31,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:31,372] [INFO] Task started: CheckM
[2024-01-25 18:55:31,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/checkm_input GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:56:21,518] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:21,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:21,540] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:21,540] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:21,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:56:21,542] [INFO] Task started: Blastn
[2024-01-25 18:56:21,542] [INFO] Running command: blastn -query GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg09f5f4c9-4708-494a-8cd9-f8a92484fa10/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:22,427] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:22,430] [INFO] Selected 19 target genomes.
[2024-01-25 18:56:22,430] [INFO] Target genome list was writen to GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:22,449] [INFO] Task started: fastANI
[2024-01-25 18:56:22,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9944dc0-675b-4eca-bb31-1a9f03450d19/GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna.gz --refList GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:44,030] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:44,042] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:44,042] [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_900111155.1	s__Pedobacter rhizosphaerae	100.0	1878	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_000708285.2	s__Pedobacter borealis	79.4241	641	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_003339865.1	s__Pedobacter chinensis	79.3685	580	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_000633455.1	s__Pedobacter jeongneungensis	79.3301	732	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_003387415.1	s__Pedobacter sp003387415	79.3105	670	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	79.3076	723	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_900100705.1	s__Pedobacter terrae	79.2559	621	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	79.2399	678	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_003664035.1	s__Pedobacter alluvionis	79.2316	637	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_004331735.1	s__Pedobacter sp004331735	79.2309	717	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_004342125.1	s__Pedobacter sp004342125	79.2022	652	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_004335085.1	s__Pedobacter nototheniae	79.1948	539	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.28	98.28	0.90	0.90	2	-
GCF_903166585.1	s__Pedobacter sp903166585	79.1716	675	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_011303555.1	s__Pedobacter sp003852395	79.1445	665	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.47	99.47	0.90	0.90	2	-
GCF_014205835.1	s__Pedobacter sp014205835	79.1236	691	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	79.1111	704	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCA_002432345.1	s__Pedobacter sp002432345	79.0005	580	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	78.8733	604	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.36	97.36	0.90	0.86	3	-
GCA_004210715.1	s__Pedobacter sp004210715	78.299	385	1887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:44,044] [INFO] GTDB search result was written to GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:44,044] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:44,048] [INFO] DFAST_QC result json was written to GCF_900111155.1_IMG-taxon_2622736586_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:56:44,048] [INFO] DFAST_QC completed!
[2024-01-25 18:56:44,048] [INFO] Total running time: 0h1m53s