[2024-01-24 14:28:16,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:16,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:16,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg64d13e34-13b5-4ef1-bff2-f0bba95dba4d/dqc_reference
[2024-01-24 14:28:17,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,698] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg90972c0a-7e8d-466c-8747-caa624a9d653/GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/cds.fna -a GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:31,522] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:31,523] [INFO] Task started: HMMsearch
[2024-01-24 14:28:31,523] [INFO] Running command: hmmsearch --tblout GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64d13e34-13b5-4ef1-bff2-f0bba95dba4d/dqc_reference/reference_markers.hmm GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:31,880] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:31,881] [INFO] Found 6/6 markers.
[2024-01-24 14:28:31,939] [INFO] Query marker FASTA was written to GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:28:31,940] [INFO] Task started: Blastn
[2024-01-24 14:28:31,940] [INFO] Running command: blastn -query GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg64d13e34-13b5-4ef1-bff2-f0bba95dba4d/dqc_reference/reference_markers.fasta -out GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:33,298] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:33,301] [INFO] Selected 18 target genomes.
[2024-01-24 14:28:33,302] [INFO] Target genome list was writen to GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:28:33,313] [INFO] Task started: fastANI
[2024-01-24 14:28:33,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg90972c0a-7e8d-466c-8747-caa624a9d653/GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna.gz --refList GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:47,854] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:47,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64d13e34-13b5-4ef1-bff2-f0bba95dba4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:47,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64d13e34-13b5-4ef1-bff2-f0bba95dba4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:47,871] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:47,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:47,871] [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
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	100.0	1433	1435	95	conclusive
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	81.9394	777	1435	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	81.6616	681	1435	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	80.4728	597	1435	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	80.4708	617	1435	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	80.2421	647	1435	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	80.1686	654	1435	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.864	470	1435	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	79.6566	504	1435	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	79.655	497	1435	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	79.6138	497	1435	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	79.4976	478	1435	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	79.3876	476	1435	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.2405	482	1435	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	79.1939	502	1435	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	78.9927	433	1435	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.6227	431	1435	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	78.4788	242	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:47,873] [INFO] DFAST Taxonomy check result was written to GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:28:47,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:47,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:47,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64d13e34-13b5-4ef1-bff2-f0bba95dba4d/dqc_reference/checkm_data
[2024-01-24 14:28:47,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:47,921] [INFO] Task started: CheckM
[2024-01-24 14:28:47,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/checkm_input GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:29:59,678] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:59,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:59,703] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:59,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:59,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:29:59,705] [INFO] Task started: Blastn
[2024-01-24 14:29:59,705] [INFO] Running command: blastn -query GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg64d13e34-13b5-4ef1-bff2-f0bba95dba4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:01,901] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:01,905] [INFO] Selected 12 target genomes.
[2024-01-24 14:30:01,906] [INFO] Target genome list was writen to GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:01,930] [INFO] Task started: fastANI
[2024-01-24 14:30:01,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg90972c0a-7e8d-466c-8747-caa624a9d653/GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna.gz --refList GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:13,027] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:13,042] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:13,042] [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_900111375.1	s__Pedococcus cremeus	100.0	1432	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	conclusive
GCF_001428025.1	s__Pedococcus sp001428025	82.2236	840	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	81.9297	778	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426245.1	s__Pedococcus sp001426245	81.6731	814	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.80	98.80	0.95	0.95	2	-
GCF_001429605.1	s__Pedococcus sp001429605	81.6659	794	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.23	98.23	0.91	0.91	2	-
GCF_013041615.1	s__Pedococcus sp013041615	81.6166	770	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707485.1	s__Pedococcus sp009707485	81.5032	696	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	81.324	696	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438965.1	s__Pedococcus bigeumensis	81.2363	787	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635045.1	s__Terracoccus luteus	79.7705	648	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	98.59	98.59	0.96	0.96	2	-
GCF_000576575.1	s__Intrasporangium_A chromatireducens	79.5622	502	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Intrasporangium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570945.1	s__Janibacter anophelis	79.3971	475	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:13,044] [INFO] GTDB search result was written to GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:13,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:13,048] [INFO] DFAST_QC result json was written to GCF_900111375.1_IMG-taxon_2671180066_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:30:13,048] [INFO] DFAST_QC completed!
[2024-01-24 14:30:13,048] [INFO] Total running time: 0h1m57s