[2024-01-24 10:47:06,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgaca4d21f-c300-4385-82d9-c36402f91a57/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,103] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b7ceec7-3b51-4215-b0c4-a3e41eb7f0b7/GCF_014643475.1_ASM1464347v1_genomic.fna.gz | prodigal -d GCF_014643475.1_ASM1464347v1_genomic.fna/cds.fna -a GCF_014643475.1_ASM1464347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:16,820] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:16,821] [INFO] Task started: HMMsearch
[2024-01-24 10:47:16,821] [INFO] Running command: hmmsearch --tblout GCF_014643475.1_ASM1464347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaca4d21f-c300-4385-82d9-c36402f91a57/dqc_reference/reference_markers.hmm GCF_014643475.1_ASM1464347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:17,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:17,146] [INFO] Found 6/6 markers.
[2024-01-24 10:47:17,181] [INFO] Query marker FASTA was written to GCF_014643475.1_ASM1464347v1_genomic.fna/markers.fasta
[2024-01-24 10:47:17,181] [INFO] Task started: Blastn
[2024-01-24 10:47:17,181] [INFO] Running command: blastn -query GCF_014643475.1_ASM1464347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaca4d21f-c300-4385-82d9-c36402f91a57/dqc_reference/reference_markers.fasta -out GCF_014643475.1_ASM1464347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,654] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,657] [INFO] Selected 24 target genomes.
[2024-01-24 10:47:19,657] [INFO] Target genome list was writen to GCF_014643475.1_ASM1464347v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:19,716] [INFO] Task started: fastANI
[2024-01-24 10:47:19,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b7ceec7-3b51-4215-b0c4-a3e41eb7f0b7/GCF_014643475.1_ASM1464347v1_genomic.fna.gz --refList GCF_014643475.1_ASM1464347v1_genomic.fna/target_genomes.txt --output GCF_014643475.1_ASM1464347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:31,116] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:31,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaca4d21f-c300-4385-82d9-c36402f91a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:31,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaca4d21f-c300-4385-82d9-c36402f91a57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:31,149] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:31,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:31,150] [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 himalayensis	strain=CGMCC 1.15533	GCA_014643475.1	1888195	1888195	type	True	100.0	677	679	95	conclusive
Streptococcus himalayensis	strain=HTS2	GCA_001708305.1	1888195	1888195	type	True	99.9942	679	679	95	conclusive
Streptococcus marmotae	strain=HTS5	GCA_001623565.1	1825069	1825069	type	True	87.8495	299	679	95	below_threshold
Streptococcus respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	83.0146	242	679	95	below_threshold
Streptococcus cuniculi	strain=CCUG 65085	GCA_001921845.1	1432788	1432788	type	True	79.969	212	679	95	below_threshold
Streptococcus xiaochunlingii	strain=E24	GCA_006385805.1	2589788	2589788	type	True	78.9679	118	679	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.9189	122	679	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000222745.2	113107	113107	type	True	78.8403	116	679	95	below_threshold
Streptococcus timonensis	strain=Marseille-P2915	GCA_900095845.1	1852387	1852387	type	True	78.7031	107	679	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_011612585.1	45634	45634	type	True	78.6965	139	679	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	78.6856	117	679	95	below_threshold
Streptococcus anginosus	strain=ATCC 33397	GCA_002088025.1	1328	1328	type	True	78.6813	137	679	95	below_threshold
Streptococcus australis	strain=ATCC 700641	GCA_000186465.1	113107	113107	type	True	78.6308	118	679	95	below_threshold
Streptococcus anginosus	strain=NCTC10713	GCA_900636475.1	1328	1328	type	True	78.6173	138	679	95	below_threshold
Streptococcus parasanguinis	strain=NCTC12854	GCA_900459355.1	1318	1318	suspected-type	True	78.5878	136	679	95	below_threshold
Streptococcus chosunense	strain=ChDC B353	GCA_003626515.1	2707003	2707003	type	True	78.5737	134	679	95	below_threshold
Streptococcus parasanguinis	strain=ATCC 15912	GCA_000164675.2	1318	1318	suspected-type	True	78.5365	135	679	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	78.494	131	679	95	below_threshold
Streptococcus anginosus	strain=SK52	GCA_000214555.2	1328	1328	type	True	78.4613	127	679	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.3919	128	679	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	78.3159	81	679	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.0635	65	679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:31,153] [INFO] DFAST Taxonomy check result was written to GCF_014643475.1_ASM1464347v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:31,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:31,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:31,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaca4d21f-c300-4385-82d9-c36402f91a57/dqc_reference/checkm_data
