[2024-01-24 13:27:46,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg60d51ead-de65-446a-9487-e8b2dd647ea2/dqc_reference
[2024-01-24 13:27:47,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,873] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,873] [INFO] Running command: gunzip -c /var/lib/cwl/stge53e1857-c7da-4281-ba92-7e91876e8fb9/GCF_000148565.1_ASM14856v1_genomic.fna.gz | prodigal -d GCF_000148565.1_ASM14856v1_genomic.fna/cds.fna -a GCF_000148565.1_ASM14856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:52,693] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:52,693] [INFO] Task started: HMMsearch
[2024-01-24 13:27:52,693] [INFO] Running command: hmmsearch --tblout GCF_000148565.1_ASM14856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60d51ead-de65-446a-9487-e8b2dd647ea2/dqc_reference/reference_markers.hmm GCF_000148565.1_ASM14856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:53,021] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:53,022] [INFO] Found 6/6 markers.
[2024-01-24 13:27:53,047] [INFO] Query marker FASTA was written to GCF_000148565.1_ASM14856v1_genomic.fna/markers.fasta
[2024-01-24 13:27:53,048] [INFO] Task started: Blastn
[2024-01-24 13:27:53,048] [INFO] Running command: blastn -query GCF_000148565.1_ASM14856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60d51ead-de65-446a-9487-e8b2dd647ea2/dqc_reference/reference_markers.fasta -out GCF_000148565.1_ASM14856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:53,702] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:53,706] [INFO] Selected 10 target genomes.
[2024-01-24 13:27:53,706] [INFO] Target genome list was writen to GCF_000148565.1_ASM14856v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:53,718] [INFO] Task started: fastANI
[2024-01-24 13:27:53,719] [INFO] Running command: fastANI --query /var/lib/cwl/stge53e1857-c7da-4281-ba92-7e91876e8fb9/GCF_000148565.1_ASM14856v1_genomic.fna.gz --refList GCF_000148565.1_ASM14856v1_genomic.fna/target_genomes.txt --output GCF_000148565.1_ASM14856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:58,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:58,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60d51ead-de65-446a-9487-e8b2dd647ea2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:58,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60d51ead-de65-446a-9487-e8b2dd647ea2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:58,106] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:27:58,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:58,107] [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
Streptococcus oralis	strain=ATCC 35037	GCA_000148565.2	1303	1303	type	True	100.0	615	616	95	conclusive
Streptococcus oralis	strain=CCUG 13229	GCA_002014885.1	1303	1303	type	True	99.9851	616	616	95	conclusive
Streptococcus oralis	strain=CCUG 24891	GCA_001639375.1	1303	1303	type	True	99.9827	613	616	95	conclusive
Streptococcus oralis	strain=ATCC 35037	GCA_000164095.1	1303	1303	type	True	99.9797	616	616	95	conclusive
Streptococcus oralis	strain=FDAARGOS_1020	GCA_016127555.1	1303	1303	type	True	99.9797	616	616	95	conclusive
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	92.3913	514	616	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	86.8561	460	616	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	86.7063	465	616	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.6351	112	616	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	77.9728	104	616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:58,108] [INFO] DFAST Taxonomy check result was written to GCF_000148565.1_ASM14856v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:58,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:58,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:58,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60d51ead-de65-446a-9487-e8b2dd647ea2/dqc_reference/checkm_data
[2024-01-24 13:27:58,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:58,134] [INFO] Task started: CheckM
[2024-01-24 13:27:58,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000148565.1_ASM14856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000148565.1_ASM14856v1_genomic.fna/checkm_input GCF_000148565.1_ASM14856v1_genomic.fna/checkm_result
[2024-01-24 13:28:20,104] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:20,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:20,123] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:20,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:20,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000148565.1_ASM14856v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:20,124] [INFO] Task started: Blastn
[2024-01-24 13:28:20,124] [INFO] Running command: blastn -query GCF_000148565.1_ASM14856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60d51ead-de65-446a-9487-e8b2dd647ea2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000148565.1_ASM14856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:20,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:20,972] [INFO] Selected 24 target genomes.
[2024-01-24 13:28:20,972] [INFO] Target genome list was writen to GCF_000148565.1_ASM14856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:21,007] [INFO] Task started: fastANI
[2024-01-24 13:28:21,007] [INFO] Running command: fastANI --query /var/lib/cwl/stge53e1857-c7da-4281-ba92-7e91876e8fb9/GCF_000148565.1_ASM14856v1_genomic.fna.gz --refList GCF_000148565.1_ASM14856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000148565.1_ASM14856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:31,987] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:32,006] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:32,006] [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_900637025.1	s__Streptococcus oralis	99.9872	615	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.04	95.11	0.90	0.80	39	conclusive
GCF_003942675.1	s__Streptococcus oralis_BC	94.9232	522	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.25	95.12	0.91	0.89	7	-
GCA_905371745.1	s__Streptococcus sp905371745	94.8433	446	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.30	95.17	0.90	0.90	6	-
GCF_001579025.1	s__Streptococcus oralis_X	94.8144	535	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000960035.1	s__Streptococcus oralis_G	94.7924	528	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.09	95.04	0.93	0.89	6	-
GCA_905221305.1	s__Streptococcus sp905221305	94.7572	525	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	95.15	0.98	0.91	6	-
GCF_001983955.1	s__Streptococcus oralis_H	94.7263	525	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.01	95.40	0.92	0.88	7	-
GCF_001075675.1	s__Streptococcus oralis_V	94.7243	531	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096435.1	s__Streptococcus oralis_AA	94.7035	550	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.40	98.81	0.98	0.95	3	-
GCF_016127915.1	s__Streptococcus oralis_BO	94.6375	541	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000831085.1	s__Streptococcus sp000831085	94.5887	538	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.77	96.77	0.93	0.93	2	-
GCA_900546335.1	s__Streptococcus sp900546335	94.3936	441	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221255.1	s__Streptococcus sp905221255	93.7987	534	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	97.53	0.94	0.94	3	-
GCF_001578935.1	s__Streptococcus oralis_R	93.5585	535	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.60	95.35	0.80	0.78	3	-
GCF_003143695.2	s__Streptococcus halitosis	93.3184	520	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.61	95.24	0.91	0.88	11	-
GCF_003942795.1	s__Streptococcus mitis_BJ	93.2946	508	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.60	99.60	0.93	0.93	2	-
GCA_905221415.1	s__Streptococcus sp905221415	93.1709	499	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002356415.1	s__Streptococcus oralis_F	92.8932	519	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.57	95.26	0.91	0.90	6	-
GCA_905221385.1	s__Streptococcus sp905221385	92.6078	499	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.72	97.71	0.92	0.92	3	-
GCF_002096685.1	s__Streptococcus oralis_AD	92.5409	512	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353325.1	s__Streptococcus sp004353325	92.3862	515	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016028255.1	s__Streptococcus oralis_AC	91.9635	511	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.16	95.70	0.95	0.93	5	-
GCF_003944215.1	s__Streptococcus oralis_BI	91.9087	482	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104285.1	s__Streptococcus sp900104285	91.5745	489	616	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:32,008] [INFO] GTDB search result was written to GCF_000148565.1_ASM14856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:32,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:32,013] [INFO] DFAST_QC result json was written to GCF_000148565.1_ASM14856v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:32,013] [INFO] DFAST_QC completed!
[2024-01-24 13:28:32,013] [INFO] Total running time: 0h0m46s