[2023-06-29 16:19:17,218] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:19:17,220] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:19:17,221] [INFO] DQC Reference Directory: /var/lib/cwl/stgc539a103-8539-42b9-bbca-f8a7c9e57930/dqc_reference
[2023-06-29 16:19:18,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:19:18,871] [INFO] Task started: Prodigal
[2023-06-29 16:19:18,872] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2ee8f89-a1cf-4f2d-8931-ccd2c77bd1ff/GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:19:23,362] [INFO] Task succeeded: Prodigal
[2023-06-29 16:19:23,362] [INFO] Task started: HMMsearch
[2023-06-29 16:19:23,362] [INFO] Running command: hmmsearch --tblout GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc539a103-8539-42b9-bbca-f8a7c9e57930/dqc_reference/reference_markers.hmm GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:19:23,647] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:19:23,649] [INFO] Found 6/6 markers.
[2023-06-29 16:19:23,708] [INFO] Query marker FASTA was written to GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:19:23,708] [INFO] Task started: Blastn
[2023-06-29 16:19:23,708] [INFO] Running command: blastn -query GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc539a103-8539-42b9-bbca-f8a7c9e57930/dqc_reference/reference_markers.fasta -out GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:24,366] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:24,370] [INFO] Selected 12 target genomes.
[2023-06-29 16:19:24,370] [INFO] Target genome list was writen to GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:19:24,373] [INFO] Task started: fastANI
[2023-06-29 16:19:24,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2ee8f89-a1cf-4f2d-8931-ccd2c77bd1ff/GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:19:30,669] [INFO] Task succeeded: fastANI
[2023-06-29 16:19:30,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc539a103-8539-42b9-bbca-f8a7c9e57930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:19:30,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc539a103-8539-42b9-bbca-f8a7c9e57930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:19:30,681] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:19:30,681] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:19:30,681] [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	94.9412	553	633	95	below_threshold
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	93.0543	498	633	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	93.0213	498	633	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	93.0126	497	633	95	below_threshold
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	92.9707	496	633	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	92.6687	505	633	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	92.1675	493	633	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	92.0707	499	633	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	91.9337	496	633	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	86.7307	448	633	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.3357	120	633	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	77.9727	116	633	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:19:30,684] [INFO] DFAST Taxonomy check result was written to GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:19:30,684] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:19:30,684] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:19:30,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc539a103-8539-42b9-bbca-f8a7c9e57930/dqc_reference/checkm_data
[2023-06-29 16:19:30,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:19:30,738] [INFO] Task started: CheckM
[2023-06-29 16:19:30,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:19:52,185] [INFO] Task succeeded: CheckM
[2023-06-29 16:19:52,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:19:52,207] [INFO] ===== Completeness check finished =====
[2023-06-29 16:19:52,207] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:19:52,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:19:52,208] [INFO] Task started: Blastn
[2023-06-29 16:19:52,208] [INFO] Running command: blastn -query GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc539a103-8539-42b9-bbca-f8a7c9e57930/dqc_reference/reference_markers_gtdb.fasta -out GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:19:53,105] [INFO] Task succeeded: Blastn
[2023-06-29 16:19:53,110] [INFO] Selected 20 target genomes.
[2023-06-29 16:19:53,110] [INFO] Target genome list was writen to GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:19:53,138] [INFO] Task started: fastANI
[2023-06-29 16:19:53,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2ee8f89-a1cf-4f2d-8931-ccd2c77bd1ff/GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:20:03,770] [INFO] Task succeeded: fastANI
[2023-06-29 16:20:03,791] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:20:03,791] [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_000222785.1	s__Streptococcus mitis_N	95.2973	543	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.68	95.43	0.88	0.87	9	conclusive
GCF_006385785.1	s__Streptococcus shenyangsis	94.9412	553	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.31	95.07	0.93	0.89	5	-
GCF_000257905.1	s__Streptococcus mitis_L	94.38	535	633	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	94.1787	561	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943935.1	s__Streptococcus mitis_BK	94.1207	552	633	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	94.0762	520	633	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	93.826	502	633	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	93.3911	514	633	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	93.2652	491	633	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	93.2573	498	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722775.1	s__Streptococcus mitis_AV	93.207	506	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.15	95.15	0.88	0.88	2	-
GCF_000148585.2	s__Streptococcus mitis	93.0583	497	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.33	95.07	0.91	0.87	25	-
GCF_001074635.1	s__Streptococcus mitis_E	92.9994	463	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221115.1	s__Streptococcus sp905221115	92.9872	516	633	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	92.8985	518	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281025.1	s__Streptococcus mitis_AK	92.7347	500	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.14	95.01	0.88	0.86	7	-
GCA_905221245.1	s__Streptococcus sp905221245	92.5563	497	633	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	92.2753	494	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.49	95.02	0.87	0.86	5	-
GCF_003942765.1	s__Streptococcus mitis_BE	92.1799	501	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.27	95.27	0.86	0.84	3	-
GCF_003626515.1	s__Streptococcus chosunense	92.0707	499	633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.51	95.33	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-29 16:20:03,794] [INFO] GTDB search result was written to GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:20:03,795] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:20:03,800] [INFO] DFAST_QC result json was written to GCA_937892355.1_ERR1332588_bin.12_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:20:03,800] [INFO] DFAST_QC completed!
[2023-06-29 16:20:03,800] [INFO] Total running time: 0h0m47s