[2024-01-25 19:00:05,805] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:05,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:05,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg78ddf19a-549a-41d0-82e3-dd36facd7346/dqc_reference
[2024-01-25 19:00:06,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:06,948] [INFO] Task started: Prodigal
[2024-01-25 19:00:06,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg4471e12e-f3ba-4f83-b3bf-187da59c197c/GCF_003627155.1_ASM362715v1_genomic.fna.gz | prodigal -d GCF_003627155.1_ASM362715v1_genomic.fna/cds.fna -a GCF_003627155.1_ASM362715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:11,025] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:11,025] [INFO] Task started: HMMsearch
[2024-01-25 19:00:11,025] [INFO] Running command: hmmsearch --tblout GCF_003627155.1_ASM362715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78ddf19a-549a-41d0-82e3-dd36facd7346/dqc_reference/reference_markers.hmm GCF_003627155.1_ASM362715v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:11,292] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:11,293] [INFO] Found 6/6 markers.
[2024-01-25 19:00:11,313] [INFO] Query marker FASTA was written to GCF_003627155.1_ASM362715v1_genomic.fna/markers.fasta
[2024-01-25 19:00:11,313] [INFO] Task started: Blastn
[2024-01-25 19:00:11,314] [INFO] Running command: blastn -query GCF_003627155.1_ASM362715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ddf19a-549a-41d0-82e3-dd36facd7346/dqc_reference/reference_markers.fasta -out GCF_003627155.1_ASM362715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:11,891] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:11,894] [INFO] Selected 16 target genomes.
[2024-01-25 19:00:11,894] [INFO] Target genome list was writen to GCF_003627155.1_ASM362715v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:11,902] [INFO] Task started: fastANI
[2024-01-25 19:00:11,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg4471e12e-f3ba-4f83-b3bf-187da59c197c/GCF_003627155.1_ASM362715v1_genomic.fna.gz --refList GCF_003627155.1_ASM362715v1_genomic.fna/target_genomes.txt --output GCF_003627155.1_ASM362715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:19,507] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:19,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78ddf19a-549a-41d0-82e3-dd36facd7346/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:19,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78ddf19a-549a-41d0-82e3-dd36facd7346/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:19,518] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:00:19,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:19,518] [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 gwangjuense	strain=ChDC B345	GCA_003627155.1	1433513	1433513	type	True	100.0	654	657	95	conclusive
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	94.5514	544	657	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	94.5374	535	657	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	94.3124	554	657	95	below_threshold
Streptococcus mitis	strain=FDAARGOS 1456	GCA_019047825.1	28037	28037	suspected-type	True	93.737	512	657	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	93.7272	506	657	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	93.6432	514	657	95	below_threshold
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	93.4851	514	657	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	93.0259	524	657	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	92.2385	509	657	95	below_threshold
Streptococcus pseudopneumoniae	strain=CCUG 49455	GCA_002087075.1	257758	257758	type	True	91.8693	476	657	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	91.3232	471	657	95	below_threshold
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	91.1944	490	657	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	87.1662	486	657	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.6426	130	657	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.0471	104	657	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:19,520] [INFO] DFAST Taxonomy check result was written to GCF_003627155.1_ASM362715v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:19,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:19,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:19,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78ddf19a-549a-41d0-82e3-dd36facd7346/dqc_reference/checkm_data
[2024-01-25 19:00:19,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:19,545] [INFO] Task started: CheckM
[2024-01-25 19:00:19,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003627155.1_ASM362715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003627155.1_ASM362715v1_genomic.fna/checkm_input GCF_003627155.1_ASM362715v1_genomic.fna/checkm_result
[2024-01-25 19:00:37,856] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:37,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:37,877] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:37,877] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:37,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003627155.1_ASM362715v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:37,877] [INFO] Task started: Blastn
[2024-01-25 19:00:37,878] [INFO] Running command: blastn -query GCF_003627155.1_ASM362715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ddf19a-549a-41d0-82e3-dd36facd7346/dqc_reference/reference_markers_gtdb.fasta -out GCF_003627155.1_ASM362715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:38,689] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:38,692] [INFO] Selected 21 target genomes.
[2024-01-25 19:00:38,692] [INFO] Target genome list was writen to GCF_003627155.1_ASM362715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:38,717] [INFO] Task started: fastANI
[2024-01-25 19:00:38,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg4471e12e-f3ba-4f83-b3bf-187da59c197c/GCF_003627155.1_ASM362715v1_genomic.fna.gz --refList GCF_003627155.1_ASM362715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003627155.1_ASM362715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:48,614] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:48,627] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:48,627] [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_003627155.1	s__Streptococcus gwangjuense	100.0	654	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006385165.1	s__Streptococcus symci	94.5439	535	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.44	95.02	0.84	0.78	21	-
GCA_000385835.1	s__Streptococcus mitis_AI	94.4663	522	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.82	97.82	0.92	0.92	2	-
GCF_016658865.1	s__Streptococcus mitis_BT	94.3488	557	657	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	94.3124	554	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.51	95.33	0.92	0.89	3	-
GCF_003942765.1	s__Streptococcus mitis_BE	94.2496	538	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.27	95.27	0.86	0.84	3	-
GCF_002096815.1	s__Streptococcus mitis_AD	94.0773	541	657	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	93.7129	365	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003942865.1	s__Streptococcus mitis_BI	93.5339	535	657	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	93.4075	503	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221155.1	s__Streptococcus sp905221155	93.4057	502	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096755.1	s__Streptococcus mitis_AC	93.3033	489	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.32	95.11	0.87	0.86	7	-
GCF_905187535.1	s__Streptococcus mitis_BS	93.2388	510	657	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	93.2283	506	657	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	93.154	516	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.49	95.02	0.87	0.86	5	-
GCF_002005545.1	s__Streptococcus mitis_I	92.8657	508	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.10	95.10	0.88	0.88	2	-
GCF_002860905.1	s__Streptococcus oralis_BA	92.8344	499	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.58	98.58	0.96	0.96	2	-
GCF_002860865.1	s__Streptococcus mitis_AT	92.8053	512	657	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	92.6801	463	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.02	95.02	0.84	0.84	2	-
GCF_903645285.1	s__Streptococcus sp903645285	92.3332	488	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.16	95.16	0.86	0.86	2	-
GCA_905221205.1	s__Streptococcus sp905221205	92.1228	496	657	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:48,630] [INFO] GTDB search result was written to GCF_003627155.1_ASM362715v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:48,630] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:48,634] [INFO] DFAST_QC result json was written to GCF_003627155.1_ASM362715v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:48,634] [INFO] DFAST_QC completed!
[2024-01-25 19:00:48,634] [INFO] Total running time: 0h0m43s