[2024-01-24 12:51:04,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:04,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:04,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg51da0913-d4f9-4b09-92c0-757cd3ecdb8e/dqc_reference
[2024-01-24 12:51:05,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:05,798] [INFO] Task started: Prodigal
[2024-01-24 12:51:05,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg1554a1f0-bcf3-47a4-8b5c-01ab412bb9ff/GCF_002014885.1_ASM201488v1_genomic.fna.gz | prodigal -d GCF_002014885.1_ASM201488v1_genomic.fna/cds.fna -a GCF_002014885.1_ASM201488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:10,420] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:10,420] [INFO] Task started: HMMsearch
[2024-01-24 12:51:10,421] [INFO] Running command: hmmsearch --tblout GCF_002014885.1_ASM201488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51da0913-d4f9-4b09-92c0-757cd3ecdb8e/dqc_reference/reference_markers.hmm GCF_002014885.1_ASM201488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:10,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:10,686] [INFO] Found 6/6 markers.
[2024-01-24 12:51:10,707] [INFO] Query marker FASTA was written to GCF_002014885.1_ASM201488v1_genomic.fna/markers.fasta
[2024-01-24 12:51:10,708] [INFO] Task started: Blastn
[2024-01-24 12:51:10,708] [INFO] Running command: blastn -query GCF_002014885.1_ASM201488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51da0913-d4f9-4b09-92c0-757cd3ecdb8e/dqc_reference/reference_markers.fasta -out GCF_002014885.1_ASM201488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:11,301] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:11,305] [INFO] Selected 11 target genomes.
[2024-01-24 12:51:11,306] [INFO] Target genome list was writen to GCF_002014885.1_ASM201488v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:11,339] [INFO] Task started: fastANI
[2024-01-24 12:51:11,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg1554a1f0-bcf3-47a4-8b5c-01ab412bb9ff/GCF_002014885.1_ASM201488v1_genomic.fna.gz --refList GCF_002014885.1_ASM201488v1_genomic.fna/target_genomes.txt --output GCF_002014885.1_ASM201488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:15,951] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:15,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51da0913-d4f9-4b09-92c0-757cd3ecdb8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:15,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51da0913-d4f9-4b09-92c0-757cd3ecdb8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:15,967] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:51:15,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:15,967] [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 oralis	strain=CCUG 13229	GCA_002014885.1	1303	1303	type	True	100.0	631	631	95	conclusive
Streptococcus oralis	strain=FDAARGOS_1020	GCA_016127555.1	1303	1303	type	True	99.9946	630	631	95	conclusive
Streptococcus oralis	strain=NCTC11427	GCA_900637025.1	1303	1303	type	True	99.9917	631	631	95	conclusive
Streptococcus oralis	strain=CCUG 24891	GCA_001639375.1	1303	1303	type	True	99.9832	626	631	95	conclusive
Streptococcus oralis	strain=ATCC 35037	GCA_000164095.1	1303	1303	type	True	99.9774	630	631	95	conclusive
Streptococcus oralis	strain=ATCC 35037	GCA_000148565.2	1303	1303	type	True	99.9703	612	631	95	conclusive
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	92.4358	523	631	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	87.1014	453	631	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	86.7761	471	631	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.8506	112	631	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.5147	94	631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:15,970] [INFO] DFAST Taxonomy check result was written to GCF_002014885.1_ASM201488v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:15,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:15,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:15,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51da0913-d4f9-4b09-92c0-757cd3ecdb8e/dqc_reference/checkm_data
[2024-01-24 12:51:15,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:15,996] [INFO] Task started: CheckM
[2024-01-24 12:51:15,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002014885.1_ASM201488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002014885.1_ASM201488v1_genomic.fna/checkm_input GCF_002014885.1_ASM201488v1_genomic.fna/checkm_result
[2024-01-24 12:51:37,106] [INFO] Task succeeded: CheckM
[2024-01-24 12:51:37,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:51:37,123] [INFO] ===== Completeness check finished =====
[2024-01-24 12:51:37,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:51:37,125] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002014885.1_ASM201488v1_genomic.fna/markers.fasta)
[2024-01-24 12:51:37,125] [INFO] Task started: Blastn
[2024-01-24 12:51:37,125] [INFO] Running command: blastn -query GCF_002014885.1_ASM201488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51da0913-d4f9-4b09-92c0-757cd3ecdb8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002014885.1_ASM201488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:37,918] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:37,923] [INFO] Selected 23 target genomes.