[2024-01-24 10:47:31,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:31,181] [INFO] Task started: CheckM
[2024-01-24 10:47:31,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643475.1_ASM1464347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643475.1_ASM1464347v1_genomic.fna/checkm_input GCF_014643475.1_ASM1464347v1_genomic.fna/checkm_result
[2024-01-24 10:47:53,078] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:53,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:53,096] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:53,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:53,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643475.1_ASM1464347v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:53,097] [INFO] Task started: Blastn
[2024-01-24 10:47:53,098] [INFO] Running command: blastn -query GCF_014643475.1_ASM1464347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaca4d21f-c300-4385-82d9-c36402f91a57/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643475.1_ASM1464347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:54,110] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:54,114] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:54,114] [INFO] Target genome list was writen to GCF_014643475.1_ASM1464347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:54,203] [INFO] Task started: fastANI
[2024-01-24 10:47:54,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b7ceec7-3b51-4215-b0c4-a3e41eb7f0b7/GCF_014643475.1_ASM1464347v1_genomic.fna.gz --refList GCF_014643475.1_ASM1464347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643475.1_ASM1464347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:04,844] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:04,865] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:04,865] [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_001708305.1	s__Streptococcus himalayensis	99.9942	679	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001623565.1	s__Streptococcus marmotae	88.0539	294	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017639855.1	s__Streptococcus sp013623465	86.7931	275	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.97	99.93	0.99	0.98	7	-
GCF_003595525.1	s__Streptococcus respiraculi	82.9814	243	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921845.1	s__Streptococcus cuniculi	79.9371	214	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570575.1	s__Streptococcus cuniculi_A	79.8454	207	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002096815.1	s__Streptococcus mitis_AD	78.9017	117	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221505.1	s__Streptococcus sp905221505	78.8127	126	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.98	0.98	3	-
GCF_016648925.1	s__Streptococcus sp900766505	78.8063	123	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.66	95.35	0.89	0.83	30	-
GCA_905221255.1	s__Streptococcus sp905221255	78.7843	116	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	97.53	0.94	0.94	3	-
GCA_000223255.2	s__Streptococcus infantis_G	78.7726	110	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314795.2	s__Streptococcus sp000314795	78.7214	121	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001072375.1	s__Streptococcus pseudopneumoniae_L	78.7211	117	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.33	95.22	0.88	0.86	3	-
GCF_900636475.1	s__Streptococcus anginosus	78.6471	137	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.16	95.41	0.84	0.78	79	-
GCF_001347015.1	s__Streptococcus pneumoniae_E	78.6306	133	679	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	78.6103	126	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000430305.1	s__Streptococcus mitis_AW	78.6076	120	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0354	95.13	95.13	0.89	0.89	2	-
GCA_905221145.1	s__Streptococcus sp905221145	78.6036	130	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001560895.1	s__Streptococcus mitis_Q	78.547	138	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.95	95.95	0.90	0.90	2	-
GCF_001811505.1	s__Streptococcus sp001811505	78.4786	125	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001073085.1	s__Streptococcus pseudopneumoniae_M	78.4496	127	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.77	95.77	0.91	0.91	2	-
GCF_900459125.1	s__Streptococcus constellatus	78.3985	131	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.83	96.57	0.88	0.81	32	-
GCF_008369405.1	s__Streptococcus cristatus_G	78.3126	140	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943815.1	s__Streptococcus cristatus_F	78.236	150	679	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015256435.1	s__Streptococcus sp015256435	77.9303	85	679	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 10:48:04,868] [INFO] GTDB search result was written to GCF_014643475.1_ASM1464347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:04,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:04,873] [INFO] DFAST_QC result json was written to GCF_014643475.1_ASM1464347v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:04,873] [INFO] DFAST_QC completed!
[2024-01-24 10:48:04,874] [INFO] Total running time: 0h0m58s