[2023-06-05 02:23:19,677] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:23:19,680] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:23:19,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg66410497-0f34-4831-9564-ca4066e5dfad/dqc_reference
[2023-06-05 02:23:21,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:23:21,208] [INFO] Task started: Prodigal
[2023-06-05 02:23:21,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg41f0d82a-9d03-4500-8a6c-a908aeeacbbf/GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna.gz | prodigal -d GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/cds.fna -a GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:23:28,178] [INFO] Task succeeded: Prodigal
[2023-06-05 02:23:28,180] [INFO] Task started: HMMsearch
[2023-06-05 02:23:28,180] [INFO] Running command: hmmsearch --tblout GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66410497-0f34-4831-9564-ca4066e5dfad/dqc_reference/reference_markers.hmm GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:23:28,499] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:23:28,501] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg41f0d82a-9d03-4500-8a6c-a908aeeacbbf/GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna.gz]
[2023-06-05 02:23:28,540] [INFO] Query marker FASTA was written to GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/markers.fasta
[2023-06-05 02:23:28,541] [INFO] Task started: Blastn
[2023-06-05 02:23:28,541] [INFO] Running command: blastn -query GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/markers.fasta -db /var/lib/cwl/stg66410497-0f34-4831-9564-ca4066e5dfad/dqc_reference/reference_markers.fasta -out GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:23:29,223] [INFO] Task succeeded: Blastn
[2023-06-05 02:23:29,227] [INFO] Selected 32 target genomes.
[2023-06-05 02:23:29,227] [INFO] Target genome list was writen to GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/target_genomes.txt
[2023-06-05 02:23:29,286] [INFO] Task started: fastANI
[2023-06-05 02:23:29,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f0d82a-9d03-4500-8a6c-a908aeeacbbf/GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna.gz --refList GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/target_genomes.txt --output GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:23:50,323] [INFO] Task succeeded: fastANI
[2023-06-05 02:23:50,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66410497-0f34-4831-9564-ca4066e5dfad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:23:50,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66410497-0f34-4831-9564-ca4066e5dfad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:23:50,348] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:23:50,348] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:23:50,348] [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
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	75.8994	59	774	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	75.8887	55	774	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	75.8637	56	774	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	75.8637	56	774	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	75.8507	58	774	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	75.7776	61	774	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	75.6022	66	774	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	75.5398	54	774	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	75.5084	54	774	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	75.1684	59	774	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	75.1279	78	774	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.0931	76	774	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	75.0861	86	774	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	75.083	72	774	95	below_threshold
Quadrisphaera setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	75.0541	72	774	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	75.0502	72	774	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	75.0502	72	774	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	75.0202	61	774	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	75.0071	108	774	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	75.0024	63	774	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	74.9586	53	774	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	74.9075	61	774	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:23:50,350] [INFO] DFAST Taxonomy check result was written to GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/tc_result.tsv
[2023-06-05 02:23:50,351] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:23:50,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:23:50,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66410497-0f34-4831-9564-ca4066e5dfad/dqc_reference/checkm_data
[2023-06-05 02:23:50,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:23:50,383] [INFO] Task started: CheckM
[2023-06-05 02:23:50,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/checkm_input GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/checkm_result
[2023-06-05 02:24:16,230] [INFO] Task succeeded: CheckM
[2023-06-05 02:24:16,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:24:16,252] [INFO] ===== Completeness check finished =====
[2023-06-05 02:24:16,253] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:24:16,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/markers.fasta)
[2023-06-05 02:24:16,253] [INFO] Task started: Blastn
[2023-06-05 02:24:16,254] [INFO] Running command: blastn -query GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/markers.fasta -db /var/lib/cwl/stg66410497-0f34-4831-9564-ca4066e5dfad/dqc_reference/reference_markers_gtdb.fasta -out GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:24:17,242] [INFO] Task succeeded: Blastn
[2023-06-05 02:24:17,245] [INFO] Selected 10 target genomes.
[2023-06-05 02:24:17,246] [INFO] Target genome list was writen to GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:24:17,250] [INFO] Task started: fastANI
[2023-06-05 02:24:17,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f0d82a-9d03-4500-8a6c-a908aeeacbbf/GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna.gz --refList GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/target_genomes_gtdb.txt --output GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:24:24,421] [INFO] Task succeeded: fastANI
[2023-06-05 02:24:24,434] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:24:24,434] [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_902790175.1	s__UBA2862 sp902790175	100.0	770	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902773515.1	s__UBA2862 sp902773515	94.0888	514	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765395.1	s__UBA2862 sp902765395	86.098	576	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800625.1	s__UBA2862 sp902800625	86.0033	591	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	97.74	97.74	0.88	0.88	2	-
GCA_902799045.1	s__UBA2862 sp902799045	85.8175	548	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315585.1	s__UBA2862 sp900315585	85.6972	554	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	98.00	97.28	0.87	0.83	5	-
GCA_902777335.1	s__UBA2862 sp902777335	84.6023	565	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540445.1	s__UBA2862 sp017540445	84.3135	469	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017480045.1	s__UBA2862 sp017480045	83.7974	449	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793245.1	s__RUG563 sp902793245	78.611	175	774	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG563	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:24:24,436] [INFO] GTDB search result was written to GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/result_gtdb.tsv
[2023-06-05 02:24:24,436] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:24:24,440] [INFO] DFAST_QC result json was written to GCA_902790175.1_Rumen_uncultured_genome_RUG13544_genomic.fna/dqc_result.json
[2023-06-05 02:24:24,441] [INFO] DFAST_QC completed!
[2023-06-05 02:24:24,441] [INFO] Total running time: 0h1m5s