[2024-01-24 13:49:40,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg085d95f6-09f2-4522-824d-d9d726a8e861/dqc_reference
[2024-01-24 13:49:41,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,414] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,414] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6aafb82-af42-450d-98c2-b5f364209e65/GCF_005405325.1_ASM540532v1_genomic.fna.gz | prodigal -d GCF_005405325.1_ASM540532v1_genomic.fna/cds.fna -a GCF_005405325.1_ASM540532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:47,300] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:47,301] [INFO] Task started: HMMsearch
[2024-01-24 13:49:47,301] [INFO] Running command: hmmsearch --tblout GCF_005405325.1_ASM540532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg085d95f6-09f2-4522-824d-d9d726a8e861/dqc_reference/reference_markers.hmm GCF_005405325.1_ASM540532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:47,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:47,552] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6aafb82-af42-450d-98c2-b5f364209e65/GCF_005405325.1_ASM540532v1_genomic.fna.gz]
[2024-01-24 13:49:47,583] [INFO] Query marker FASTA was written to GCF_005405325.1_ASM540532v1_genomic.fna/markers.fasta
[2024-01-24 13:49:47,584] [INFO] Task started: Blastn
[2024-01-24 13:49:47,584] [INFO] Running command: blastn -query GCF_005405325.1_ASM540532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg085d95f6-09f2-4522-824d-d9d726a8e861/dqc_reference/reference_markers.fasta -out GCF_005405325.1_ASM540532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,187] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,190] [INFO] Selected 11 target genomes.
[2024-01-24 13:49:48,191] [INFO] Target genome list was writen to GCF_005405325.1_ASM540532v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:48,193] [INFO] Task started: fastANI
[2024-01-24 13:49:48,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6aafb82-af42-450d-98c2-b5f364209e65/GCF_005405325.1_ASM540532v1_genomic.fna.gz --refList GCF_005405325.1_ASM540532v1_genomic.fna/target_genomes.txt --output GCF_005405325.1_ASM540532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:01,750] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:01,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg085d95f6-09f2-4522-824d-d9d726a8e861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:01,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg085d95f6-09f2-4522-824d-d9d726a8e861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:01,765] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:01,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:01,765] [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
Companilactobacillus heilongjiangensis	strain=S4-3	GCA_005405325.1	1074467	1074467	type	True	100.0	896	897	95	conclusive
Companilactobacillus heilongjiangensis	strain=DSM 28069	GCA_000831645.3	1074467	1074467	type	True	99.9958	897	897	95	conclusive
Companilactobacillus huachuanensis	strain=395-6.2	GCA_005404815.1	2559914	2559914	type	True	87.3016	747	897	95	below_threshold
Companilactobacillus nantensis	strain=DSM 16982	GCA_001435815.1	305793	305793	type	True	84.8238	645	897	95	below_threshold
Companilactobacillus zhachilii	strain=HBUAS52074	GCA_003606365.2	2304606	2304606	type	True	84.3857	629	897	95	below_threshold
Companilactobacillus musae	strain=313	GCA_003573575.1	1903258	1903258	type	True	82.7834	485	897	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	81.4933	407	897	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	81.4712	429	897	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.3522	241	897	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	78.818	205	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,767] [INFO] DFAST Taxonomy check result was written to GCF_005405325.1_ASM540532v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:01,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:01,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:01,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg085d95f6-09f2-4522-824d-d9d726a8e861/dqc_reference/checkm_data
[2024-01-24 13:50:01,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:01,797] [INFO] Task started: CheckM
[2024-01-24 13:50:01,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405325.1_ASM540532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405325.1_ASM540532v1_genomic.fna/checkm_input GCF_005405325.1_ASM540532v1_genomic.fna/checkm_result
[2024-01-24 13:50:26,176] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:26,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,197] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:26,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:26,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405325.1_ASM540532v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:26,198] [INFO] Task started: Blastn
[2024-01-24 13:50:26,199] [INFO] Running command: blastn -query GCF_005405325.1_ASM540532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg085d95f6-09f2-4522-824d-d9d726a8e861/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405325.1_ASM540532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:26,981] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:26,997] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:26,997] [INFO] Target genome list was writen to GCF_005405325.1_ASM540532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:27,004] [INFO] Task started: fastANI
[2024-01-24 13:50:27,004] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6aafb82-af42-450d-98c2-b5f364209e65/GCF_005405325.1_ASM540532v1_genomic.fna.gz --refList GCF_005405325.1_ASM540532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405325.1_ASM540532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:37,452] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:37,459] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:37,460] [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_000831645.3	s__Companilactobacillus heilongjiangensis	99.9958	897	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_005404815.1	s__Companilactobacillus huachuanensis	87.3384	744	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435815.1	s__Companilactobacillus nantensis	84.8363	644	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003606365.2	s__Companilactobacillus zhachilii	84.4122	628	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.75	97.75	0.87	0.87	2	-
GCF_003967595.1	s__Companilactobacillus musae	82.7469	477	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001434275.1	s__Companilactobacillus mindensis	82.4604	459	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001435445.1	s__Companilactobacillus kimchii	81.4687	426	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.97	1.00	1.00	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,462] [INFO] GTDB search result was written to GCF_005405325.1_ASM540532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:37,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:37,465] [INFO] DFAST_QC result json was written to GCF_005405325.1_ASM540532v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:37,465] [INFO] DFAST_QC completed!
[2024-01-24 13:50:37,465] [INFO] Total running time: 0h0m57s