[2024-01-24 12:46:56,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:56,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:56,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg207f8a3b-5bdc-41b9-9f78-fdcca9e2762e/dqc_reference
[2024-01-24 12:46:58,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:58,336] [INFO] Task started: Prodigal
[2024-01-24 12:46:58,336] [INFO] Running command: gunzip -c /var/lib/cwl/stga048b83b-17ce-4966-b169-2fcad6c0d24d/GCF_004136565.1_ASM413656v1_genomic.fna.gz | prodigal -d GCF_004136565.1_ASM413656v1_genomic.fna/cds.fna -a GCF_004136565.1_ASM413656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:05,006] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:05,007] [INFO] Task started: HMMsearch
[2024-01-24 12:47:05,007] [INFO] Running command: hmmsearch --tblout GCF_004136565.1_ASM413656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg207f8a3b-5bdc-41b9-9f78-fdcca9e2762e/dqc_reference/reference_markers.hmm GCF_004136565.1_ASM413656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:05,241] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:05,242] [INFO] Found 6/6 markers.
[2024-01-24 12:47:05,263] [INFO] Query marker FASTA was written to GCF_004136565.1_ASM413656v1_genomic.fna/markers.fasta
[2024-01-24 12:47:05,263] [INFO] Task started: Blastn
[2024-01-24 12:47:05,263] [INFO] Running command: blastn -query GCF_004136565.1_ASM413656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg207f8a3b-5bdc-41b9-9f78-fdcca9e2762e/dqc_reference/reference_markers.fasta -out GCF_004136565.1_ASM413656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:06,508] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:06,512] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:06,513] [INFO] Target genome list was writen to GCF_004136565.1_ASM413656v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:06,520] [INFO] Task started: fastANI
[2024-01-24 12:47:06,521] [INFO] Running command: fastANI --query /var/lib/cwl/stga048b83b-17ce-4966-b169-2fcad6c0d24d/GCF_004136565.1_ASM413656v1_genomic.fna.gz --refList GCF_004136565.1_ASM413656v1_genomic.fna/target_genomes.txt --output GCF_004136565.1_ASM413656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:15,376] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:15,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg207f8a3b-5bdc-41b9-9f78-fdcca9e2762e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:15,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg207f8a3b-5bdc-41b9-9f78-fdcca9e2762e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:15,397] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:47:15,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:15,398] [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
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	100.0	779	780	95	conclusive
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	99.999	779	780	95	conclusive
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	99.1312	751	780	95	conclusive
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	79.7258	379	780	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	79.3845	413	780	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	79.3498	381	780	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	79.2554	373	780	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	79.2494	403	780	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_004136575.1	592378	592378	type	True	78.7275	278	780	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_009734705.1	592378	592378	type	True	78.6984	283	780	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	78.5744	275	780	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.3838	256	780	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	77.7526	134	780	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.6609	214	780	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.5829	218	780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:15,400] [INFO] DFAST Taxonomy check result was written to GCF_004136565.1_ASM413656v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:15,401] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:15,401] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:15,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg207f8a3b-5bdc-41b9-9f78-fdcca9e2762e/dqc_reference/checkm_data
[2024-01-24 12:47:15,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:15,427] [INFO] Task started: CheckM
[2024-01-24 12:47:15,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004136565.1_ASM413656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004136565.1_ASM413656v1_genomic.fna/checkm_input GCF_004136565.1_ASM413656v1_genomic.fna/checkm_result
[2024-01-24 12:47:51,897] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:51,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:51,917] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:51,917] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:51,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004136565.1_ASM413656v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:51,918] [INFO] Task started: Blastn
[2024-01-24 12:47:51,918] [INFO] Running command: blastn -query GCF_004136565.1_ASM413656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg207f8a3b-5bdc-41b9-9f78-fdcca9e2762e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004136565.1_ASM413656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:53,993] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:53,995] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:53,996] [INFO] Target genome list was writen to GCF_004136565.1_ASM413656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:54,008] [INFO] Task started: fastANI
[2024-01-24 12:47:54,009] [INFO] Running command: fastANI --query /var/lib/cwl/stga048b83b-17ce-4966-b169-2fcad6c0d24d/GCF_004136565.1_ASM413656v1_genomic.fna.gz --refList GCF_004136565.1_ASM413656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004136565.1_ASM413656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:01,969] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:01,980] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:01,980] [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_001570865.1	s__Rothia kristinae	99.1312	751	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	conclusive
GCF_004136635.1	s__Rothia halotolerans	81.4267	471	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580365.1	s__Kocuria turfanensis	79.7258	379	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_001482365.1	s__Kocuria flava	79.3552	415	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_014636775.1	s__Kocuria dechangensis	79.3371	382	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483755.1	s__Kocuria polaris_A	79.3029	372	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006094695.1	s__Kocuria rosea	79.2681	381	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_007666205.1	s__Kocuria palustris_A	79.001	318	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007681555.1	s__Kocuria salsicia	78.9934	322	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.09	95.42	0.92	0.89	8	-
GCF_004136575.1	s__Rothia koreensis	78.745	276	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.36	98.73	0.95	0.92	3	-
GCF_000710345.2	s__Rothia sp000710345	78.5543	312	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001766675.1	s__Arthrobacter_G sp001766675	77.6715	214	780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:01,981] [INFO] GTDB search result was written to GCF_004136565.1_ASM413656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:01,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:01,986] [INFO] DFAST_QC result json was written to GCF_004136565.1_ASM413656v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:01,986] [INFO] DFAST_QC completed!
[2024-01-24 12:48:01,986] [INFO] Total running time: 0h1m5s