[2024-01-24 13:13:51,450] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,453] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcfb3cdd-58e5-4766-9ea5-5bc71de05157/dqc_reference
[2024-01-24 13:13:52,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,711] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,711] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6ea400c-5e82-4b2b-835d-1bbc5dcde0fb/GCF_017884005.1_ASM1788400v1_genomic.fna.gz | prodigal -d GCF_017884005.1_ASM1788400v1_genomic.fna/cds.fna -a GCF_017884005.1_ASM1788400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:59,190] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:59,190] [INFO] Task started: HMMsearch
[2024-01-24 13:13:59,190] [INFO] Running command: hmmsearch --tblout GCF_017884005.1_ASM1788400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcfb3cdd-58e5-4766-9ea5-5bc71de05157/dqc_reference/reference_markers.hmm GCF_017884005.1_ASM1788400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:59,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:59,574] [INFO] Found 6/6 markers.
[2024-01-24 13:13:59,604] [INFO] Query marker FASTA was written to GCF_017884005.1_ASM1788400v1_genomic.fna/markers.fasta
[2024-01-24 13:13:59,604] [INFO] Task started: Blastn
[2024-01-24 13:13:59,604] [INFO] Running command: blastn -query GCF_017884005.1_ASM1788400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcfb3cdd-58e5-4766-9ea5-5bc71de05157/dqc_reference/reference_markers.fasta -out GCF_017884005.1_ASM1788400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,382] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,385] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:00,386] [INFO] Target genome list was writen to GCF_017884005.1_ASM1788400v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:00,451] [INFO] Task started: fastANI
[2024-01-24 13:14:00,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ea400c-5e82-4b2b-835d-1bbc5dcde0fb/GCF_017884005.1_ASM1788400v1_genomic.fna.gz --refList GCF_017884005.1_ASM1788400v1_genomic.fna/target_genomes.txt --output GCF_017884005.1_ASM1788400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:08,832] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:08,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcfb3cdd-58e5-4766-9ea5-5bc71de05157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:08,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcfb3cdd-58e5-4766-9ea5-5bc71de05157/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:08,941] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:14:08,942] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:14:08,943] [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=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	81.4234	500	898	95	below_threshold
Streptococcus sanguinis	strain=NCTC 7863	GCA_001593525.1	1305	1305	suspected-type	True	81.4056	465	898	95	below_threshold
Streptococcus sanguinis	strain=SK1	GCA_000194945.1	1305	1305	suspected-type	True	81.3182	491	898	95	below_threshold
Streptococcus gordonii	strain=ATCC 10558	GCA_001469295.1	1302	1302	suspected-type	True	80.0495	260	898	95	below_threshold
Streptococcus gordonii	strain=FDAARGOS 1454	GCA_019046945.1	1302	1302	suspected-type	True	80.0015	265	898	95	below_threshold
Streptococcus sinensis	strain=HKU4	GCA_000767835.1	176090	176090	type	True	79.8681	316	898	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_000222765.2	45634	45634	type	True	79.5398	330	898	95	below_threshold
Streptococcus cristatus	strain=NCTC12479	GCA_900475445.1	45634	45634	type	True	79.5317	324	898	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_000187855.1	45634	45634	type	True	79.4778	327	898	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_011612585.1	45634	45634	type	True	79.428	338	898	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.1889	129	898	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.551	126	898	95	below_threshold
Streptococcus peroris	strain=ATCC 700780	GCA_000187585.1	68891	68891	type	True	78.3336	99	898	95	below_threshold
Streptococcus massiliensis	strain=NCTC13765	GCA_900459365.1	313439	313439	type	True	78.3143	176	898	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.1611	68	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:08,946] [INFO] DFAST Taxonomy check result was written to GCF_017884005.1_ASM1788400v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:08,947] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:08,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:08,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcfb3cdd-58e5-4766-9ea5-5bc71de05157/dqc_reference/checkm_data
[2024-01-24 13:14:08,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:08,982] [INFO] Task started: CheckM
[2024-01-24 13:14:08,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017884005.1_ASM1788400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017884005.1_ASM1788400v1_genomic.fna/checkm_input GCF_017884005.1_ASM1788400v1_genomic.fna/checkm_result
[2024-01-24 13:14:37,335] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:37,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:37,412] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:37,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:37,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017884005.1_ASM1788400v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:37,414] [INFO] Task started: Blastn
[2024-01-24 13:14:37,414] [INFO] Running command: blastn -query GCF_017884005.1_ASM1788400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcfb3cdd-58e5-4766-9ea5-5bc71de05157/dqc_reference/reference_markers_gtdb.fasta -out GCF_017884005.1_ASM1788400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:38,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:38,440] [INFO] Selected 16 target genomes.
[2024-01-24 13:14:38,441] [INFO] Target genome list was writen to GCF_017884005.1_ASM1788400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:38,468] [INFO] Task started: fastANI
[2024-01-24 13:14:38,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6ea400c-5e82-4b2b-835d-1bbc5dcde0fb/GCF_017884005.1_ASM1788400v1_genomic.fna.gz --refList GCF_017884005.1_ASM1788400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017884005.1_ASM1788400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:46,998] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:47,015] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:47,015] [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_017884005.1	s__Streptococcus panodentis	100.0	895	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.49	98.49	0.90	0.90	2	conclusive
GCF_000212855.1	s__Streptococcus sanguinis_A	81.6883	506	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212815.1	s__Streptococcus sanguinis_C	81.6567	466	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.73	95.65	0.92	0.92	3	-
GCA_905372115.1	s__Streptococcus sp905372115	81.639	469	898	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	81.4955	493	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.44	97.44	0.92	0.92	2	-
GCF_003943655.1	s__Streptococcus sanguinis_F	81.4902	484	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	96.90	0.96	0.95	3	-
GCF_000194945.1	s__Streptococcus sanguinis	81.3318	490	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.01	0.93	0.89	47	-
GCF_003943735.1	s__Streptococcus sanguinis_E	81.3191	483	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.70	95.02	0.91	0.89	6	-
GCF_001078705.1	s__Streptococcus sanguinis_D	81.3018	502	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013378335.1	s__Streptococcus sanguinis_I	81.1935	474	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.17	96.17	0.87	0.87	2	-
GCA_001578795.1	s__Streptococcus gordonii_A	80.9747	266	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001578775.1	s__Streptococcus cristatus_A	80.2343	336	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943465.1	s__Streptococcus cristatus_C	79.7917	335	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.24	95.10	0.94	0.90	8	-
GCF_902460355.1	s__Streptococcus sp902460355	79.7816	324	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369405.1	s__Streptococcus cristatus_G	79.6768	316	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222765.1	s__Streptococcus cristatus	79.5411	331	898	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.39	95.04	0.92	0.87	17	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:47,018] [INFO] GTDB search result was written to GCF_017884005.1_ASM1788400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:47,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:47,023] [INFO] DFAST_QC result json was written to GCF_017884005.1_ASM1788400v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:47,023] [INFO] DFAST_QC completed!
[2024-01-24 13:14:47,023] [INFO] Total running time: 0h0m56s