[2024-01-25 17:34:07,127] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b389b6a-9fc7-4e5a-8aa3-13a976c1a559/dqc_reference
[2024-01-25 17:34:09,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,029] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg2474d084-3e0e-4709-85d0-626ab2084af6/GCF_014646555.1_ASM1464655v1_genomic.fna.gz | prodigal -d GCF_014646555.1_ASM1464655v1_genomic.fna/cds.fna -a GCF_014646555.1_ASM1464655v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:17,992] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:17,992] [INFO] Task started: HMMsearch
[2024-01-25 17:34:17,992] [INFO] Running command: hmmsearch --tblout GCF_014646555.1_ASM1464655v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b389b6a-9fc7-4e5a-8aa3-13a976c1a559/dqc_reference/reference_markers.hmm GCF_014646555.1_ASM1464655v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:18,190] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:18,191] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2474d084-3e0e-4709-85d0-626ab2084af6/GCF_014646555.1_ASM1464655v1_genomic.fna.gz]
[2024-01-25 17:34:18,215] [INFO] Query marker FASTA was written to GCF_014646555.1_ASM1464655v1_genomic.fna/markers.fasta
[2024-01-25 17:34:18,215] [INFO] Task started: Blastn
[2024-01-25 17:34:18,215] [INFO] Running command: blastn -query GCF_014646555.1_ASM1464655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b389b6a-9fc7-4e5a-8aa3-13a976c1a559/dqc_reference/reference_markers.fasta -out GCF_014646555.1_ASM1464655v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:18,671] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:18,679] [INFO] Selected 4 target genomes.
[2024-01-25 17:34:18,679] [INFO] Target genome list was writen to GCF_014646555.1_ASM1464655v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:18,681] [INFO] Task started: fastANI
[2024-01-25 17:34:18,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg2474d084-3e0e-4709-85d0-626ab2084af6/GCF_014646555.1_ASM1464655v1_genomic.fna.gz --refList GCF_014646555.1_ASM1464655v1_genomic.fna/target_genomes.txt --output GCF_014646555.1_ASM1464655v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:21,173] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:21,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b389b6a-9fc7-4e5a-8aa3-13a976c1a559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:21,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b389b6a-9fc7-4e5a-8aa3-13a976c1a559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:21,205] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:21,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:21,205] [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
Vulcanisaeta souniana	strain=JCM 11219	GCA_014646555.1	164452	164452	type	True	100.0	795	796	95	conclusive
Vulcanisaeta souniana	strain=JCM 11219	GCA_001316025.1	164452	164452	type	True	99.6327	768	796	95	conclusive
Vulcanisaeta distributa	strain=DSM 14429	GCA_000148385.1	164451	164451	suspected-type	True	83.1952	535	796	95	below_threshold
Vulcanisaeta moutnovskia	strain=768-28	GCA_000190315.1	985052	985052	type	True	80.2395	452	796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:21,207] [INFO] DFAST Taxonomy check result was written to GCF_014646555.1_ASM1464655v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:21,207] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:21,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:21,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b389b6a-9fc7-4e5a-8aa3-13a976c1a559/dqc_reference/checkm_data
[2024-01-25 17:34:21,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:21,241] [INFO] Task started: CheckM
[2024-01-25 17:34:21,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646555.1_ASM1464655v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646555.1_ASM1464655v1_genomic.fna/checkm_input GCF_014646555.1_ASM1464655v1_genomic.fna/checkm_result
[2024-01-25 17:34:52,958] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:52,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:34:52,976] [INFO] ===== Completeness check finished =====
[2024-01-25 17:34:52,976] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:34:52,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646555.1_ASM1464655v1_genomic.fna/markers.fasta)
[2024-01-25 17:34:52,976] [INFO] Task started: Blastn
[2024-01-25 17:34:52,976] [INFO] Running command: blastn -query GCF_014646555.1_ASM1464655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b389b6a-9fc7-4e5a-8aa3-13a976c1a559/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646555.1_ASM1464655v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:53,455] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:53,458] [INFO] Selected 5 target genomes.
[2024-01-25 17:34:53,459] [INFO] Target genome list was writen to GCF_014646555.1_ASM1464655v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:34:53,462] [INFO] Task started: fastANI
[2024-01-25 17:34:53,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg2474d084-3e0e-4709-85d0-626ab2084af6/GCF_014646555.1_ASM1464655v1_genomic.fna.gz --refList GCF_014646555.1_ASM1464655v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646555.1_ASM1464655v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:34:56,175] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:56,185] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:34:56,185] [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_014646555.1	s__Vulcanisaeta souniana	100.0	795	796	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Vulcanisaeta	95.0	99.65	99.65	1.00	1.00	2	conclusive
GCA_002496475.1	s__Vulcanisaeta sp002496475	86.161	402	796	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Vulcanisaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000148385.1	s__Vulcanisaeta distributa	83.1794	536	796	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Vulcanisaeta	95.0	96.46	96.46	0.88	0.88	2	-
GCF_000190315.1	s__Vulcanisaeta moutnovskia	80.2395	452	796	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Vulcanisaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001316245.1	s__Vulcanisaeta sp001316245	79.0387	394	796	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Vulcanisaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:34:56,192] [INFO] GTDB search result was written to GCF_014646555.1_ASM1464655v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:34:56,193] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:34:56,195] [INFO] DFAST_QC result json was written to GCF_014646555.1_ASM1464655v1_genomic.fna/dqc_result.json
[2024-01-25 17:34:56,195] [INFO] DFAST_QC completed!
[2024-01-25 17:34:56,195] [INFO] Total running time: 0h0m49s