[2024-01-24 12:51:37,923] [INFO] Target genome list was writen to GCF_002014885.1_ASM201488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:51:37,948] [INFO] Task started: fastANI
[2024-01-24 12:51:37,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg1554a1f0-bcf3-47a4-8b5c-01ab412bb9ff/GCF_002014885.1_ASM201488v1_genomic.fna.gz --refList GCF_002014885.1_ASM201488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002014885.1_ASM201488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:51:47,760] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:47,778] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:51:47,779] [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_900637025.1	s__Streptococcus oralis	99.9917	631	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.04	95.11	0.90	0.80	39	conclusive
GCF_001075675.1	s__Streptococcus oralis_V	94.9054	528	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_001579025.1	s__Streptococcus oralis_X	94.8624	545	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905371745.1	s__Streptococcus sp905371745	94.8343	456	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.30	95.17	0.90	0.90	6	-
GCF_003942675.1	s__Streptococcus oralis_BC	94.7692	537	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.25	95.12	0.91	0.89	7	-
GCF_000960035.1	s__Streptococcus oralis_G	94.7685	538	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.09	95.04	0.93	0.89	6	-
GCA_905221305.1	s__Streptococcus sp905221305	94.7354	538	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	95.15	0.98	0.91	6	-
GCF_001983955.1	s__Streptococcus oralis_H	94.7013	537	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.01	95.40	0.92	0.88	7	-
GCF_002096435.1	s__Streptococcus oralis_AA	94.6888	561	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.40	98.81	0.98	0.95	3	-
GCF_016127915.1	s__Streptococcus oralis_BO	94.5645	553	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000831085.1	s__Streptococcus sp000831085	94.4809	550	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.77	96.77	0.93	0.93	2	-
GCA_900546335.1	s__Streptococcus sp900546335	94.33	452	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221255.1	s__Streptococcus sp905221255	93.8278	540	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	97.53	0.94	0.94	3	-
GCF_003942795.1	s__Streptococcus mitis_BJ	93.3169	514	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.60	99.60	0.93	0.93	2	-
GCF_003143695.2	s__Streptococcus halitosis	93.311	519	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.61	95.24	0.91	0.88	11	-
GCA_905221415.1	s__Streptococcus sp905221415	93.2201	510	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002356415.1	s__Streptococcus oralis_F	92.8464	524	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.57	95.26	0.91	0.90	6	-
GCA_905221385.1	s__Streptococcus sp905221385	92.5832	498	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.72	97.71	0.92	0.92	3	-
GCF_004353325.1	s__Streptococcus sp004353325	92.4358	523	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_002096685.1	s__Streptococcus oralis_AD	92.3835	519	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_016028255.1	s__Streptococcus oralis_AC	91.9063	519	631	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.16	95.70	0.95	0.93	5	-
GCF_003944215.1	s__Streptococcus oralis_BI	91.7212	500	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_900104285.1	s__Streptococcus sp900104285	91.6302	500	631	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 12:51:47,780] [INFO] GTDB search result was written to GCF_002014885.1_ASM201488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:51:47,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:51:47,785] [INFO] DFAST_QC result json was written to GCF_002014885.1_ASM201488v1_genomic.fna/dqc_result.json
[2024-01-24 12:51:47,785] [INFO] DFAST_QC completed!
[2024-01-24 12:51:47,785] [INFO] Total running time: 0h0m43s