[2024-01-24 13:42:57,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg14eebc4d-bbc2-4522-bf34-b088adf4c093/dqc_reference
[2024-01-24 13:42:58,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,479] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,479] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c4af281-134e-46fe-8250-0e054412189e/GCF_024346585.1_ASM2434658v1_genomic.fna.gz | prodigal -d GCF_024346585.1_ASM2434658v1_genomic.fna/cds.fna -a GCF_024346585.1_ASM2434658v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:03,305] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:03,305] [INFO] Task started: HMMsearch
[2024-01-24 13:43:03,305] [INFO] Running command: hmmsearch --tblout GCF_024346585.1_ASM2434658v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14eebc4d-bbc2-4522-bf34-b088adf4c093/dqc_reference/reference_markers.hmm GCF_024346585.1_ASM2434658v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:03,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:03,582] [INFO] Found 6/6 markers.
[2024-01-24 13:43:03,609] [INFO] Query marker FASTA was written to GCF_024346585.1_ASM2434658v1_genomic.fna/markers.fasta
[2024-01-24 13:43:03,610] [INFO] Task started: Blastn
[2024-01-24 13:43:03,610] [INFO] Running command: blastn -query GCF_024346585.1_ASM2434658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14eebc4d-bbc2-4522-bf34-b088adf4c093/dqc_reference/reference_markers.fasta -out GCF_024346585.1_ASM2434658v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:04,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:04,210] [INFO] Selected 17 target genomes.
[2024-01-24 13:43:04,210] [INFO] Target genome list was writen to GCF_024346585.1_ASM2434658v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:04,236] [INFO] Task started: fastANI
[2024-01-24 13:43:04,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c4af281-134e-46fe-8250-0e054412189e/GCF_024346585.1_ASM2434658v1_genomic.fna.gz --refList GCF_024346585.1_ASM2434658v1_genomic.fna/target_genomes.txt --output GCF_024346585.1_ASM2434658v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:12,634] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:12,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14eebc4d-bbc2-4522-bf34-b088adf4c093/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:12,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14eebc4d-bbc2-4522-bf34-b088adf4c093/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:12,653] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:12,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:12,654] [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 toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	100.0	684	685	95	conclusive
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	94.2612	538	685	95	below_threshold
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	94.2605	533	685	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	94.2526	546	685	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	94.1788	550	685	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	93.2534	500	685	95	below_threshold
Streptococcus gwangjuense	strain=ChDC B345	GCA_003627155.1	1433513	1433513	type	True	93.2097	521	685	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	93.0016	508	685	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	92.9853	505	685	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	92.6515	529	685	95	below_threshold
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	92.582	455	685	95	below_threshold
Streptococcus pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	92.4976	529	685	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	92.0957	520	685	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	92.0435	495	685	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	87.2924	467	685	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	80.7006	137	685	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.8669	131	685	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:12,655] [INFO] DFAST Taxonomy check result was written to GCF_024346585.1_ASM2434658v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:12,656] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:12,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:12,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14eebc4d-bbc2-4522-bf34-b088adf4c093/dqc_reference/checkm_data
[2024-01-24 13:43:12,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:12,696] [INFO] Task started: CheckM
[2024-01-24 13:43:12,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346585.1_ASM2434658v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346585.1_ASM2434658v1_genomic.fna/checkm_input GCF_024346585.1_ASM2434658v1_genomic.fna/checkm_result
[2024-01-24 13:43:34,447] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:34,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:34,466] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:34,467] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:34,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346585.1_ASM2434658v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:34,468] [INFO] Task started: Blastn
[2024-01-24 13:43:34,468] [INFO] Running command: blastn -query GCF_024346585.1_ASM2434658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14eebc4d-bbc2-4522-bf34-b088adf4c093/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346585.1_ASM2434658v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:35,320] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:35,323] [INFO] Selected 26 target genomes.
[2024-01-24 13:43:35,323] [INFO] Target genome list was writen to GCF_024346585.1_ASM2434658v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:35,363] [INFO] Task started: fastANI
[2024-01-24 13:43:35,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c4af281-134e-46fe-8250-0e054412189e/GCF_024346585.1_ASM2434658v1_genomic.fna.gz --refList GCF_024346585.1_ASM2434658v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346585.1_ASM2434658v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:48,159] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:48,183] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:43:48,184] [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_001281025.1	s__Streptococcus mitis_AK	94.4028	554	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.14	95.01	0.88	0.86	7	-
GCF_000148585.2	s__Streptococcus mitis	94.2526	546	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.33	95.07	0.91	0.87	25	-
GCF_001070815.1	s__Streptococcus pseudopneumoniae_P	93.9257	518	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096925.1	s__Streptococcus mitis_AF	93.8789	497	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905187535.1	s__Streptococcus mitis_BS	93.8192	538	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001810785.1	s__Streptococcus sp001810785	93.8062	533	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220045.1	s__Streptococcus mitis_AP	93.7161	534	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096895.1	s__Streptococcus mitis_AH	93.7002	510	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096855.1	s__Streptococcus mitis_Y	93.6812	522	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.03	96.03	0.87	0.87	2	-
GCF_002096835.1	s__Streptococcus mitis_W	93.6015	510	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905369855.1	s__Streptococcus oralis_BN	93.5573	374	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650315.1	s__Streptococcus sp001650315	93.4823	511	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.60	97.60	0.91	0.91	2	-
GCF_000148525.1	s__Streptococcus mitis_H	93.2879	514	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096845.1	s__Streptococcus mitis_A	93.1553	524	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013305725.1	s__Streptococcus mitis_BO	93.0892	522	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626515.1	s__Streptococcus chosunense	93.0096	503	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.51	95.33	0.92	0.89	3	-
GCF_016658865.1	s__Streptococcus mitis_BT	92.9207	507	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001113365.1	s__Streptococcus pneumoniae_C	92.8962	544	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.29	95.29	0.90	0.90	2	-
GCA_905221085.1	s__Streptococcus sp905221085	92.8613	518	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001074975.1	s__Streptococcus pseudopneumoniae_D	92.6013	502	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001560895.1	s__Streptococcus mitis_Q	92.4419	511	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.95	95.95	0.90	0.90	2	-
GCF_001074825.1	s__Streptococcus pseudopneumoniae_C	92.4075	493	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0354	97.20	97.20	0.89	0.89	2	-
GCA_905221125.1	s__Streptococcus sp905221125	92.3834	528	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221235.1	s__Streptococcus sp905221235	92.264	511	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000430305.1	s__Streptococcus mitis_AW	92.2585	494	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0354	95.13	95.13	0.89	0.89	2	-
GCF_005844455.1	s__Streptococcus mitis_BF	91.6542	473	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:48,185] [INFO] GTDB search result was written to GCF_024346585.1_ASM2434658v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:48,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:48,190] [INFO] DFAST_QC result json was written to GCF_024346585.1_ASM2434658v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:48,190] [INFO] DFAST_QC completed!
[2024-01-24 13:43:48,190] [INFO] Total running time: 0h0m51s