[2024-01-24 11:34:54,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:54,328] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:54,335] [INFO] DQC Reference Directory: /var/lib/cwl/stgff0816eb-8489-4d48-a983-d94337cd2143/dqc_reference
[2024-01-24 11:34:56,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,207] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,207] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaee3086-6dc0-4e98-ba96-b130f14519db/GCF_003172995.1_ASM317299v1_genomic.fna.gz | prodigal -d GCF_003172995.1_ASM317299v1_genomic.fna/cds.fna -a GCF_003172995.1_ASM317299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:01,427] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:01,428] [INFO] Task started: HMMsearch
[2024-01-24 11:35:01,428] [INFO] Running command: hmmsearch --tblout GCF_003172995.1_ASM317299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff0816eb-8489-4d48-a983-d94337cd2143/dqc_reference/reference_markers.hmm GCF_003172995.1_ASM317299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:01,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:01,666] [INFO] Found 6/6 markers.
[2024-01-24 11:35:01,690] [INFO] Query marker FASTA was written to GCF_003172995.1_ASM317299v1_genomic.fna/markers.fasta
[2024-01-24 11:35:01,690] [INFO] Task started: Blastn
[2024-01-24 11:35:01,690] [INFO] Running command: blastn -query GCF_003172995.1_ASM317299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0816eb-8489-4d48-a983-d94337cd2143/dqc_reference/reference_markers.fasta -out GCF_003172995.1_ASM317299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:02,329] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:02,332] [INFO] Selected 9 target genomes.
[2024-01-24 11:35:02,333] [INFO] Target genome list was writen to GCF_003172995.1_ASM317299v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:02,346] [INFO] Task started: fastANI
[2024-01-24 11:35:02,347] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaee3086-6dc0-4e98-ba96-b130f14519db/GCF_003172995.1_ASM317299v1_genomic.fna.gz --refList GCF_003172995.1_ASM317299v1_genomic.fna/target_genomes.txt --output GCF_003172995.1_ASM317299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:07,625] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:07,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff0816eb-8489-4d48-a983-d94337cd2143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:07,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff0816eb-8489-4d48-a983-d94337cd2143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:07,637] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:35:07,638] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:07,638] [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 sobrinus	strain=SL1	GCA_003172995.1	1310	1310	type	True	100.0	730	732	95	conclusive
Streptococcus sobrinus	strain=NCTC12279	GCA_900475395.1	1310	1310	type	True	99.9941	729	732	95	conclusive
Streptococcus sobrinus	strain=ATCC 33478	GCA_000439045.1	1310	1310	type	True	99.9504	681	732	95	conclusive
Streptococcus sobrinus	strain=DSM 20742	GCA_000686605.1	1310	1310	type	True	99.9463	680	732	95	conclusive
Streptococcus downei	strain=NCTC 11391	GCA_900459175.1	1317	1317	type	True	86.9227	538	732	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	81.1888	65	732	95	below_threshold
Streptococcus criceti	strain=HS-6	GCA_000187975.3	1333	1333	type	True	80.4947	418	732	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.2057	62	732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:07,640] [INFO] DFAST Taxonomy check result was written to GCF_003172995.1_ASM317299v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:07,641] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:07,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:07,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff0816eb-8489-4d48-a983-d94337cd2143/dqc_reference/checkm_data
[2024-01-24 11:35:07,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:07,676] [INFO] Task started: CheckM
[2024-01-24 11:35:07,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003172995.1_ASM317299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003172995.1_ASM317299v1_genomic.fna/checkm_input GCF_003172995.1_ASM317299v1_genomic.fna/checkm_result
[2024-01-24 11:35:30,640] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:30,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:30,664] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:30,664] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:30,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003172995.1_ASM317299v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:30,665] [INFO] Task started: Blastn
[2024-01-24 11:35:30,665] [INFO] Running command: blastn -query GCF_003172995.1_ASM317299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0816eb-8489-4d48-a983-d94337cd2143/dqc_reference/reference_markers_gtdb.fasta -out GCF_003172995.1_ASM317299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:31,564] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:31,568] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:31,568] [INFO] Target genome list was writen to GCF_003172995.1_ASM317299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:31,577] [INFO] Task started: fastANI
[2024-01-24 11:35:31,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaee3086-6dc0-4e98-ba96-b130f14519db/GCF_003172995.1_ASM317299v1_genomic.fna.gz --refList GCF_003172995.1_ASM317299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003172995.1_ASM317299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:37,062] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:37,082] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:37,083] [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_000686605.1	s__Streptococcus sobrinus	99.9463	680	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.93	98.60	0.95	0.92	52	conclusive
GCF_900459175.1	s__Streptococcus downei	86.9175	535	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.20	97.65	0.95	0.94	6	-
GCF_000187975.2	s__Streptococcus criceti	80.4986	417	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011038795.1	s__Streptococcus sp011038795	79.9225	387	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	99.03	0.90	0.90	2	-
GCF_010604095.1	s__Streptococcus sp000187445	78.763	98	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_000376985.1	s__Streptococcus henryi	78.411	98	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_905187535.1	s__Streptococcus mitis_BS	78.3713	73	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423745.1	s__Streptococcus plurextorum	78.2618	67	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017883985.1	s__Streptococcus oricebi	78.2117	74	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760245.1	s__Streptococcus suis_I	78.0692	67	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002960625.1	s__Streptococcus suis_T	78.0028	81	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	77.8787	116	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017884005.1	s__Streptococcus panodentis	77.4155	88	732	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.49	98.49	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:37,085] [INFO] GTDB search result was written to GCF_003172995.1_ASM317299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:37,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:37,089] [INFO] DFAST_QC result json was written to GCF_003172995.1_ASM317299v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:37,090] [INFO] DFAST_QC completed!
[2024-01-24 11:35:37,090] [INFO] Total running time: 0h0m43s