[2024-01-25 17:42:35,367] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:35,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:35,368] [INFO] DQC Reference Directory: /var/lib/cwl/stgdec76955-7a46-426b-8d46-f1f4c77862db/dqc_reference
[2024-01-25 17:42:36,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:36,496] [INFO] Task started: Prodigal
[2024-01-25 17:42:36,496] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeb300f9-ba80-4ff2-8ac8-0203ae115027/GCF_903645285.1_Q2617_genomic.fna.gz | prodigal -d GCF_903645285.1_Q2617_genomic.fna/cds.fna -a GCF_903645285.1_Q2617_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:40,990] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:40,991] [INFO] Task started: HMMsearch
[2024-01-25 17:42:40,991] [INFO] Running command: hmmsearch --tblout GCF_903645285.1_Q2617_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdec76955-7a46-426b-8d46-f1f4c77862db/dqc_reference/reference_markers.hmm GCF_903645285.1_Q2617_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:41,216] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:41,217] [INFO] Found 6/6 markers.
[2024-01-25 17:42:41,236] [INFO] Query marker FASTA was written to GCF_903645285.1_Q2617_genomic.fna/markers.fasta
[2024-01-25 17:42:41,237] [INFO] Task started: Blastn
[2024-01-25 17:42:41,237] [INFO] Running command: blastn -query GCF_903645285.1_Q2617_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec76955-7a46-426b-8d46-f1f4c77862db/dqc_reference/reference_markers.fasta -out GCF_903645285.1_Q2617_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:41,785] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:41,789] [INFO] Selected 16 target genomes.
[2024-01-25 17:42:41,789] [INFO] Target genome list was writen to GCF_903645285.1_Q2617_genomic.fna/target_genomes.txt
[2024-01-25 17:42:41,805] [INFO] Task started: fastANI
[2024-01-25 17:42:41,805] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb300f9-ba80-4ff2-8ac8-0203ae115027/GCF_903645285.1_Q2617_genomic.fna.gz --refList GCF_903645285.1_Q2617_genomic.fna/target_genomes.txt --output GCF_903645285.1_Q2617_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:50,950] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:50,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdec76955-7a46-426b-8d46-f1f4c77862db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:50,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdec76955-7a46-426b-8d46-f1f4c77862db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:50,961] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:42:50,961] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:42:50,961] [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 pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	93.7882	530	674	95	below_threshold
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	93.7138	459	674	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	93.1255	531	674	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	93.1165	492	674	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	92.9474	532	674	95	below_threshold
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	92.9221	491	674	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	92.8482	502	674	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	92.8307	499	674	95	below_threshold
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	92.8242	497	674	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	92.4481	516	674	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	92.2853	473	674	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	92.1403	476	674	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	92.1003	478	674	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	86.5011	442	674	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.1102	121	674	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.8029	124	674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:50,963] [INFO] DFAST Taxonomy check result was written to GCF_903645285.1_Q2617_genomic.fna/tc_result.tsv
[2024-01-25 17:42:50,963] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:50,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:50,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdec76955-7a46-426b-8d46-f1f4c77862db/dqc_reference/checkm_data
[2024-01-25 17:42:50,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:50,987] [INFO] Task started: CheckM
[2024-01-25 17:42:50,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903645285.1_Q2617_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903645285.1_Q2617_genomic.fna/checkm_input GCF_903645285.1_Q2617_genomic.fna/checkm_result
[2024-01-25 17:43:10,725] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:10,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:10,742] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:10,743] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:10,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903645285.1_Q2617_genomic.fna/markers.fasta)
[2024-01-25 17:43:10,743] [INFO] Task started: Blastn
[2024-01-25 17:43:10,743] [INFO] Running command: blastn -query GCF_903645285.1_Q2617_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec76955-7a46-426b-8d46-f1f4c77862db/dqc_reference/reference_markers_gtdb.fasta -out GCF_903645285.1_Q2617_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:11,645] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:11,648] [INFO] Selected 22 target genomes.
[2024-01-25 17:43:11,649] [INFO] Target genome list was writen to GCF_903645285.1_Q2617_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:11,669] [INFO] Task started: fastANI
[2024-01-25 17:43:11,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb300f9-ba80-4ff2-8ac8-0203ae115027/GCF_903645285.1_Q2617_genomic.fna.gz --refList GCF_903645285.1_Q2617_genomic.fna/target_genomes_gtdb.txt --output GCF_903645285.1_Q2617_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:24,863] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:24,877] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:24,878] [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_903645285.1	s__Streptococcus sp903645285	100.0	672	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.16	95.16	0.86	0.86	2	conclusive
GCF_001347015.1	s__Streptococcus pneumoniae_E	94.6717	574	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013277415.1	s__Streptococcus sp013277415	94.6579	569	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.52	95.41	0.90	0.87	4	-
GCF_900411395.1	s__Streptococcus mitis_BA	94.6119	584	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.49	95.11	0.89	0.86	15	-
GCF_001113365.1	s__Streptococcus pneumoniae_C	94.5605	583	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.29	95.29	0.90	0.90	2	-
GCF_001171885.1	s__Streptococcus pneumoniae_A	94.4083	579	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013276795.1	s__Streptococcus sp013276795	94.2881	524	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.33	95.34	0.95	0.89	5	-
GCF_001070715.1	s__Streptococcus pseudopneumoniae_H	93.9245	476	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001579035.1	s__Streptococcus mitis_J	93.8461	539	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002087075.1	s__Streptococcus pseudopneumoniae	93.7882	530	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.77	96.15	0.92	0.85	120	-
GCF_001579045.1	s__Streptococcus mitis_D	93.3639	521	674	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	93.1747	534	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.15	95.15	0.88	0.88	2	-
GCF_001074635.1	s__Streptococcus mitis_E	93.1737	477	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005545.1	s__Streptococcus mitis_I	93.0958	522	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.10	95.10	0.88	0.88	2	-
GCF_000148525.1	s__Streptococcus mitis_H	92.9849	523	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221245.1	s__Streptococcus sp905221245	92.7072	502	674	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	92.6999	512	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.14	95.01	0.88	0.86	7	-
GCA_905221225.1	s__Streptococcus sp905221225	92.6107	497	674	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	92.5979	473	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003942965.1	s__Streptococcus mitis_BH	92.5643	470	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496205.1	s__Streptococcus mitis_BN	92.4167	468	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.48	95.48	0.97	0.94	4	-
GCF_001579665.1	s__Streptococcus mitis_S	92.042	478	674	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.64	95.33	0.87	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:24,883] [INFO] GTDB search result was written to GCF_903645285.1_Q2617_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:24,885] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:24,890] [INFO] DFAST_QC result json was written to GCF_903645285.1_Q2617_genomic.fna/dqc_result.json
[2024-01-25 17:43:24,890] [INFO] DFAST_QC completed!
[2024-01-25 17:43:24,890] [INFO] Total running time: 0h0m50s