[2024-01-24 14:46:55,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgd989b69b-903f-46ac-8c2c-cf8906627f64/dqc_reference
[2024-01-24 14:46:58,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,017] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg90ec6169-126a-48e4-a153-345e32457b51/GCF_006385785.1_ASM638578v1_genomic.fna.gz | prodigal -d GCF_006385785.1_ASM638578v1_genomic.fna/cds.fna -a GCF_006385785.1_ASM638578v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:02,957] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:02,957] [INFO] Task started: HMMsearch
[2024-01-24 14:47:02,957] [INFO] Running command: hmmsearch --tblout GCF_006385785.1_ASM638578v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd989b69b-903f-46ac-8c2c-cf8906627f64/dqc_reference/reference_markers.hmm GCF_006385785.1_ASM638578v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:03,273] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:03,274] [INFO] Found 6/6 markers.
[2024-01-24 14:47:03,296] [INFO] Query marker FASTA was written to GCF_006385785.1_ASM638578v1_genomic.fna/markers.fasta
[2024-01-24 14:47:03,297] [INFO] Task started: Blastn
[2024-01-24 14:47:03,297] [INFO] Running command: blastn -query GCF_006385785.1_ASM638578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd989b69b-903f-46ac-8c2c-cf8906627f64/dqc_reference/reference_markers.fasta -out GCF_006385785.1_ASM638578v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:04,380] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:04,386] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:04,386] [INFO] Target genome list was writen to GCF_006385785.1_ASM638578v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:04,425] [INFO] Task started: fastANI
[2024-01-24 14:47:04,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ec6169-126a-48e4-a153-345e32457b51/GCF_006385785.1_ASM638578v1_genomic.fna.gz --refList GCF_006385785.1_ASM638578v1_genomic.fna/target_genomes.txt --output GCF_006385785.1_ASM638578v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:12,024] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:12,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd989b69b-903f-46ac-8c2c-cf8906627f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:12,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd989b69b-903f-46ac-8c2c-cf8906627f64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:12,040] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:12,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:12,040] [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 shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	100.0	663	663	95	conclusive
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	92.8057	516	663	95	below_threshold
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	92.7435	517	663	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	92.7163	524	663	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	92.6901	517	663	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	92.6879	540	663	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	92.369	500	663	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	92.0571	508	663	95	below_threshold
Streptococcus pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	91.9965	512	663	95	below_threshold
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	91.9248	456	663	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	91.6112	520	663	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	91.5773	509	663	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	86.5961	470	663	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.0449	133	663	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.7962	117	663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:12,042] [INFO] DFAST Taxonomy check result was written to GCF_006385785.1_ASM638578v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:12,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:12,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:12,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd989b69b-903f-46ac-8c2c-cf8906627f64/dqc_reference/checkm_data
[2024-01-24 14:47:12,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:12,070] [INFO] Task started: CheckM
[2024-01-24 14:47:12,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385785.1_ASM638578v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385785.1_ASM638578v1_genomic.fna/checkm_input GCF_006385785.1_ASM638578v1_genomic.fna/checkm_result
[2024-01-24 14:47:34,495] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:34,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:34,519] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:34,519] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:34,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385785.1_ASM638578v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:34,521] [INFO] Task started: Blastn
[2024-01-24 14:47:34,521] [INFO] Running command: blastn -query GCF_006385785.1_ASM638578v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd989b69b-903f-46ac-8c2c-cf8906627f64/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385785.1_ASM638578v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:35,555] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:35,562] [INFO] Selected 22 target genomes.
[2024-01-24 14:47:35,563] [INFO] Target genome list was writen to GCF_006385785.1_ASM638578v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:35,596] [INFO] Task started: fastANI
[2024-01-24 14:47:35,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ec6169-126a-48e4-a153-345e32457b51/GCF_006385785.1_ASM638578v1_genomic.fna.gz --refList GCF_006385785.1_ASM638578v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385785.1_ASM638578v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:47,980] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:47,999] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:48,000] [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_006385785.1	s__Streptococcus shenyangsis	100.0	663	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.31	95.07	0.93	0.89	5	conclusive
GCF_000222785.1	s__Streptococcus mitis_N	94.7068	567	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.68	95.43	0.88	0.87	9	-
GCF_003943935.1	s__Streptococcus mitis_BK	94.3047	566	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000257905.1	s__Streptococcus mitis_L	94.2946	548	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722685.1	s__Streptococcus mitis_M	94.2654	582	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221085.1	s__Streptococcus sp905221085	93.9245	539	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001074825.1	s__Streptococcus pseudopneumoniae_C	93.5503	526	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0354	97.20	97.20	0.89	0.89	2	-
GCF_002860905.1	s__Streptococcus oralis_BA	93.1743	533	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.58	98.58	0.96	0.96	2	-
GCA_018364455.1	s__Streptococcus mitis_BR	93.1644	497	663	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	93.0978	506	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860865.1	s__Streptococcus mitis_AT	93.0458	535	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.74	95.72	0.90	0.90	3	-
GCF_000148545.1	s__Streptococcus mitis_C	92.9879	493	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.02	95.02	0.84	0.84	2	-
GCF_002005545.1	s__Streptococcus mitis_I	92.9257	529	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.10	95.10	0.88	0.88	2	-
GCF_001076775.1	s__Streptococcus pseudopneumoniae_G	92.8593	520	663	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	92.7732	535	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001070815.1	s__Streptococcus pseudopneumoniae_P	92.7473	501	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496155.1	s__Streptococcus mitis_BQ	92.7447	531	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148585.2	s__Streptococcus mitis	92.6549	518	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.33	95.07	0.91	0.87	25	-
GCF_001281025.1	s__Streptococcus mitis_AK	92.6338	528	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.14	95.01	0.88	0.86	7	-
GCF_001810785.1	s__Streptococcus sp001810785	92.3958	513	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144795.1	s__Streptococcus mitis_BB	92.1197	507	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.49	95.02	0.87	0.86	5	-
GCF_003942865.1	s__Streptococcus mitis_BI	92.035	519	663	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 14:47:48,002] [INFO] GTDB search result was written to GCF_006385785.1_ASM638578v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:48,002] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:48,009] [INFO] DFAST_QC result json was written to GCF_006385785.1_ASM638578v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:48,009] [INFO] DFAST_QC completed!
[2024-01-24 14:47:48,010] [INFO] Total running time: 0h0m53s