[2024-01-24 11:12:57,918] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cdace1f-2c11-4ef5-8d75-6ef38ddf7143/dqc_reference
[2024-01-24 11:12:59,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,323] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg51feb7a2-4420-4661-bdc4-0352a25ac7ba/GCF_002087075.1_ASM208707v1_genomic.fna.gz | prodigal -d GCF_002087075.1_ASM208707v1_genomic.fna/cds.fna -a GCF_002087075.1_ASM208707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:04,154] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:04,154] [INFO] Task started: HMMsearch
[2024-01-24 11:13:04,154] [INFO] Running command: hmmsearch --tblout GCF_002087075.1_ASM208707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cdace1f-2c11-4ef5-8d75-6ef38ddf7143/dqc_reference/reference_markers.hmm GCF_002087075.1_ASM208707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:04,439] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:04,440] [INFO] Found 6/6 markers.
[2024-01-24 11:13:04,467] [INFO] Query marker FASTA was written to GCF_002087075.1_ASM208707v1_genomic.fna/markers.fasta
[2024-01-24 11:13:04,467] [INFO] Task started: Blastn
[2024-01-24 11:13:04,467] [INFO] Running command: blastn -query GCF_002087075.1_ASM208707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cdace1f-2c11-4ef5-8d75-6ef38ddf7143/dqc_reference/reference_markers.fasta -out GCF_002087075.1_ASM208707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:05,114] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:05,117] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:05,117] [INFO] Target genome list was writen to GCF_002087075.1_ASM208707v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:05,143] [INFO] Task started: fastANI
[2024-01-24 11:13:05,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg51feb7a2-4420-4661-bdc4-0352a25ac7ba/GCF_002087075.1_ASM208707v1_genomic.fna.gz --refList GCF_002087075.1_ASM208707v1_genomic.fna/target_genomes.txt --output GCF_002087075.1_ASM208707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:13,748] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:13,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cdace1f-2c11-4ef5-8d75-6ef38ddf7143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:13,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cdace1f-2c11-4ef5-8d75-6ef38ddf7143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:13,761] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:13,761] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:13,761] [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	100.0	681	683	95	conclusive
Streptococcus pseudopneumoniae	strain=ATCC BAA-960	GCA_000257825.1	257758	257758	type	True	99.7183	551	683	95	conclusive
Streptococcus pneumoniae	strain=NCTC7465	GCA_001457635.1	1313	1313	type	True	94.5025	531	683	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	94.3695	511	683	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	92.4214	532	683	95	below_threshold
Streptococcus mitis	strain=CCUG 31611	GCA_002014755.1	28037	28037	suspected-type	True	92.2345	486	683	95	below_threshold
Streptococcus mitis	strain=NCTC 12261	GCA_000148585.3	28037	28037	suspected-type	True	92.2135	477	683	95	below_threshold
Streptococcus mitis	strain=NCTC12261	GCA_900459425.1	28037	28037	suspected-type	True	92.1735	490	683	95	below_threshold
Streptococcus shenyangsis	strain=D19	GCA_006385785.1	2589786	2589786	type	True	92.0797	508	683	95	below_threshold
Streptococcus gwangjuense	strain=ChDC B345	GCA_003627155.1	1433513	1433513	type	True	91.9191	481	683	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	91.8482	477	683	95	below_threshold
Streptococcus symci	strain=C17	GCA_006385165.1	2588991	2588991	type	True	91.4686	485	683	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	86.7541	445	683	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.9276	122	683	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.2927	98	683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:13,763] [INFO] DFAST Taxonomy check result was written to GCF_002087075.1_ASM208707v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:13,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:13,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:13,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cdace1f-2c11-4ef5-8d75-6ef38ddf7143/dqc_reference/checkm_data
[2024-01-24 11:13:13,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:13,796] [INFO] Task started: CheckM
[2024-01-24 11:13:13,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002087075.1_ASM208707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002087075.1_ASM208707v1_genomic.fna/checkm_input GCF_002087075.1_ASM208707v1_genomic.fna/checkm_result
[2024-01-24 11:13:36,138] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:36,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:36,158] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:36,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:36,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002087075.1_ASM208707v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:36,160] [INFO] Task started: Blastn
[2024-01-24 11:13:36,160] [INFO] Running command: blastn -query GCF_002087075.1_ASM208707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cdace1f-2c11-4ef5-8d75-6ef38ddf7143/dqc_reference/reference_markers_gtdb.fasta -out GCF_002087075.1_ASM208707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:37,107] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:37,113] [INFO] Selected 21 target genomes.
[2024-01-24 11:13:37,113] [INFO] Target genome list was writen to GCF_002087075.1_ASM208707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:37,150] [INFO] Task started: fastANI
[2024-01-24 11:13:37,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg51feb7a2-4420-4661-bdc4-0352a25ac7ba/GCF_002087075.1_ASM208707v1_genomic.fna.gz --refList GCF_002087075.1_ASM208707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002087075.1_ASM208707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:49,895] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:49,923] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:49,924] [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_002087075.1	s__Streptococcus pseudopneumoniae	100.0	681	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.77	96.15	0.92	0.85	120	conclusive
GCF_001457635.1	s__Streptococcus pneumoniae	94.5355	530	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.62	97.54	0.92	0.81	8452	-
GCF_001347015.1	s__Streptococcus pneumoniae_E	94.0921	557	683	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	93.9637	562	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.29	95.29	0.90	0.90	2	-
GCF_903645285.1	s__Streptococcus sp903645285	93.7217	539	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.16	95.16	0.86	0.86	2	-
GCF_001171885.1	s__Streptococcus pneumoniae_A	93.656	541	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013277515.1	s__Streptococcus sp013277515	93.5422	517	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013276795.1	s__Streptococcus sp013276795	93.5062	510	683	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	93.0425	477	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148545.1	s__Streptococcus mitis_C	92.7366	469	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.02	95.02	0.84	0.84	2	-
GCF_001579045.1	s__Streptococcus mitis_D	92.6549	527	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148525.1	s__Streptococcus mitis_H	92.4745	500	683	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	92.401	363	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860905.1	s__Streptococcus oralis_BA	92.3729	487	683	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	92.2899	515	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.74	95.72	0.90	0.90	3	-
GCF_000148585.2	s__Streptococcus mitis	92.1855	478	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.33	95.07	0.91	0.87	25	-
GCF_002096925.1	s__Streptococcus mitis_AF	92.1317	465	683	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	91.7795	472	683	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	91.7614	507	683	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	91.6131	469	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.51	95.33	0.92	0.89	3	-
GCF_006385165.1	s__Streptococcus symci	91.4294	488	683	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.44	95.02	0.84	0.78	21	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:49,926] [INFO] GTDB search result was written to GCF_002087075.1_ASM208707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:49,926] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:49,936] [INFO] DFAST_QC result json was written to GCF_002087075.1_ASM208707v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:49,937] [INFO] DFAST_QC completed!
[2024-01-24 11:13:49,937] [INFO] Total running time: 0h0m52s