[2023-06-28 01:43:27,565] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:43:27,567] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:43:27,567] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcd143d4-08ac-46d3-a65e-0cad3c176fe6/dqc_reference
[2023-06-28 01:43:28,901] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:43:28,903] [INFO] Task started: Prodigal
[2023-06-28 01:43:28,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f064381-8f9f-4055-b773-8b37fca6241b/GCA_026041435.1_ASM2604143v1_genomic.fna.gz | prodigal -d GCA_026041435.1_ASM2604143v1_genomic.fna/cds.fna -a GCA_026041435.1_ASM2604143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:43:38,819] [INFO] Task succeeded: Prodigal
[2023-06-28 01:43:38,819] [INFO] Task started: HMMsearch
[2023-06-28 01:43:38,819] [INFO] Running command: hmmsearch --tblout GCA_026041435.1_ASM2604143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcd143d4-08ac-46d3-a65e-0cad3c176fe6/dqc_reference/reference_markers.hmm GCA_026041435.1_ASM2604143v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:43:39,129] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:43:39,130] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4f064381-8f9f-4055-b773-8b37fca6241b/GCA_026041435.1_ASM2604143v1_genomic.fna.gz]
[2023-06-28 01:43:39,168] [INFO] Query marker FASTA was written to GCA_026041435.1_ASM2604143v1_genomic.fna/markers.fasta
[2023-06-28 01:43:39,168] [INFO] Task started: Blastn
[2023-06-28 01:43:39,168] [INFO] Running command: blastn -query GCA_026041435.1_ASM2604143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd143d4-08ac-46d3-a65e-0cad3c176fe6/dqc_reference/reference_markers.fasta -out GCA_026041435.1_ASM2604143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:39,899] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:39,903] [INFO] Selected 25 target genomes.
[2023-06-28 01:43:39,904] [INFO] Target genome list was writen to GCA_026041435.1_ASM2604143v1_genomic.fna/target_genomes.txt
[2023-06-28 01:43:39,906] [INFO] Task started: fastANI
[2023-06-28 01:43:39,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f064381-8f9f-4055-b773-8b37fca6241b/GCA_026041435.1_ASM2604143v1_genomic.fna.gz --refList GCA_026041435.1_ASM2604143v1_genomic.fna/target_genomes.txt --output GCA_026041435.1_ASM2604143v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:43:55,922] [INFO] Task succeeded: fastANI
[2023-06-28 01:43:55,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcd143d4-08ac-46d3-a65e-0cad3c176fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:43:55,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcd143d4-08ac-46d3-a65e-0cad3c176fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:43:55,928] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:43:55,928] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:43:55,928] [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
Sedimenticola thiotaurini	strain=SIP-G1	GCA_001007875.1	1543721	1543721	type	True	76.4593	76	1073	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	75.747	50	1073	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.5626	50	1073	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:43:55,930] [INFO] DFAST Taxonomy check result was written to GCA_026041435.1_ASM2604143v1_genomic.fna/tc_result.tsv
[2023-06-28 01:43:55,931] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:43:55,931] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:43:55,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcd143d4-08ac-46d3-a65e-0cad3c176fe6/dqc_reference/checkm_data
[2023-06-28 01:43:55,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:43:55,981] [INFO] Task started: CheckM
[2023-06-28 01:43:55,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026041435.1_ASM2604143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026041435.1_ASM2604143v1_genomic.fna/checkm_input GCA_026041435.1_ASM2604143v1_genomic.fna/checkm_result
[2023-06-28 01:44:31,865] [INFO] Task succeeded: CheckM
[2023-06-28 01:44:31,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 01:44:31,890] [INFO] ===== Completeness check finished =====
[2023-06-28 01:44:31,890] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:44:31,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026041435.1_ASM2604143v1_genomic.fna/markers.fasta)
[2023-06-28 01:44:31,891] [INFO] Task started: Blastn
[2023-06-28 01:44:31,891] [INFO] Running command: blastn -query GCA_026041435.1_ASM2604143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd143d4-08ac-46d3-a65e-0cad3c176fe6/dqc_reference/reference_markers_gtdb.fasta -out GCA_026041435.1_ASM2604143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:44:32,993] [INFO] Task succeeded: Blastn
[2023-06-28 01:44:32,997] [INFO] Selected 6 target genomes.
[2023-06-28 01:44:32,998] [INFO] Target genome list was writen to GCA_026041435.1_ASM2604143v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:44:33,001] [INFO] Task started: fastANI
[2023-06-28 01:44:33,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f064381-8f9f-4055-b773-8b37fca6241b/GCA_026041435.1_ASM2604143v1_genomic.fna.gz --refList GCA_026041435.1_ASM2604143v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026041435.1_ASM2604143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:44:38,563] [INFO] Task succeeded: fastANI
[2023-06-28 01:44:38,575] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:44:38,576] [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
GCA_001709035.1	s__Thiodiazotropha endoloripes_B	99.258	997	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.26	97.31	0.93	0.86	11	conclusive
GCF_001708965.1	s__Thiodiazotropha endoloripes	91.8041	913	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.62	99.43	0.97	0.94	9	-
GCA_016842065.1	s__Thiodiazotropha sp016842065	88.8656	878	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003676145.1	s__Thiodiazotropha endolucinida	88.6021	882	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	97.91	96.39	0.93	0.89	26	-
GCA_019100305.1	s__Thiodiazotropha sp019100305	88.4727	721	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003058495.1	s__Thiodiazotropha sp003058495	77.9023	255	1073	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiodiazotropha	95.0	99.61	99.54	0.96	0.95	6	-
--------------------------------------------------------------------------------
[2023-06-28 01:44:38,578] [INFO] GTDB search result was written to GCA_026041435.1_ASM2604143v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:44:38,578] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:44:38,581] [INFO] DFAST_QC result json was written to GCA_026041435.1_ASM2604143v1_genomic.fna/dqc_result.json
[2023-06-28 01:44:38,581] [INFO] DFAST_QC completed!
[2023-06-28 01:44:38,581] [INFO] Total running time: 0h1m11s