[2024-01-24 14:14:00,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,263] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfc59cd8-fbb5-45ed-a3f2-a3a88ad5de4f/dqc_reference
[2024-01-24 14:14:01,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:01,562] [INFO] Task started: Prodigal
[2024-01-24 14:14:01,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg30cfb4b1-ab12-4da2-8d8a-231345a2cd47/GCF_001593525.1_ASM159352v1_genomic.fna.gz | prodigal -d GCF_001593525.1_ASM159352v1_genomic.fna/cds.fna -a GCF_001593525.1_ASM159352v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:06,688] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:06,688] [INFO] Task started: HMMsearch
[2024-01-24 14:14:06,688] [INFO] Running command: hmmsearch --tblout GCF_001593525.1_ASM159352v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfc59cd8-fbb5-45ed-a3f2-a3a88ad5de4f/dqc_reference/reference_markers.hmm GCF_001593525.1_ASM159352v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:07,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:07,038] [INFO] Found 6/6 markers.
[2024-01-24 14:14:07,089] [INFO] Query marker FASTA was written to GCF_001593525.1_ASM159352v1_genomic.fna/markers.fasta
[2024-01-24 14:14:07,090] [INFO] Task started: Blastn
[2024-01-24 14:14:07,090] [INFO] Running command: blastn -query GCF_001593525.1_ASM159352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfc59cd8-fbb5-45ed-a3f2-a3a88ad5de4f/dqc_reference/reference_markers.fasta -out GCF_001593525.1_ASM159352v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:08,060] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:08,078] [INFO] Selected 13 target genomes.
[2024-01-24 14:14:08,078] [INFO] Target genome list was writen to GCF_001593525.1_ASM159352v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:08,117] [INFO] Task started: fastANI
[2024-01-24 14:14:08,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg30cfb4b1-ab12-4da2-8d8a-231345a2cd47/GCF_001593525.1_ASM159352v1_genomic.fna.gz --refList GCF_001593525.1_ASM159352v1_genomic.fna/target_genomes.txt --output GCF_001593525.1_ASM159352v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:16,761] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:16,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfc59cd8-fbb5-45ed-a3f2-a3a88ad5de4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:16,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfc59cd8-fbb5-45ed-a3f2-a3a88ad5de4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:16,777] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:14:16,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:16,778] [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 sanguinis	strain=NCTC 7863	GCA_001593525.1	1305	1305	suspected-type	True	100.0	727	728	95	conclusive
Streptococcus sanguinis	strain=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	99.9922	724	728	95	conclusive
Streptococcus sanguinis	strain=SK1	GCA_000194945.1	1305	1305	suspected-type	True	99.988	724	728	95	conclusive
Streptococcus gordonii	strain=FDAARGOS 1454	GCA_019046945.1	1302	1302	suspected-type	True	86.294	412	728	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_000187855.1	45634	45634	type	True	85.0702	407	728	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_011612585.1	45634	45634	type	True	85.0373	408	728	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_000222765.2	45634	45634	type	True	85.0347	401	728	95	below_threshold
Streptococcus sinensis	strain=HKU4	GCA_000767835.1	176090	176090	type	True	84.7885	380	728	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.9589	173	728	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.6023	158	728	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.5613	166	728	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	79.3308	159	728	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.2672	101	728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:16,782] [INFO] DFAST Taxonomy check result was written to GCF_001593525.1_ASM159352v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:16,783] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:16,783] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:16,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfc59cd8-fbb5-45ed-a3f2-a3a88ad5de4f/dqc_reference/checkm_data
[2024-01-24 14:14:16,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:16,821] [INFO] Task started: CheckM
[2024-01-24 14:14:16,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001593525.1_ASM159352v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001593525.1_ASM159352v1_genomic.fna/checkm_input GCF_001593525.1_ASM159352v1_genomic.fna/checkm_result
[2024-01-24 14:14:43,792] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:43,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:43,816] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:43,817] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:43,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001593525.1_ASM159352v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:43,818] [INFO] Task started: Blastn
[2024-01-24 14:14:43,818] [INFO] Running command: blastn -query GCF_001593525.1_ASM159352v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfc59cd8-fbb5-45ed-a3f2-a3a88ad5de4f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001593525.1_ASM159352v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:44,706] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:44,709] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:44,710] [INFO] Target genome list was writen to GCF_001593525.1_ASM159352v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:44,719] [INFO] Task started: fastANI
[2024-01-24 14:14:44,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg30cfb4b1-ab12-4da2-8d8a-231345a2cd47/GCF_001593525.1_ASM159352v1_genomic.fna.gz --refList GCF_001593525.1_ASM159352v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001593525.1_ASM159352v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:51,060] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:51,076] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:51,077] [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_000194945.1	s__Streptococcus sanguinis	99.988	724	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.01	0.93	0.89	47	conclusive
GCF_013343115.1	s__Streptococcus sanguinis_H	94.9493	668	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.75	95.06	0.92	0.88	13	-
GCF_003943735.1	s__Streptococcus sanguinis_E	94.9328	653	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.70	95.02	0.91	0.89	6	-
GCF_000212815.1	s__Streptococcus sanguinis_C	94.5365	626	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.73	95.65	0.92	0.92	3	-
GCF_003943655.1	s__Streptococcus sanguinis_F	94.3981	635	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	96.90	0.96	0.95	3	-
GCF_001078705.1	s__Streptococcus sanguinis_D	94.2224	661	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372115.1	s__Streptococcus sp905372115	94.1768	617	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635155.1	s__Streptococcus sanguinis_G	93.9658	652	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.44	97.44	0.92	0.92	2	-
GCF_000212855.1	s__Streptococcus sanguinis_A	93.8572	655	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001578795.1	s__Streptococcus gordonii_A	85.9262	403	728	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	85.2638	404	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000767835.1	s__Streptococcus sinensis	84.7885	380	728	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.90	95.29	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:51,079] [INFO] GTDB search result was written to GCF_001593525.1_ASM159352v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:51,080] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:51,087] [INFO] DFAST_QC result json was written to GCF_001593525.1_ASM159352v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:51,087] [INFO] DFAST_QC completed!
[2024-01-24 14:14:51,087] [INFO] Total running time: 0h0m51s