[2024-01-24 14:28:02,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b7664bd-2b94-4570-8400-310716365ce2/dqc_reference
[2024-01-24 14:28:03,912] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:03,913] [INFO] Task started: Prodigal
[2024-01-24 14:28:03,913] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5a1fa0f-7ba7-4bd0-b4ba-6288d5bed12f/GCF_000154985.1_ASM15498v1_genomic.fna.gz | prodigal -d GCF_000154985.1_ASM15498v1_genomic.fna/cds.fna -a GCF_000154985.1_ASM15498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:08,212] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:08,212] [INFO] Task started: HMMsearch
[2024-01-24 14:28:08,213] [INFO] Running command: hmmsearch --tblout GCF_000154985.1_ASM15498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b7664bd-2b94-4570-8400-310716365ce2/dqc_reference/reference_markers.hmm GCF_000154985.1_ASM15498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:08,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:08,455] [INFO] Found 6/6 markers.
[2024-01-24 14:28:08,479] [INFO] Query marker FASTA was written to GCF_000154985.1_ASM15498v1_genomic.fna/markers.fasta
[2024-01-24 14:28:08,479] [INFO] Task started: Blastn
[2024-01-24 14:28:08,479] [INFO] Running command: blastn -query GCF_000154985.1_ASM15498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7664bd-2b94-4570-8400-310716365ce2/dqc_reference/reference_markers.fasta -out GCF_000154985.1_ASM15498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:09,073] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:09,076] [INFO] Selected 13 target genomes.
[2024-01-24 14:28:09,077] [INFO] Target genome list was writen to GCF_000154985.1_ASM15498v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:09,085] [INFO] Task started: fastANI
[2024-01-24 14:28:09,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a1fa0f-7ba7-4bd0-b4ba-6288d5bed12f/GCF_000154985.1_ASM15498v1_genomic.fna.gz --refList GCF_000154985.1_ASM15498v1_genomic.fna/target_genomes.txt --output GCF_000154985.1_ASM15498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:14,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:14,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b7664bd-2b94-4570-8400-310716365ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:14,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b7664bd-2b94-4570-8400-310716365ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:14,735] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:28:14,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:14,736] [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 infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	100.0	630	631	95	conclusive
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	99.9872	630	631	95	conclusive
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	99.987	629	631	95	conclusive
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	94.1781	510	631	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	94.1747	504	631	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	93.881	511	631	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	90.2389	520	631	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	85.0011	468	631	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.2304	59	631	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.2016	72	631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:14,740] [INFO] DFAST Taxonomy check result was written to GCF_000154985.1_ASM15498v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:14,740] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:14,740] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:14,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b7664bd-2b94-4570-8400-310716365ce2/dqc_reference/checkm_data
[2024-01-24 14:28:14,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:14,764] [INFO] Task started: CheckM
[2024-01-24 14:28:14,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000154985.1_ASM15498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000154985.1_ASM15498v1_genomic.fna/checkm_input GCF_000154985.1_ASM15498v1_genomic.fna/checkm_result
[2024-01-24 14:28:36,664] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:36,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:36,683] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:36,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:36,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000154985.1_ASM15498v1_genomic.fna/markers.fasta)
[2024-01-24 14:28:36,684] [INFO] Task started: Blastn
[2024-01-24 14:28:36,684] [INFO] Running command: blastn -query GCF_000154985.1_ASM15498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b7664bd-2b94-4570-8400-310716365ce2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000154985.1_ASM15498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:37,511] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:37,514] [INFO] Selected 8 target genomes.
[2024-01-24 14:28:37,514] [INFO] Target genome list was writen to GCF_000154985.1_ASM15498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:37,836] [INFO] Task started: fastANI
[2024-01-24 14:28:37,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5a1fa0f-7ba7-4bd0-b4ba-6288d5bed12f/GCF_000154985.1_ASM15498v1_genomic.fna.gz --refList GCF_000154985.1_ASM15498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000154985.1_ASM15498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:28:42,390] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:42,398] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:28:42,398] [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_000154985.1	s__Streptococcus infantarius	100.0	629	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	conclusive
GCF_900101445.1	s__Streptococcus equinus_B	94.281	519	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_900475675.1	s__Streptococcus lutetiensis	94.1781	510	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_900104225.1	s__Streptococcus equinus_D	90.2689	493	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461705.1	s__Streptococcus vicugnae	90.2277	521	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCA_000283635.1	s__Streptococcus macedonicus	86.0488	473	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_002000985.1	s__Streptococcus gallolyticus	85.0109	467	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCA_900478025.1	s__Streptococcus pasteurianus	84.6746	448	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.1304	99.06	98.58	0.89	0.84	22	-
--------------------------------------------------------------------------------
[2024-01-24 14:28:42,400] [INFO] GTDB search result was written to GCF_000154985.1_ASM15498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:28:42,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:28:42,403] [INFO] DFAST_QC result json was written to GCF_000154985.1_ASM15498v1_genomic.fna/dqc_result.json
[2024-01-24 14:28:42,403] [INFO] DFAST_QC completed!
[2024-01-24 14:28:42,403] [INFO] Total running time: 0h0m40s