[2024-01-25 19:02:20,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:20,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:20,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg9573f1a5-e992-466a-baa0-dc6a3eeda17e/dqc_reference
[2024-01-25 19:02:21,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:21,774] [INFO] Task started: Prodigal
[2024-01-25 19:02:21,775] [INFO] Running command: gunzip -c /var/lib/cwl/stge814e67f-2bdf-43f7-bf34-f28f5d049fd0/GCF_900459175.1_52087_B01_genomic.fna.gz | prodigal -d GCF_900459175.1_52087_B01_genomic.fna/cds.fna -a GCF_900459175.1_52087_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:26,333] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:26,333] [INFO] Task started: HMMsearch
[2024-01-25 19:02:26,333] [INFO] Running command: hmmsearch --tblout GCF_900459175.1_52087_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9573f1a5-e992-466a-baa0-dc6a3eeda17e/dqc_reference/reference_markers.hmm GCF_900459175.1_52087_B01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:26,553] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:26,555] [INFO] Found 6/6 markers.
[2024-01-25 19:02:26,579] [INFO] Query marker FASTA was written to GCF_900459175.1_52087_B01_genomic.fna/markers.fasta
[2024-01-25 19:02:26,580] [INFO] Task started: Blastn
[2024-01-25 19:02:26,580] [INFO] Running command: blastn -query GCF_900459175.1_52087_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9573f1a5-e992-466a-baa0-dc6a3eeda17e/dqc_reference/reference_markers.fasta -out GCF_900459175.1_52087_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:27,161] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:27,164] [INFO] Selected 10 target genomes.
[2024-01-25 19:02:27,165] [INFO] Target genome list was writen to GCF_900459175.1_52087_B01_genomic.fna/target_genomes.txt
[2024-01-25 19:02:27,173] [INFO] Task started: fastANI
[2024-01-25 19:02:27,173] [INFO] Running command: fastANI --query /var/lib/cwl/stge814e67f-2bdf-43f7-bf34-f28f5d049fd0/GCF_900459175.1_52087_B01_genomic.fna.gz --refList GCF_900459175.1_52087_B01_genomic.fna/target_genomes.txt --output GCF_900459175.1_52087_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:32,923] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:32,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9573f1a5-e992-466a-baa0-dc6a3eeda17e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:32,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9573f1a5-e992-466a-baa0-dc6a3eeda17e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:32,931] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:32,931] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:32,931] [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 downei	strain=NCTC 11391	GCA_900459175.1	1317	1317	type	True	100.0	742	743	95	conclusive
Streptococcus sobrinus	strain=SL1	GCA_003172995.1	1310	1310	type	True	87.112	539	743	95	below_threshold
Streptococcus sobrinus	strain=NCTC12279	GCA_900475395.1	1310	1310	type	True	87.0544	542	743	95	below_threshold
Streptococcus sobrinus	strain=DSM 20742	GCA_000686605.1	1310	1310	type	True	86.916	517	743	95	below_threshold
Streptococcus sobrinus	strain=ATCC 33478	GCA_000439045.1	1310	1310	type	True	86.8045	528	743	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.5024	65	743	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.4907	76	743	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.3098	87	743	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.1873	71	743	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	77.6849	76	743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:32,933] [INFO] DFAST Taxonomy check result was written to GCF_900459175.1_52087_B01_genomic.fna/tc_result.tsv
[2024-01-25 19:02:32,933] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:32,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:32,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9573f1a5-e992-466a-baa0-dc6a3eeda17e/dqc_reference/checkm_data
[2024-01-25 19:02:32,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:32,958] [INFO] Task started: CheckM
[2024-01-25 19:02:32,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459175.1_52087_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459175.1_52087_B01_genomic.fna/checkm_input GCF_900459175.1_52087_B01_genomic.fna/checkm_result
[2024-01-25 19:02:52,231] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:52,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:52,253] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:52,254] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:52,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459175.1_52087_B01_genomic.fna/markers.fasta)
[2024-01-25 19:02:52,254] [INFO] Task started: Blastn
[2024-01-25 19:02:52,254] [INFO] Running command: blastn -query GCF_900459175.1_52087_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9573f1a5-e992-466a-baa0-dc6a3eeda17e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459175.1_52087_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:53,068] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:53,071] [INFO] Selected 15 target genomes.
[2024-01-25 19:02:53,071] [INFO] Target genome list was writen to GCF_900459175.1_52087_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:53,086] [INFO] Task started: fastANI
[2024-01-25 19:02:53,087] [INFO] Running command: fastANI --query /var/lib/cwl/stge814e67f-2bdf-43f7-bf34-f28f5d049fd0/GCF_900459175.1_52087_B01_genomic.fna.gz --refList GCF_900459175.1_52087_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900459175.1_52087_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:00,347] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:00,356] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:00,357] [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_900459175.1	s__Streptococcus downei	100.0	743	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.20	97.65	0.95	0.94	6	conclusive
GCF_000686605.1	s__Streptococcus sobrinus	86.8749	521	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.93	98.60	0.95	0.92	52	-
GCF_000187975.2	s__Streptococcus criceti	80.5536	385	743	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	79.9804	378	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	99.03	0.90	0.90	2	-
GCF_000963255.1	s__Streptococcus infantis_F	79.0352	70	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.05	95.05	0.86	0.86	2	-
GCF_002000985.1	s__Streptococcus gallolyticus	78.9011	101	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCF_001074565.1	s__Streptococcus pseudopneumoniae_J	78.6848	70	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154985.1	s__Streptococcus infantarius	78.0068	88	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_000212855.1	s__Streptococcus sanguinis_A	77.9159	88	743	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	77.78	75	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943655.1	s__Streptococcus sanguinis_F	77.7091	96	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	96.90	0.96	0.95	3	-
GCF_002964045.1	s__Streptococcus suis_U	77.707	75	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.50	95.50	0.81	0.81	2	-
GCF_002960625.1	s__Streptococcus suis_T	77.543	81	743	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	77.4133	89	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.49	98.49	0.90	0.90	2	-
GCF_002760245.1	s__Streptococcus suis_I	77.1415	89	743	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:00,358] [INFO] GTDB search result was written to GCF_900459175.1_52087_B01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:00,358] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:00,361] [INFO] DFAST_QC result json was written to GCF_900459175.1_52087_B01_genomic.fna/dqc_result.json
[2024-01-25 19:03:00,361] [INFO] DFAST_QC completed!
[2024-01-25 19:03:00,361] [INFO] Total running time: 0h0m40s