[2024-01-24 10:47:22,631] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:22,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:22,736] [INFO] DQC Reference Directory: /var/lib/cwl/stgf080fc8d-d174-4785-ab7d-c60f0c0bc299/dqc_reference
[2024-01-24 10:47:26,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,183] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stgf816ad6b-c0c8-4317-b46c-467146fccd31/GCF_020736445.1_ASM2073644v1_genomic.fna.gz | prodigal -d GCF_020736445.1_ASM2073644v1_genomic.fna/cds.fna -a GCF_020736445.1_ASM2073644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:33,972] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:33,973] [INFO] Task started: HMMsearch
[2024-01-24 10:47:33,973] [INFO] Running command: hmmsearch --tblout GCF_020736445.1_ASM2073644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf080fc8d-d174-4785-ab7d-c60f0c0bc299/dqc_reference/reference_markers.hmm GCF_020736445.1_ASM2073644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:34,190] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:34,191] [INFO] Found 6/6 markers.
[2024-01-24 10:47:34,858] [INFO] Query marker FASTA was written to GCF_020736445.1_ASM2073644v1_genomic.fna/markers.fasta
[2024-01-24 10:47:34,859] [INFO] Task started: Blastn
[2024-01-24 10:47:34,859] [INFO] Running command: blastn -query GCF_020736445.1_ASM2073644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf080fc8d-d174-4785-ab7d-c60f0c0bc299/dqc_reference/reference_markers.fasta -out GCF_020736445.1_ASM2073644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:35,758] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:35,762] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:35,763] [INFO] Target genome list was writen to GCF_020736445.1_ASM2073644v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:35,773] [INFO] Task started: fastANI
[2024-01-24 10:47:35,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgf816ad6b-c0c8-4317-b46c-467146fccd31/GCF_020736445.1_ASM2073644v1_genomic.fna.gz --refList GCF_020736445.1_ASM2073644v1_genomic.fna/target_genomes.txt --output GCF_020736445.1_ASM2073644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:46,067] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:46,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf080fc8d-d174-4785-ab7d-c60f0c0bc299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:46,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf080fc8d-d174-4785-ab7d-c60f0c0bc299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:46,086] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:47:46,086] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:47:46,086] [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
Dermabacter jinjuensis	strain=FDAARGOS_1555	GCA_020736445.1	1667168	1667168	type	True	100.0	789	791	95	inconclusive
Dermabacter jinjuensis	strain=32T	GCA_002443115.1	1667168	1667168	type	True	99.9931	791	791	95	inconclusive
Dermabacter hominis	strain=NBRC 106157	GCA_001570785.1	36740	36740	type	True	95.9242	653	791	95	inconclusive
Dermabacter vaginalis	strain=AD1-86	GCA_001678905.1	1630135	1630135	type	True	87.2491	635	791	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	78.0172	168	791	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	77.92	166	791	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	77.8181	171	791	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	77.6387	154	791	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	77.4049	162	791	95	below_threshold
Brachybacterium subflavum	strain=CFH 10395	GCA_009299795.1	2585206	2585206	type	True	77.3176	169	791	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	76.8904	68	791	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.4768	83	791	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.4236	91	791	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	75.7457	57	791	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	75.6309	65	791	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:46,088] [INFO] DFAST Taxonomy check result was written to GCF_020736445.1_ASM2073644v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:46,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:46,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:46,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf080fc8d-d174-4785-ab7d-c60f0c0bc299/dqc_reference/checkm_data
[2024-01-24 10:47:46,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:46,114] [INFO] Task started: CheckM
[2024-01-24 10:47:46,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020736445.1_ASM2073644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020736445.1_ASM2073644v1_genomic.fna/checkm_input GCF_020736445.1_ASM2073644v1_genomic.fna/checkm_result
[2024-01-24 10:48:14,176] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:14,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:14,203] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:14,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:14,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020736445.1_ASM2073644v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:14,204] [INFO] Task started: Blastn
[2024-01-24 10:48:14,204] [INFO] Running command: blastn -query GCF_020736445.1_ASM2073644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf080fc8d-d174-4785-ab7d-c60f0c0bc299/dqc_reference/reference_markers_gtdb.fasta -out GCF_020736445.1_ASM2073644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:15,601] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:15,605] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:15,605] [INFO] Target genome list was writen to GCF_020736445.1_ASM2073644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:15,684] [INFO] Task started: fastANI
[2024-01-24 10:48:15,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgf816ad6b-c0c8-4317-b46c-467146fccd31/GCF_020736445.1_ASM2073644v1_genomic.fna.gz --refList GCF_020736445.1_ASM2073644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020736445.1_ASM2073644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:27,510] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:27,530] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:27,530] [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_001570785.1	s__Dermabacter hominis	95.9242	653	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Dermabacter	95.0	96.01	95.75	0.93	0.91	8	conclusive
GCF_001678905.1	s__Dermabacter vaginalis	87.2623	634	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Dermabacter	95.0	96.46	96.40	0.93	0.93	3	-
GCF_001403775.1	s__Dermabacter massiliensis_A	84.9629	583	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Dermabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191425.1	s__Helcobacillus massiliensis	79.3602	190	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Helcobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871795.1	s__Brachybacterium sp002871795	78.1831	158	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163655.1	s__Brachybacterium nesterenkovii	78.0373	167	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005490785.1	s__Brachybacterium sp005490785	77.7131	187	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623465.1	s__Brachybacterium halotolerans	77.6182	155	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130585.1	s__Brachybacterium endophyticum	77.5965	143	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023405.1	s__Brachybacterium faecium	77.3649	162	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299795.1	s__Brachybacterium subflavum	77.333	168	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873755.1	s__Amycolatopsis lexingtonensis	77.0493	69	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCA_019118275.1	s__Brachybacterium merdavium	76.8901	95	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220945.1	s__Amycolatopsis mediterranei	76.7731	67	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	0.99	7	-
GCF_001420995.1	s__Pseudonocardia sp001420995	76.1181	58	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.03	98.66	0.91	0.86	8	-
GCF_003937945.1	s__Amycolatopsis eburnea	75.6309	65	791	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,532] [INFO] GTDB search result was written to GCF_020736445.1_ASM2073644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:27,533] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:27,536] [INFO] DFAST_QC result json was written to GCF_020736445.1_ASM2073644v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:27,537] [INFO] DFAST_QC completed!
[2024-01-24 10:48:27,537] [INFO] Total running time: 0h1m5s