[2024-01-24 12:06:23,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:23,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:23,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg30d6194a-86a0-4a74-89f9-ecbd70ea5159/dqc_reference
[2024-01-24 12:06:25,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,362] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b70aa34-e8a6-4c53-8f63-26319eb96e79/GCF_016127555.1_ASM1612755v1_genomic.fna.gz | prodigal -d GCF_016127555.1_ASM1612755v1_genomic.fna/cds.fna -a GCF_016127555.1_ASM1612755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:29,977] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:29,977] [INFO] Task started: HMMsearch
[2024-01-24 12:06:29,977] [INFO] Running command: hmmsearch --tblout GCF_016127555.1_ASM1612755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30d6194a-86a0-4a74-89f9-ecbd70ea5159/dqc_reference/reference_markers.hmm GCF_016127555.1_ASM1612755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:30,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:30,241] [INFO] Found 6/6 markers.
[2024-01-24 12:06:30,264] [INFO] Query marker FASTA was written to GCF_016127555.1_ASM1612755v1_genomic.fna/markers.fasta
[2024-01-24 12:06:30,265] [INFO] Task started: Blastn
[2024-01-24 12:06:30,265] [INFO] Running command: blastn -query GCF_016127555.1_ASM1612755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30d6194a-86a0-4a74-89f9-ecbd70ea5159/dqc_reference/reference_markers.fasta -out GCF_016127555.1_ASM1612755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:30,827] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:30,830] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:30,830] [INFO] Target genome list was writen to GCF_016127555.1_ASM1612755v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:30,851] [INFO] Task started: fastANI
[2024-01-24 12:06:30,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b70aa34-e8a6-4c53-8f63-26319eb96e79/GCF_016127555.1_ASM1612755v1_genomic.fna.gz --refList GCF_016127555.1_ASM1612755v1_genomic.fna/target_genomes.txt --output GCF_016127555.1_ASM1612755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:36,255] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:36,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30d6194a-86a0-4a74-89f9-ecbd70ea5159/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:36,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30d6194a-86a0-4a74-89f9-ecbd70ea5159/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:36,271] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:06:36,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:36,271] [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=FDAARGOS_1020	GCA_016127555.1	1303	1303	type	True	100.0	640	643	95	conclusive
Streptococcus oralis	strain=NCTC11427	GCA_900637025.1	1303	1303	type	True	99.9992	640	643	95	conclusive
Streptococcus oralis	strain=CCUG 13229	GCA_002014885.1	1303	1303	type	True	99.9861	631	643	95	conclusive
Streptococcus oralis	strain=CCUG 24891	GCA_001639375.1	1303	1303	type	True	99.9802	626	643	95	conclusive
Streptococcus oralis	strain=ATCC 35037	GCA_000148565.2	1303	1303	type	True	99.9655	612	643	95	conclusive
Streptococcus oralis	strain=ATCC 35037	GCA_000164095.1	1303	1303	type	True	99.9632	633	643	95	conclusive
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	92.3183	522	643	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	87.1569	465	643	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	86.9394	461	643	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.23	108	643	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.1069	123	643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:36,273] [INFO] DFAST Taxonomy check result was written to GCF_016127555.1_ASM1612755v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:36,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:36,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:36,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30d6194a-86a0-4a74-89f9-ecbd70ea5159/dqc_reference/checkm_data
[2024-01-24 12:06:36,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:36,304] [INFO] Task started: CheckM
[2024-01-24 12:06:36,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127555.1_ASM1612755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127555.1_ASM1612755v1_genomic.fna/checkm_input GCF_016127555.1_ASM1612755v1_genomic.fna/checkm_result
[2024-01-24 12:06:56,963] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:56,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:56,980] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:56,980] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:56,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127555.1_ASM1612755v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:56,981] [INFO] Task started: Blastn
[2024-01-24 12:06:56,981] [INFO] Running command: blastn -query GCF_016127555.1_ASM1612755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30d6194a-86a0-4a74-89f9-ecbd70ea5159/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127555.1_ASM1612755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:57,904] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:57,907] [INFO] Selected 23 target genomes.
[2024-01-24 12:06:57,907] [INFO] Target genome list was writen to GCF_016127555.1_ASM1612755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:57,924] [INFO] Task started: fastANI
[2024-01-24 12:06:57,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b70aa34-e8a6-4c53-8f63-26319eb96e79/GCF_016127555.1_ASM1612755v1_genomic.fna.gz --refList GCF_016127555.1_ASM1612755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127555.1_ASM1612755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:08,350] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:08,370] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:08,371] [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	99.9992	640	643	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_003942675.1	s__Streptococcus oralis_BC	94.8882	529	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.25	95.12	0.91	0.89	7	-
GCF_001075675.1	s__Streptococcus oralis_V	94.815	534	643	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	94.7894	461	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.30	95.17	0.90	0.90	6	-
GCF_000960035.1	s__Streptococcus oralis_G	94.7649	544	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.09	95.04	0.93	0.89	6	-
GCF_001579025.1	s__Streptococcus oralis_X	94.7628	552	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096435.1	s__Streptococcus oralis_AA	94.7476	561	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.40	98.81	0.98	0.95	3	-
GCF_001983955.1	s__Streptococcus oralis_H	94.7382	549	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.01	95.40	0.92	0.88	7	-
GCA_905221305.1	s__Streptococcus sp905221305	94.7185	541	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	95.15	0.98	0.91	6	-
GCF_016127915.1	s__Streptococcus oralis_BO	94.63	562	643	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	94.5146	551	643	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	94.2601	453	643	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	93.8446	535	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.55	97.53	0.94	0.94	3	-
GCF_003143695.2	s__Streptococcus halitosis	93.2975	523	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.61	95.24	0.91	0.88	11	-
GCF_003942795.1	s__Streptococcus mitis_BJ	93.2673	512	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.60	99.60	0.93	0.93	2	-
GCA_905221415.1	s__Streptococcus sp905221415	93.0794	516	643	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	93.0557	531	643	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	92.5487	503	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.72	97.71	0.92	0.92	3	-
GCF_002096685.1	s__Streptococcus oralis_AD	92.4566	525	643	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353325.1	s__Streptococcus sp004353325	92.3183	522	643	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	92.0667	513	643	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	91.8639	502	643	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	91.6269	505	643	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 12:07:08,374] [INFO] GTDB search result was written to GCF_016127555.1_ASM1612755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:08,374] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:08,378] [INFO] DFAST_QC result json was written to GCF_016127555.1_ASM1612755v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:08,378] [INFO] DFAST_QC completed!
[2024-01-24 12:07:08,378] [INFO] Total running time: 0h0m44s