[2024-01-24 11:34:38,231] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,233] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e889eac-4d36-42cb-a5e5-c36c9ccbcfa2/dqc_reference
[2024-01-24 11:34:39,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:39,642] [INFO] Task started: Prodigal
[2024-01-24 11:34:39,643] [INFO] Running command: gunzip -c /var/lib/cwl/stge8bcd015-6e1f-466d-bc26-329cff308ffc/GCF_006739205.1_ASM673920v1_genomic.fna.gz | prodigal -d GCF_006739205.1_ASM673920v1_genomic.fna/cds.fna -a GCF_006739205.1_ASM673920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:43,809] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:43,810] [INFO] Task started: HMMsearch
[2024-01-24 11:34:43,810] [INFO] Running command: hmmsearch --tblout GCF_006739205.1_ASM673920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e889eac-4d36-42cb-a5e5-c36c9ccbcfa2/dqc_reference/reference_markers.hmm GCF_006739205.1_ASM673920v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:44,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:44,212] [INFO] Found 6/6 markers.
[2024-01-24 11:34:44,231] [INFO] Query marker FASTA was written to GCF_006739205.1_ASM673920v1_genomic.fna/markers.fasta
[2024-01-24 11:34:44,232] [INFO] Task started: Blastn
[2024-01-24 11:34:44,232] [INFO] Running command: blastn -query GCF_006739205.1_ASM673920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e889eac-4d36-42cb-a5e5-c36c9ccbcfa2/dqc_reference/reference_markers.fasta -out GCF_006739205.1_ASM673920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:46,478] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:46,482] [INFO] Selected 8 target genomes.
[2024-01-24 11:34:46,482] [INFO] Target genome list was writen to GCF_006739205.1_ASM673920v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:46,495] [INFO] Task started: fastANI
[2024-01-24 11:34:46,495] [INFO] Running command: fastANI --query /var/lib/cwl/stge8bcd015-6e1f-466d-bc26-329cff308ffc/GCF_006739205.1_ASM673920v1_genomic.fna.gz --refList GCF_006739205.1_ASM673920v1_genomic.fna/target_genomes.txt --output GCF_006739205.1_ASM673920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:34:50,429] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:50,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e889eac-4d36-42cb-a5e5-c36c9ccbcfa2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:34:50,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e889eac-4d36-42cb-a5e5-c36c9ccbcfa2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:34:50,436] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:34:50,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:34:50,436] [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 mutans	strain=NBRC 13955	GCA_006739205.1	1309	1309	type	True	100.0	670	672	95	conclusive
Streptococcus mutans	strain=FDAARGOS 1458	GCA_019048645.1	1309	1309	type	True	99.9989	669	672	95	conclusive
Streptococcus mutans	strain=NCTC10449	GCA_900475095.1	1309	1309	type	True	99.9989	670	672	95	conclusive
Streptococcus mutans	strain=ATCC 25175	GCA_000347875.1	1309	1309	type	True	99.9774	654	672	95	conclusive
Streptococcus mutans	strain=DSM 20523	GCA_000375505.1	1309	1309	type	True	99.9521	653	672	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:34:50,438] [INFO] DFAST Taxonomy check result was written to GCF_006739205.1_ASM673920v1_genomic.fna/tc_result.tsv
[2024-01-24 11:34:50,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:34:50,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:34:50,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e889eac-4d36-42cb-a5e5-c36c9ccbcfa2/dqc_reference/checkm_data
[2024-01-24 11:34:50,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:34:50,461] [INFO] Task started: CheckM
[2024-01-24 11:34:50,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006739205.1_ASM673920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006739205.1_ASM673920v1_genomic.fna/checkm_input GCF_006739205.1_ASM673920v1_genomic.fna/checkm_result
[2024-01-24 11:35:11,521] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:11,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:11,544] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:11,544] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:11,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006739205.1_ASM673920v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:11,545] [INFO] Task started: Blastn
[2024-01-24 11:35:11,545] [INFO] Running command: blastn -query GCF_006739205.1_ASM673920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e889eac-4d36-42cb-a5e5-c36c9ccbcfa2/dqc_reference/reference_markers_gtdb.fasta -out GCF_006739205.1_ASM673920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:12,418] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:12,421] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:12,421] [INFO] Target genome list was writen to GCF_006739205.1_ASM673920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:12,432] [INFO] Task started: fastANI
[2024-01-24 11:35:12,433] [INFO] Running command: fastANI --query /var/lib/cwl/stge8bcd015-6e1f-466d-bc26-329cff308ffc/GCF_006739205.1_ASM673920v1_genomic.fna.gz --refList GCF_006739205.1_ASM673920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006739205.1_ASM673920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:18,632] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:18,645] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:18,645] [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_006739205.1	s__Streptococcus mutans	100.0	669	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.12	98.73	0.95	0.87	261	conclusive
GCF_002355215.1	s__Streptococcus troglodytae	94.8583	591	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286075.1	s__Streptococcus ratti	80.0327	378	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_001431045.1	s__Streptococcus orisasini	79.5609	359	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187995.2	s__Streptococcus macacae	79.3216	311	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001937065.1	s__Streptococcus sp001937065	79.1778	325	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423725.1	s__Streptococcus devriesei	78.6017	307	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379985.1	s__Streptococcus caballi	78.5503	151	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000283635.1	s__Streptococcus macedonicus	78.5141	147	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	78.5	121	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188055.2	s__Streptococcus urinalis	78.1599	126	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.98	99.96	0.98	0.97	3	-
GCF_010604095.1	s__Streptococcus sp000187445	77.8842	109	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_000376985.1	s__Streptococcus henryi	77.8308	144	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_000380005.1	s__Streptococcus didelphis	77.6623	102	672	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 11:35:18,648] [INFO] GTDB search result was written to GCF_006739205.1_ASM673920v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:18,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:18,652] [INFO] DFAST_QC result json was written to GCF_006739205.1_ASM673920v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:18,652] [INFO] DFAST_QC completed!
[2024-01-24 11:35:18,652] [INFO] Total running time: 0h0m40s