[2024-01-24 13:01:10,950] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:10,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:10,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb501423-682e-48a6-b9ec-2ef222c71968/dqc_reference
[2024-01-24 13:01:12,228] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:12,229] [INFO] Task started: Prodigal
[2024-01-24 13:01:12,229] [INFO] Running command: gunzip -c /var/lib/cwl/stg46c4881b-8bf1-4fe1-8567-616f28a68213/GCF_900447955.1_43366_G01_genomic.fna.gz | prodigal -d GCF_900447955.1_43366_G01_genomic.fna/cds.fna -a GCF_900447955.1_43366_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:23,001] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:23,002] [INFO] Task started: HMMsearch
[2024-01-24 13:01:23,002] [INFO] Running command: hmmsearch --tblout GCF_900447955.1_43366_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb501423-682e-48a6-b9ec-2ef222c71968/dqc_reference/reference_markers.hmm GCF_900447955.1_43366_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:23,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:23,356] [INFO] Found 6/6 markers.
[2024-01-24 13:01:23,405] [INFO] Query marker FASTA was written to GCF_900447955.1_43366_G01_genomic.fna/markers.fasta
[2024-01-24 13:01:23,405] [INFO] Task started: Blastn
[2024-01-24 13:01:23,405] [INFO] Running command: blastn -query GCF_900447955.1_43366_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb501423-682e-48a6-b9ec-2ef222c71968/dqc_reference/reference_markers.fasta -out GCF_900447955.1_43366_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:24,063] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:24,066] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:24,067] [INFO] Target genome list was writen to GCF_900447955.1_43366_G01_genomic.fna/target_genomes.txt
[2024-01-24 13:01:24,073] [INFO] Task started: fastANI
[2024-01-24 13:01:24,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c4881b-8bf1-4fe1-8567-616f28a68213/GCF_900447955.1_43366_G01_genomic.fna.gz --refList GCF_900447955.1_43366_G01_genomic.fna/target_genomes.txt --output GCF_900447955.1_43366_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:34,381] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:34,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb501423-682e-48a6-b9ec-2ef222c71968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:34,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb501423-682e-48a6-b9ec-2ef222c71968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:34,390] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:01:34,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:34,390] [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
Enterococcus malodoratus	strain=NCTC12365	GCA_900447955.1	71451	71451	type	True	100.0	1540	1542	95	conclusive
Enterococcus malodoratus	strain=ATCC 43197	GCA_000407185.1	71451	71451	type	True	99.9995	1534	1542	95	conclusive
Enterococcus malodoratus	strain=ATCC 43197	GCA_000393875.1	71451	71451	type	True	99.9811	1525	1542	95	conclusive
Enterococcus malodoratus	strain=DSM 20681	GCA_001886025.1	71451	71451	type	True	99.9441	1447	1542	95	conclusive
Enterococcus hulanensis	strain=190-7	GCA_005405485.1	2559929	2559929	type	True	82.0428	932	1542	95	below_threshold
Enterococcus avium	strain=DSM 20679	GCA_001885775.1	33945	33945	type	True	81.9363	793	1542	95	below_threshold
Enterococcus raffinosus	strain=NBRC 100492	GCA_001544115.1	71452	71452	type	True	81.6276	793	1542	95	below_threshold
Vagococcus xieshaowenii	strain=personal::cf-49	GCA_004792515.1	2562451	2562451	type	True	79.9759	62	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:34,394] [INFO] DFAST Taxonomy check result was written to GCF_900447955.1_43366_G01_genomic.fna/tc_result.tsv
[2024-01-24 13:01:34,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:34,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:34,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb501423-682e-48a6-b9ec-2ef222c71968/dqc_reference/checkm_data
[2024-01-24 13:01:34,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:34,448] [INFO] Task started: CheckM
[2024-01-24 13:01:34,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447955.1_43366_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447955.1_43366_G01_genomic.fna/checkm_input GCF_900447955.1_43366_G01_genomic.fna/checkm_result
[2024-01-24 13:02:11,001] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:11,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:11,023] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:11,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:11,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447955.1_43366_G01_genomic.fna/markers.fasta)
[2024-01-24 13:02:11,024] [INFO] Task started: Blastn
[2024-01-24 13:02:11,024] [INFO] Running command: blastn -query GCF_900447955.1_43366_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb501423-682e-48a6-b9ec-2ef222c71968/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447955.1_43366_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:11,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:11,825] [INFO] Selected 11 target genomes.
[2024-01-24 13:02:11,825] [INFO] Target genome list was writen to GCF_900447955.1_43366_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:11,833] [INFO] Task started: fastANI
[2024-01-24 13:02:11,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg46c4881b-8bf1-4fe1-8567-616f28a68213/GCF_900447955.1_43366_G01_genomic.fna.gz --refList GCF_900447955.1_43366_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447955.1_43366_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:20,956] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:20,966] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:20,966] [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_000407185.1	s__Enterococcus_A malodoratus	99.9995	1534	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.33	98.27	0.94	0.84	8	conclusive
GCF_000406965.1	s__Enterococcus_A avium	82.2029	828	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.01	97.91	0.91	0.78	43	-
GCF_005405485.1	s__Enterococcus_A hulanensis	82.0507	931	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	97.15	97.02	0.83	0.81	4	-
GCF_017315985.1	s__Enterococcus_A sp017315985	81.8467	838	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917525.1	s__Enterococcus_A raffinosus_A	81.6903	834	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886185.1	s__Enterococcus_A raffinosus	81.6769	779	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	99.27	97.96	0.91	0.87	12	-
GCF_000407545.1	s__Enterococcus_A gilvus	81.6433	705	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.79	97.90	0.91	0.83	8	-
GCF_001544295.1	s__Enterococcus_A pseudoavium	81.506	535	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885905.1	s__Enterococcus_A devriesei	80.9104	569	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	98.13	98.05	0.88	0.86	3	-
GCF_005405225.1	s__Enterococcus_A dongliensis	80.8798	393	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885945.1	s__Enterococcus_A hermanniensis	80.2404	438	1542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,968] [INFO] GTDB search result was written to GCF_900447955.1_43366_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:20,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:20,972] [INFO] DFAST_QC result json was written to GCF_900447955.1_43366_G01_genomic.fna/dqc_result.json
[2024-01-24 13:02:20,972] [INFO] DFAST_QC completed!
[2024-01-24 13:02:20,972] [INFO] Total running time: 0h1m10s