[2023-06-19 03:48:17,263] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:48:17,265] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:48:17,265] [INFO] DQC Reference Directory: /var/lib/cwl/stgf60829a1-ae0a-4dac-8d46-9e7075c874a4/dqc_reference
[2023-06-19 03:48:19,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:48:19,244] [INFO] Task started: Prodigal
[2023-06-19 03:48:19,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg1caa7b20-5b47-4efd-bfaa-2eee547ac345/GCA_018373175.1_ASM1837317v1_genomic.fna.gz | prodigal -d GCA_018373175.1_ASM1837317v1_genomic.fna/cds.fna -a GCA_018373175.1_ASM1837317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:48:27,817] [INFO] Task succeeded: Prodigal
[2023-06-19 03:48:27,817] [INFO] Task started: HMMsearch
[2023-06-19 03:48:27,817] [INFO] Running command: hmmsearch --tblout GCA_018373175.1_ASM1837317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf60829a1-ae0a-4dac-8d46-9e7075c874a4/dqc_reference/reference_markers.hmm GCA_018373175.1_ASM1837317v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:48:28,075] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:48:28,077] [INFO] Found 6/6 markers.
[2023-06-19 03:48:28,105] [INFO] Query marker FASTA was written to GCA_018373175.1_ASM1837317v1_genomic.fna/markers.fasta
[2023-06-19 03:48:28,106] [INFO] Task started: Blastn
[2023-06-19 03:48:28,106] [INFO] Running command: blastn -query GCA_018373175.1_ASM1837317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf60829a1-ae0a-4dac-8d46-9e7075c874a4/dqc_reference/reference_markers.fasta -out GCA_018373175.1_ASM1837317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:48:29,202] [INFO] Task succeeded: Blastn
[2023-06-19 03:48:29,207] [INFO] Selected 12 target genomes.
[2023-06-19 03:48:29,208] [INFO] Target genome list was writen to GCA_018373175.1_ASM1837317v1_genomic.fna/target_genomes.txt
[2023-06-19 03:48:29,210] [INFO] Task started: fastANI
[2023-06-19 03:48:29,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg1caa7b20-5b47-4efd-bfaa-2eee547ac345/GCA_018373175.1_ASM1837317v1_genomic.fna.gz --refList GCA_018373175.1_ASM1837317v1_genomic.fna/target_genomes.txt --output GCA_018373175.1_ASM1837317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:48:37,080] [INFO] Task succeeded: fastANI
[2023-06-19 03:48:37,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf60829a1-ae0a-4dac-8d46-9e7075c874a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:48:37,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf60829a1-ae0a-4dac-8d46-9e7075c874a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:48:37,095] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:48:37,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:48:37,095] [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
Kocuria varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	88.0224	752	886	95	below_threshold
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	86.1834	713	886	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	85.9735	656	886	95	below_threshold
Kocuria tytonicola	strain=DSM 104133	GCA_003687455.1	2055946	2055946	type	True	85.8154	621	886	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_900177335.1	1049583	1049583	type	True	84.9127	688	886	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	84.9096	685	886	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	84.8976	689	886	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.4664	212	886	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.3783	221	886	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.0818	194	886	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	76.7507	117	886	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.7078	181	886	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:48:37,098] [INFO] DFAST Taxonomy check result was written to GCA_018373175.1_ASM1837317v1_genomic.fna/tc_result.tsv
[2023-06-19 03:48:37,098] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:48:37,099] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:48:37,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf60829a1-ae0a-4dac-8d46-9e7075c874a4/dqc_reference/checkm_data
[2023-06-19 03:48:37,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:48:37,135] [INFO] Task started: CheckM
[2023-06-19 03:48:37,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018373175.1_ASM1837317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018373175.1_ASM1837317v1_genomic.fna/checkm_input GCA_018373175.1_ASM1837317v1_genomic.fna/checkm_result
[2023-06-19 03:49:10,322] [INFO] Task succeeded: CheckM
[2023-06-19 03:49:10,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:49:10,347] [INFO] ===== Completeness check finished =====
[2023-06-19 03:49:10,347] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:49:10,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018373175.1_ASM1837317v1_genomic.fna/markers.fasta)
[2023-06-19 03:49:10,348] [INFO] Task started: Blastn
[2023-06-19 03:49:10,348] [INFO] Running command: blastn -query GCA_018373175.1_ASM1837317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf60829a1-ae0a-4dac-8d46-9e7075c874a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018373175.1_ASM1837317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:49:12,077] [INFO] Task succeeded: Blastn
[2023-06-19 03:49:12,082] [INFO] Selected 8 target genomes.
[2023-06-19 03:49:12,082] [INFO] Target genome list was writen to GCA_018373175.1_ASM1837317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:49:12,087] [INFO] Task started: fastANI
[2023-06-19 03:49:12,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg1caa7b20-5b47-4efd-bfaa-2eee547ac345/GCA_018373175.1_ASM1837317v1_genomic.fna.gz --refList GCA_018373175.1_ASM1837317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018373175.1_ASM1837317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:49:17,599] [INFO] Task succeeded: fastANI
[2023-06-19 03:49:17,611] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:49:17,611] [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_007681555.1	s__Kocuria salsicia	99.1946	850	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.09	95.42	0.92	0.89	8	conclusive
GCF_006539885.1	s__Kocuria varians	88.0401	751	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	-
GCF_000010285.1	s__Kocuria rhizophila_A	86.8571	748	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_003226895.2	s__Kocuria tytonis	86.1834	713	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667225.1	s__Kocuria rhizophila	85.9911	655	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.80	97.11	0.92	0.85	19	-
GCF_003687455.1	s__Kocuria tytonicola	85.8154	621	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.95	98.95	0.94	0.94	2	-
GCA_014652975.1	s__Kocuria marina	84.9705	689	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	98.16	96.52	0.91	0.86	16	-
GCF_000786655.1	s__Kocuria marina_A	84.8214	675	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	96.52	96.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-19 03:49:17,613] [INFO] GTDB search result was written to GCA_018373175.1_ASM1837317v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:49:17,613] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:49:17,616] [INFO] DFAST_QC result json was written to GCA_018373175.1_ASM1837317v1_genomic.fna/dqc_result.json
[2023-06-19 03:49:17,617] [INFO] DFAST_QC completed!
[2023-06-19 03:49:17,617] [INFO] Total running time: 0h1m0s