[2024-01-25 18:06:05,533] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,534] [INFO] DQC Reference Directory: /var/lib/cwl/stgd200141a-d5c8-4a61-90b6-13e7bd26729d/dqc_reference
[2024-01-25 18:06:06,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,692] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4cb0871-1b86-4464-b5b0-0892258a6571/GCF_900459045.1_41975_B01_genomic.fna.gz | prodigal -d GCF_900459045.1_41975_B01_genomic.fna/cds.fna -a GCF_900459045.1_41975_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:11,715] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:11,715] [INFO] Task started: HMMsearch
[2024-01-25 18:06:11,715] [INFO] Running command: hmmsearch --tblout GCF_900459045.1_41975_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd200141a-d5c8-4a61-90b6-13e7bd26729d/dqc_reference/reference_markers.hmm GCF_900459045.1_41975_B01_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:11,937] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:11,939] [INFO] Found 6/6 markers.
[2024-01-25 18:06:11,959] [INFO] Query marker FASTA was written to GCF_900459045.1_41975_B01_genomic.fna/markers.fasta
[2024-01-25 18:06:11,959] [INFO] Task started: Blastn
[2024-01-25 18:06:11,959] [INFO] Running command: blastn -query GCF_900459045.1_41975_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd200141a-d5c8-4a61-90b6-13e7bd26729d/dqc_reference/reference_markers.fasta -out GCF_900459045.1_41975_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:12,502] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:12,504] [INFO] Selected 11 target genomes.
[2024-01-25 18:06:12,505] [INFO] Target genome list was writen to GCF_900459045.1_41975_B01_genomic.fna/target_genomes.txt
[2024-01-25 18:06:12,513] [INFO] Task started: fastANI
[2024-01-25 18:06:12,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4cb0871-1b86-4464-b5b0-0892258a6571/GCF_900459045.1_41975_B01_genomic.fna.gz --refList GCF_900459045.1_41975_B01_genomic.fna/target_genomes.txt --output GCF_900459045.1_41975_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:25,467] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:25,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd200141a-d5c8-4a61-90b6-13e7bd26729d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:25,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd200141a-d5c8-4a61-90b6-13e7bd26729d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:25,476] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:06:25,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:25,477] [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 acidominimus	strain=NCTC12957	GCA_900459045.1	1326	1326	type	True	100.0	806	812	95	conclusive
Streptococcus acidominimus	strain=CCUG 27296	GCA_001921825.1	1326	1326	type	True	99.8652	696	812	95	conclusive
Streptococcus cuniculi	strain=CCUG 65085	GCA_001921845.1	1432788	1432788	type	True	82.5948	462	812	95	below_threshold
Streptococcus respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	82.4566	447	812	95	below_threshold
Streptococcus azizii	strain=12-5202	GCA_001984715.1	1579424	1579424	type	True	81.5655	460	812	95	below_threshold
Streptococcus marmotae	strain=HTS5	GCA_001623565.1	1825069	1825069	type	True	80.6887	376	812	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	79.0508	116	812	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.8464	149	812	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	78.421	87	812	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.3478	166	812	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.1708	104	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:25,478] [INFO] DFAST Taxonomy check result was written to GCF_900459045.1_41975_B01_genomic.fna/tc_result.tsv
[2024-01-25 18:06:25,479] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:25,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:25,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd200141a-d5c8-4a61-90b6-13e7bd26729d/dqc_reference/checkm_data
[2024-01-25 18:06:25,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:25,506] [INFO] Task started: CheckM
[2024-01-25 18:06:25,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459045.1_41975_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459045.1_41975_B01_genomic.fna/checkm_input GCF_900459045.1_41975_B01_genomic.fna/checkm_result
[2024-01-25 18:06:46,551] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:46,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:46,568] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:46,568] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:46,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459045.1_41975_B01_genomic.fna/markers.fasta)
[2024-01-25 18:06:46,569] [INFO] Task started: Blastn
[2024-01-25 18:06:46,569] [INFO] Running command: blastn -query GCF_900459045.1_41975_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgd200141a-d5c8-4a61-90b6-13e7bd26729d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459045.1_41975_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:47,389] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:47,391] [INFO] Selected 7 target genomes.
[2024-01-25 18:06:47,391] [INFO] Target genome list was writen to GCF_900459045.1_41975_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:47,400] [INFO] Task started: fastANI
[2024-01-25 18:06:47,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4cb0871-1b86-4464-b5b0-0892258a6571/GCF_900459045.1_41975_B01_genomic.fna.gz --refList GCF_900459045.1_41975_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900459045.1_41975_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:57,592] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:57,598] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:57,598] [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_001921825.1	s__Streptococcus acidominimus	99.8652	696	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.52	97.98	0.90	0.85	5	conclusive
GCF_004570575.1	s__Streptococcus cuniculi_A	84.0708	439	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004569635.1	s__Streptococcus sp004569635	83.5408	499	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001921845.1	s__Streptococcus cuniculi	82.6358	459	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003595525.1	s__Streptococcus respiraculi	82.4168	450	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984715.1	s__Streptococcus azizii	81.5574	460	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.97	99.96	0.99	0.99	5	-
GCF_017639855.1	s__Streptococcus sp013623465	81.0104	387	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.97	99.93	0.99	0.98	7	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:57,599] [INFO] GTDB search result was written to GCF_900459045.1_41975_B01_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:57,600] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:57,610] [INFO] DFAST_QC result json was written to GCF_900459045.1_41975_B01_genomic.fna/dqc_result.json
[2024-01-25 18:06:57,610] [INFO] DFAST_QC completed!
[2024-01-25 18:06:57,610] [INFO] Total running time: 0h0m52s