[2024-01-24 14:54:55,632] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:55,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:55,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb8c86e3-1d92-4714-9037-9de829cc85dc/dqc_reference
[2024-01-24 14:54:57,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,028] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,028] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf70e51b-bd69-4443-9bf8-4e2b535cb0ce/GCF_014646815.1_ASM1464681v1_genomic.fna.gz | prodigal -d GCF_014646815.1_ASM1464681v1_genomic.fna/cds.fna -a GCF_014646815.1_ASM1464681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:10,967] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:10,968] [INFO] Task started: HMMsearch
[2024-01-24 14:55:10,968] [INFO] Running command: hmmsearch --tblout GCF_014646815.1_ASM1464681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb8c86e3-1d92-4714-9037-9de829cc85dc/dqc_reference/reference_markers.hmm GCF_014646815.1_ASM1464681v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:11,272] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:11,273] [INFO] Found 6/6 markers.
[2024-01-24 14:55:11,323] [INFO] Query marker FASTA was written to GCF_014646815.1_ASM1464681v1_genomic.fna/markers.fasta
[2024-01-24 14:55:11,324] [INFO] Task started: Blastn
[2024-01-24 14:55:11,324] [INFO] Running command: blastn -query GCF_014646815.1_ASM1464681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb8c86e3-1d92-4714-9037-9de829cc85dc/dqc_reference/reference_markers.fasta -out GCF_014646815.1_ASM1464681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:12,612] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:12,615] [INFO] Selected 21 target genomes.
[2024-01-24 14:55:12,615] [INFO] Target genome list was writen to GCF_014646815.1_ASM1464681v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:12,623] [INFO] Task started: fastANI
[2024-01-24 14:55:12,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf70e51b-bd69-4443-9bf8-4e2b535cb0ce/GCF_014646815.1_ASM1464681v1_genomic.fna.gz --refList GCF_014646815.1_ASM1464681v1_genomic.fna/target_genomes.txt --output GCF_014646815.1_ASM1464681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:30,651] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:30,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb8c86e3-1d92-4714-9037-9de829cc85dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:30,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb8c86e3-1d92-4714-9037-9de829cc85dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:30,669] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:30,669] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:30,669] [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
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	81.5453	671	1558	95	below_threshold
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	81.5388	768	1558	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	80.2627	639	1558	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	80.2155	629	1558	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	80.1446	668	1558	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.8856	687	1558	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.8812	665	1558	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	79.8118	540	1558	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.6919	636	1558	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	79.6786	532	1558	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.623	479	1558	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	79.516	542	1558	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	79.4638	473	1558	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.4539	586	1558	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	79.0733	499	1558	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	78.9846	444	1558	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.9465	519	1558	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.8683	540	1558	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	78.5425	464	1558	95	below_threshold
Mobilicoccus massiliensis	strain=SIT2	GCA_000826525.2	1522310	1522310	type	True	78.4653	424	1558	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.3383	403	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:30,672] [INFO] DFAST Taxonomy check result was written to GCF_014646815.1_ASM1464681v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:30,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:30,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:30,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb8c86e3-1d92-4714-9037-9de829cc85dc/dqc_reference/checkm_data
[2024-01-24 14:55:30,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:30,725] [INFO] Task started: CheckM
[2024-01-24 14:55:30,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646815.1_ASM1464681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646815.1_ASM1464681v1_genomic.fna/checkm_input GCF_014646815.1_ASM1464681v1_genomic.fna/checkm_result
[2024-01-24 14:56:42,275] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:42,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:42,298] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:42,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:42,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646815.1_ASM1464681v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:42,299] [INFO] Task started: Blastn
[2024-01-24 14:56:42,299] [INFO] Running command: blastn -query GCF_014646815.1_ASM1464681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb8c86e3-1d92-4714-9037-9de829cc85dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646815.1_ASM1464681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:44,333] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:44,336] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:44,337] [INFO] Target genome list was writen to GCF_014646815.1_ASM1464681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:44,347] [INFO] Task started: fastANI
[2024-01-24 14:56:44,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf70e51b-bd69-4443-9bf8-4e2b535cb0ce/GCF_014646815.1_ASM1464681v1_genomic.fna.gz --refList GCF_014646815.1_ASM1464681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646815.1_ASM1464681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:59,446] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:59,461] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:59,461] [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_014646815.1	s__Terrabacter tumescens	100.0	1554	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_006716915.1	s__Terrabacter sp006716915	89.1768	1300	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991735.1	s__Terrabacter aerolatus	88.755	1202	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429185.1	s__Terrabacter sp001429185	88.2748	1255	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.06	99.06	0.95	0.95	2	-
GCF_000383675.1	s__Terrabacter sp000383675	88.1366	1254	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	88.0074	1243	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCA_000620545.1	s__Terrabacter sp000620545	86.9042	1116	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014518425.1	s__Terrabacter sp014518425	85.8792	1104	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716675.1	s__Humibacillus xanthopallidus	84.9512	1087	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717145.1	s__Humibacillus xanthopallidus_A	84.74	1106	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758225.1	s__Terracoccus sp001758225	81.3221	832	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:59,462] [INFO] GTDB search result was written to GCF_014646815.1_ASM1464681v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:59,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:59,467] [INFO] DFAST_QC result json was written to GCF_014646815.1_ASM1464681v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:59,467] [INFO] DFAST_QC completed!
[2024-01-24 14:56:59,467] [INFO] Total running time: 0h2m4s