[2023-06-29 21:52:04,768] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:52:04,771] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:52:04,771] [INFO] DQC Reference Directory: /var/lib/cwl/stgdefef45c-594b-4578-ab72-7f14019d520a/dqc_reference
[2023-06-29 21:52:05,940] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:52:05,941] [INFO] Task started: Prodigal
[2023-06-29 21:52:05,941] [INFO] Running command: gunzip -c /var/lib/cwl/stgff35d73c-7428-4c9b-b4ea-fc2abb2dceea/GCA_016708855.1_ASM1670885v1_genomic.fna.gz | prodigal -d GCA_016708855.1_ASM1670885v1_genomic.fna/cds.fna -a GCA_016708855.1_ASM1670885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:52:16,904] [INFO] Task succeeded: Prodigal
[2023-06-29 21:52:16,904] [INFO] Task started: HMMsearch
[2023-06-29 21:52:16,904] [INFO] Running command: hmmsearch --tblout GCA_016708855.1_ASM1670885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdefef45c-594b-4578-ab72-7f14019d520a/dqc_reference/reference_markers.hmm GCA_016708855.1_ASM1670885v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:52:17,164] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:52:17,166] [INFO] Found 6/6 markers.
[2023-06-29 21:52:17,200] [INFO] Query marker FASTA was written to GCA_016708855.1_ASM1670885v1_genomic.fna/markers.fasta
[2023-06-29 21:52:17,200] [INFO] Task started: Blastn
[2023-06-29 21:52:17,200] [INFO] Running command: blastn -query GCA_016708855.1_ASM1670885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefef45c-594b-4578-ab72-7f14019d520a/dqc_reference/reference_markers.fasta -out GCA_016708855.1_ASM1670885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:52:18,128] [INFO] Task succeeded: Blastn
[2023-06-29 21:52:18,133] [INFO] Selected 20 target genomes.
[2023-06-29 21:52:18,133] [INFO] Target genome list was writen to GCA_016708855.1_ASM1670885v1_genomic.fna/target_genomes.txt
[2023-06-29 21:52:18,145] [INFO] Task started: fastANI
[2023-06-29 21:52:18,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgff35d73c-7428-4c9b-b4ea-fc2abb2dceea/GCA_016708855.1_ASM1670885v1_genomic.fna.gz --refList GCA_016708855.1_ASM1670885v1_genomic.fna/target_genomes.txt --output GCA_016708855.1_ASM1670885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:52:33,505] [INFO] Task succeeded: fastANI
[2023-06-29 21:52:33,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdefef45c-594b-4578-ab72-7f14019d520a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:52:33,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdefef45c-594b-4578-ab72-7f14019d520a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:52:33,524] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:52:33,524] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:52:33,524] [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 badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	78.7332	340	1181	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	78.7264	367	1181	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	78.7148	404	1181	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	78.6801	323	1181	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	78.6521	379	1181	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	78.6063	361	1181	95	below_threshold
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	78.5694	361	1181	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.5176	328	1181	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.463	315	1181	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.4478	325	1181	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.3343	316	1181	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	78.2981	283	1181	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	78.1501	299	1181	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	78.1187	312	1181	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	78.0819	291	1181	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	78.0372	282	1181	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	77.9909	264	1181	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.9463	270	1181	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	77.4278	222	1181	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	76.4618	268	1181	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:52:33,526] [INFO] DFAST Taxonomy check result was written to GCA_016708855.1_ASM1670885v1_genomic.fna/tc_result.tsv
[2023-06-29 21:52:33,527] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:52:33,527] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:52:33,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdefef45c-594b-4578-ab72-7f14019d520a/dqc_reference/checkm_data
[2023-06-29 21:52:33,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:52:33,568] [INFO] Task started: CheckM
[2023-06-29 21:52:33,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708855.1_ASM1670885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708855.1_ASM1670885v1_genomic.fna/checkm_input GCA_016708855.1_ASM1670885v1_genomic.fna/checkm_result
[2023-06-29 21:53:13,052] [INFO] Task succeeded: CheckM
[2023-06-29 21:53:13,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 21:53:13,078] [INFO] ===== Completeness check finished =====
[2023-06-29 21:53:13,078] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:53:13,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708855.1_ASM1670885v1_genomic.fna/markers.fasta)
[2023-06-29 21:53:13,079] [INFO] Task started: Blastn
[2023-06-29 21:53:13,079] [INFO] Running command: blastn -query GCA_016708855.1_ASM1670885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdefef45c-594b-4578-ab72-7f14019d520a/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708855.1_ASM1670885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:53:14,407] [INFO] Task succeeded: Blastn
[2023-06-29 21:53:14,412] [INFO] Selected 11 target genomes.
[2023-06-29 21:53:14,412] [INFO] Target genome list was writen to GCA_016708855.1_ASM1670885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:53:14,421] [INFO] Task started: fastANI
[2023-06-29 21:53:14,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgff35d73c-7428-4c9b-b4ea-fc2abb2dceea/GCA_016708855.1_ASM1670885v1_genomic.fna.gz --refList GCA_016708855.1_ASM1670885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708855.1_ASM1670885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:53:23,006] [INFO] Task succeeded: fastANI
[2023-06-29 21:53:23,018] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:53:23,018] [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
GCA_016704565.1	s__GCA-2748155 sp016704565	98.5482	1093	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	97.96	97.36	0.89	0.86	3	conclusive
GCA_016707175.1	s__GCA-2748155 sp016707175	84.2607	840	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	98.89	98.81	0.91	0.85	4	-
GCA_016710645.1	s__GCA-2748155 sp016710645	80.4319	534	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711095.1	s__GCA-2748155 sp016711095	80.3983	560	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710385.1	s__GCA-2748155 sp016710385	80.3594	580	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__GCA-2748155	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.8215	407	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	78.6686	408	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_900104525.1	s__Pedococcus dokdonensis	78.6628	378	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000184685.1	s__Intrasporangium calvum	78.5695	361	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Intrasporangium	95.0	99.10	99.10	0.92	0.92	2	-
GCF_014518425.1	s__Terrabacter sp014518425	78.4066	390	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297495.1	s__Janibacter hoylei	78.0693	292	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 21:53:23,021] [INFO] GTDB search result was written to GCA_016708855.1_ASM1670885v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:53:23,021] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:53:23,025] [INFO] DFAST_QC result json was written to GCA_016708855.1_ASM1670885v1_genomic.fna/dqc_result.json
[2023-06-29 21:53:23,025] [INFO] DFAST_QC completed!
[2023-06-29 21:53:23,026] [INFO] Total running time: 0h1m18s