[2024-01-24 11:26:36,052] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:36,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:36,056] [INFO] DQC Reference Directory: /var/lib/cwl/stg78c4c5ca-60d0-4e62-a928-140d4dff522f/dqc_reference
[2024-01-24 11:26:37,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:37,339] [INFO] Task started: Prodigal
[2024-01-24 11:26:37,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg1af0ad27-4aee-485d-9960-896f86f34315/GCF_003841405.1_ASM384140v1_genomic.fna.gz | prodigal -d GCF_003841405.1_ASM384140v1_genomic.fna/cds.fna -a GCF_003841405.1_ASM384140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:42,515] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:42,515] [INFO] Task started: HMMsearch
[2024-01-24 11:26:42,516] [INFO] Running command: hmmsearch --tblout GCF_003841405.1_ASM384140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78c4c5ca-60d0-4e62-a928-140d4dff522f/dqc_reference/reference_markers.hmm GCF_003841405.1_ASM384140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:42,773] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:42,775] [INFO] Found 6/6 markers.
[2024-01-24 11:26:42,800] [INFO] Query marker FASTA was written to GCF_003841405.1_ASM384140v1_genomic.fna/markers.fasta
[2024-01-24 11:26:42,801] [INFO] Task started: Blastn
[2024-01-24 11:26:42,801] [INFO] Running command: blastn -query GCF_003841405.1_ASM384140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c4c5ca-60d0-4e62-a928-140d4dff522f/dqc_reference/reference_markers.fasta -out GCF_003841405.1_ASM384140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:43,432] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:43,436] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:43,437] [INFO] Target genome list was writen to GCF_003841405.1_ASM384140v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:43,483] [INFO] Task started: fastANI
[2024-01-24 11:26:43,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg1af0ad27-4aee-485d-9960-896f86f34315/GCF_003841405.1_ASM384140v1_genomic.fna.gz --refList GCF_003841405.1_ASM384140v1_genomic.fna/target_genomes.txt --output GCF_003841405.1_ASM384140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:50,810] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:50,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78c4c5ca-60d0-4e62-a928-140d4dff522f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:50,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78c4c5ca-60d0-4e62-a928-140d4dff522f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:50,817] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:50,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:50,817] [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
Tetragenococcus halophilus subsp. halophilus	strain=DSM 20339	GCA_003841405.1	1513897	51669	type	True	100.0	860	863	95	conclusive
Tetragenococcus halophilus subsp. flandriensis	strain=DSM 23766	GCA_002922845.1	1513898	51669	type	True	96.0817	625	863	95	conclusive
Tetragenococcus solitarius	strain=NBRC 100494	GCA_001544195.1	71453	71453	type	True	81.5214	471	863	95	below_threshold
Tetragenococcus muriaticus	strain=DSM 15685	GCA_000423785.1	64642	64642	type	True	81.2531	410	863	95	below_threshold
Tetragenococcus koreensis	strain=KCTC 3924	GCA_003795145.1	290335	290335	type	True	80.8931	514	863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:50,819] [INFO] DFAST Taxonomy check result was written to GCF_003841405.1_ASM384140v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:50,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:50,820] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:50,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78c4c5ca-60d0-4e62-a928-140d4dff522f/dqc_reference/checkm_data
[2024-01-24 11:26:50,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:50,850] [INFO] Task started: CheckM
[2024-01-24 11:26:50,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003841405.1_ASM384140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003841405.1_ASM384140v1_genomic.fna/checkm_input GCF_003841405.1_ASM384140v1_genomic.fna/checkm_result
[2024-01-24 11:27:12,790] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:12,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:12,813] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:12,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:12,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003841405.1_ASM384140v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:12,814] [INFO] Task started: Blastn
[2024-01-24 11:27:12,814] [INFO] Running command: blastn -query GCF_003841405.1_ASM384140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78c4c5ca-60d0-4e62-a928-140d4dff522f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003841405.1_ASM384140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:13,605] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:13,609] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:13,609] [INFO] Target genome list was writen to GCF_003841405.1_ASM384140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:13,642] [INFO] Task started: fastANI
[2024-01-24 11:27:13,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg1af0ad27-4aee-485d-9960-896f86f34315/GCF_003841405.1_ASM384140v1_genomic.fna.gz --refList GCF_003841405.1_ASM384140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003841405.1_ASM384140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:21,265] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:21,277] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:21,277] [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_003841405.1	s__Tetragenococcus halophilus	100.0	861	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	97.86	96.17	0.89	0.79	30	conclusive
GCF_003795125.1	s__Tetragenococcus osmophilus	82.179	456	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544195.1	s__Tetragenococcus solitarius	81.5025	473	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423785.1	s__Tetragenococcus muriaticus	81.2978	411	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	98.93	98.87	0.88	0.86	3	-
GCF_003795145.1	s__Tetragenococcus koreensis	80.9039	517	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Tetragenococcus	95.0	99.21	98.98	0.92	0.90	7	-
GCF_011397115.1	s__Enterococcus_C saigonensis	78.8687	95	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377505.1	s__Enterococcus sp017377505	77.238	51	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	95.67	95.67	0.83	0.83	2	-
GCF_017426705.1	s__Enterococcus_F sp017426705	77.0733	120	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148425.1	s__Enterococcus sp002148425	76.9661	60	863	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus	95.0	98.91	98.88	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,279] [INFO] GTDB search result was written to GCF_003841405.1_ASM384140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:21,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:21,283] [INFO] DFAST_QC result json was written to GCF_003841405.1_ASM384140v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:21,283] [INFO] DFAST_QC completed!
[2024-01-24 11:27:21,283] [INFO] Total running time: 0h0m45s