[2024-01-25 20:12:05,937] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg13579375-5575-4013-a1dd-0af961825e3a/dqc_reference
[2024-01-25 20:12:07,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:07,104] [INFO] Task started: Prodigal
[2024-01-25 20:12:07,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg898c998a-c89e-42fb-b7f7-9949d34807ae/GCF_900636475.1_42197_F01_genomic.fna.gz | prodigal -d GCF_900636475.1_42197_F01_genomic.fna/cds.fna -a GCF_900636475.1_42197_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:11,057] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:11,057] [INFO] Task started: HMMsearch
[2024-01-25 20:12:11,057] [INFO] Running command: hmmsearch --tblout GCF_900636475.1_42197_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13579375-5575-4013-a1dd-0af961825e3a/dqc_reference/reference_markers.hmm GCF_900636475.1_42197_F01_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:11,273] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:11,274] [INFO] Found 6/6 markers.
[2024-01-25 20:12:11,292] [INFO] Query marker FASTA was written to GCF_900636475.1_42197_F01_genomic.fna/markers.fasta
[2024-01-25 20:12:11,292] [INFO] Task started: Blastn
[2024-01-25 20:12:11,292] [INFO] Running command: blastn -query GCF_900636475.1_42197_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg13579375-5575-4013-a1dd-0af961825e3a/dqc_reference/reference_markers.fasta -out GCF_900636475.1_42197_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:11,836] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:11,841] [INFO] Selected 11 target genomes.
[2024-01-25 20:12:11,841] [INFO] Target genome list was writen to GCF_900636475.1_42197_F01_genomic.fna/target_genomes.txt
[2024-01-25 20:12:11,867] [INFO] Task started: fastANI
[2024-01-25 20:12:11,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg898c998a-c89e-42fb-b7f7-9949d34807ae/GCF_900636475.1_42197_F01_genomic.fna.gz --refList GCF_900636475.1_42197_F01_genomic.fna/target_genomes.txt --output GCF_900636475.1_42197_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:16,351] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:16,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13579375-5575-4013-a1dd-0af961825e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:16,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13579375-5575-4013-a1dd-0af961825e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:16,358] [INFO] Found 9 fastANI hits (6 hits with ANI > threshold)
[2024-01-25 20:12:16,359] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:16,359] [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 anginosus	strain=NCTC10713	GCA_900636475.1	1328	1328	type	True	100.0	645	651	95	conclusive
Streptococcus anginosus subsp. anginosus	strain=FDAARGOS_1569	GCA_020735765.1	1671923	1328	type	True	99.9997	624	651	95	conclusive
Streptococcus anginosus	strain=ATCC 33397	GCA_002088025.1	1328	1328	type	True	99.9933	629	651	95	conclusive
Streptococcus anginosus	strain=SK52	GCA_000474055.1	1328	1328	type	True	99.975	623	651	95	conclusive
Streptococcus anginosus	strain=DSM 20563	GCA_000373605.1	1328	1328	type	True	99.9739	632	651	95	conclusive
Streptococcus anginosus	strain=SK52	GCA_000214555.2	1328	1328	type	True	99.864	566	651	95	conclusive
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	90.0168	509	651	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.4854	132	651	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.0735	100	651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:16,360] [INFO] DFAST Taxonomy check result was written to GCF_900636475.1_42197_F01_genomic.fna/tc_result.tsv
[2024-01-25 20:12:16,360] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:16,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:16,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13579375-5575-4013-a1dd-0af961825e3a/dqc_reference/checkm_data
[2024-01-25 20:12:16,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:16,384] [INFO] Task started: CheckM
[2024-01-25 20:12:16,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900636475.1_42197_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900636475.1_42197_F01_genomic.fna/checkm_input GCF_900636475.1_42197_F01_genomic.fna/checkm_result
[2024-01-25 20:12:34,352] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:34,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:34,382] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:34,382] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:34,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900636475.1_42197_F01_genomic.fna/markers.fasta)
[2024-01-25 20:12:34,383] [INFO] Task started: Blastn
[2024-01-25 20:12:34,383] [INFO] Running command: blastn -query GCF_900636475.1_42197_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg13579375-5575-4013-a1dd-0af961825e3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900636475.1_42197_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:35,167] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:35,170] [INFO] Selected 5 target genomes.
[2024-01-25 20:12:35,170] [INFO] Target genome list was writen to GCF_900636475.1_42197_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:35,181] [INFO] Task started: fastANI
[2024-01-25 20:12:35,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg898c998a-c89e-42fb-b7f7-9949d34807ae/GCF_900636475.1_42197_F01_genomic.fna.gz --refList GCF_900636475.1_42197_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900636475.1_42197_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:37,766] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:37,770] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:37,770] [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_900636475.1	s__Streptococcus anginosus	100.0	643	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.16	95.41	0.84	0.78	79	conclusive
GCF_001697145.1	s__Streptococcus anginosus_C	94.8721	558	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.71	95.87	0.90	0.80	41	-
GCF_902167705.1	s__Streptococcus constellatus_A	91.6423	515	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900459125.1	s__Streptococcus constellatus	90.058	515	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.83	96.57	0.88	0.81	32	-
GCF_000413475.1	s__Streptococcus intermedius	87.3901	477	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.44	98.07	0.89	0.81	45	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:37,772] [INFO] GTDB search result was written to GCF_900636475.1_42197_F01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:37,772] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:37,774] [INFO] DFAST_QC result json was written to GCF_900636475.1_42197_F01_genomic.fna/dqc_result.json
[2024-01-25 20:12:37,775] [INFO] DFAST_QC completed!
[2024-01-25 20:12:37,775] [INFO] Total running time: 0h0m32s