[2024-01-24 12:44:42,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:42,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:42,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg434246fa-1e14-42d8-9519-c56df052dcba/dqc_reference
[2024-01-24 12:44:43,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:43,785] [INFO] Task started: Prodigal
[2024-01-24 12:44:43,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg496b0874-282e-4b1a-a629-c566bf7c5e15/GCF_900475445.1_42727_F01_genomic.fna.gz | prodigal -d GCF_900475445.1_42727_F01_genomic.fna/cds.fna -a GCF_900475445.1_42727_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:48,717] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:48,717] [INFO] Task started: HMMsearch
[2024-01-24 12:44:48,717] [INFO] Running command: hmmsearch --tblout GCF_900475445.1_42727_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg434246fa-1e14-42d8-9519-c56df052dcba/dqc_reference/reference_markers.hmm GCF_900475445.1_42727_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:48,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:48,964] [INFO] Found 6/6 markers.
[2024-01-24 12:44:48,992] [INFO] Query marker FASTA was written to GCF_900475445.1_42727_F01_genomic.fna/markers.fasta
[2024-01-24 12:44:48,992] [INFO] Task started: Blastn
[2024-01-24 12:44:48,992] [INFO] Running command: blastn -query GCF_900475445.1_42727_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg434246fa-1e14-42d8-9519-c56df052dcba/dqc_reference/reference_markers.fasta -out GCF_900475445.1_42727_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:49,602] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:49,606] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:49,606] [INFO] Target genome list was writen to GCF_900475445.1_42727_F01_genomic.fna/target_genomes.txt
[2024-01-24 12:44:49,640] [INFO] Task started: fastANI
[2024-01-24 12:44:49,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg496b0874-282e-4b1a-a629-c566bf7c5e15/GCF_900475445.1_42727_F01_genomic.fna.gz --refList GCF_900475445.1_42727_F01_genomic.fna/target_genomes.txt --output GCF_900475445.1_42727_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:55,253] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:55,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg434246fa-1e14-42d8-9519-c56df052dcba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:55,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg434246fa-1e14-42d8-9519-c56df052dcba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:55,264] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:44:55,265] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:55,265] [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 cristatus	strain=NCTC12479	GCA_900475445.1	45634	45634	type	True	100.0	665	666	95	conclusive
Streptococcus cristatus	strain=ATCC 51100	GCA_000222765.2	45634	45634	type	True	99.9714	657	666	95	conclusive
Streptococcus cristatus	strain=ATCC 51100	GCA_000187855.1	45634	45634	type	True	99.9591	654	666	95	conclusive
Streptococcus cristatus	strain=ATCC 51100	GCA_011612585.1	45634	45634	type	True	95.1648	599	666	95	conclusive
Streptococcus sinensis	strain=HKU4	GCA_000767835.1	176090	176090	type	True	87.8069	443	666	95	below_threshold
Streptococcus sanguinis	strain=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	85.2496	420	666	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	81.7851	217	666	95	below_threshold
Streptococcus pneumoniae	strain=CCUG 28588	GCA_001679535.1	1313	1313	type	True	81.3214	193	666	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	80.8442	202	666	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	80.6721	126	666	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.4042	113	666	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.3653	80	666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:55,266] [INFO] DFAST Taxonomy check result was written to GCF_900475445.1_42727_F01_genomic.fna/tc_result.tsv
[2024-01-24 12:44:55,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:55,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:55,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg434246fa-1e14-42d8-9519-c56df052dcba/dqc_reference/checkm_data
[2024-01-24 12:44:55,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:55,291] [INFO] Task started: CheckM
[2024-01-24 12:44:55,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475445.1_42727_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475445.1_42727_F01_genomic.fna/checkm_input GCF_900475445.1_42727_F01_genomic.fna/checkm_result
[2024-01-24 12:45:18,062] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:18,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:18,083] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:18,083] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:18,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475445.1_42727_F01_genomic.fna/markers.fasta)
[2024-01-24 12:45:18,084] [INFO] Task started: Blastn
[2024-01-24 12:45:18,084] [INFO] Running command: blastn -query GCF_900475445.1_42727_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg434246fa-1e14-42d8-9519-c56df052dcba/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475445.1_42727_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:19,024] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:19,028] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:19,029] [INFO] Target genome list was writen to GCF_900475445.1_42727_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:19,051] [INFO] Task started: fastANI
[2024-01-24 12:45:19,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg496b0874-282e-4b1a-a629-c566bf7c5e15/GCF_900475445.1_42727_F01_genomic.fna.gz --refList GCF_900475445.1_42727_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475445.1_42727_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:25,751] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:25,764] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:45:25,764] [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_000222765.1	s__Streptococcus cristatus	99.9714	657	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.39	95.04	0.92	0.87	17	inconclusive
GCF_003943815.1	s__Streptococcus cristatus_F	95.005	576	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_003943465.1	s__Streptococcus cristatus_C	94.8527	579	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.24	95.10	0.94	0.90	8	-
GCF_003943515.1	s__Streptococcus cristatus_D	94.7183	561	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001578775.1	s__Streptococcus cristatus_A	94.5229	567	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003943505.1	s__Streptococcus cristatus_E	94.4233	569	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902460355.1	s__Streptococcus sp902460355	94.0456	589	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369405.1	s__Streptococcus cristatus_G	93.1514	586	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385925.1	s__Streptococcus cristatus_B	92.8523	573	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.95	99.95	1.00	0.99	3	-
GCF_900635155.1	s__Streptococcus sanguinis_G	85.1725	417	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.44	97.44	0.92	0.92	2	-
GCA_905372115.1	s__Streptococcus sp905372115	85.1627	375	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212855.1	s__Streptococcus sanguinis_A	85.0291	400	666	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:25,765] [INFO] GTDB search result was written to GCF_900475445.1_42727_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:25,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:25,770] [INFO] DFAST_QC result json was written to GCF_900475445.1_42727_F01_genomic.fna/dqc_result.json
[2024-01-24 12:45:25,770] [INFO] DFAST_QC completed!
[2024-01-24 12:45:25,770] [INFO] Total running time: 0h0m43s