[2024-01-24 13:57:31,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,268] [INFO] DQC Reference Directory: /var/lib/cwl/stgd930d79c-00d0-4772-9666-e812765d8a76/dqc_reference
[2024-01-24 13:57:32,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:32,563] [INFO] Task started: Prodigal
[2024-01-24 13:57:32,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg41f1bcb7-ed30-4207-aff9-106b11a9e108/GCF_000746435.1_ASM74643v1_genomic.fna.gz | prodigal -d GCF_000746435.1_ASM74643v1_genomic.fna/cds.fna -a GCF_000746435.1_ASM74643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:35,567] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:35,567] [INFO] Task started: HMMsearch
[2024-01-24 13:57:35,567] [INFO] Running command: hmmsearch --tblout GCF_000746435.1_ASM74643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd930d79c-00d0-4772-9666-e812765d8a76/dqc_reference/reference_markers.hmm GCF_000746435.1_ASM74643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:35,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:35,745] [INFO] Found 6/6 markers.
[2024-01-24 13:57:35,765] [INFO] Query marker FASTA was written to GCF_000746435.1_ASM74643v1_genomic.fna/markers.fasta
[2024-01-24 13:57:35,765] [INFO] Task started: Blastn
[2024-01-24 13:57:35,765] [INFO] Running command: blastn -query GCF_000746435.1_ASM74643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd930d79c-00d0-4772-9666-e812765d8a76/dqc_reference/reference_markers.fasta -out GCF_000746435.1_ASM74643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:36,340] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:36,343] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:36,343] [INFO] Target genome list was writen to GCF_000746435.1_ASM74643v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:36,347] [INFO] Task started: fastANI
[2024-01-24 13:57:36,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f1bcb7-ed30-4207-aff9-106b11a9e108/GCF_000746435.1_ASM74643v1_genomic.fna.gz --refList GCF_000746435.1_ASM74643v1_genomic.fna/target_genomes.txt --output GCF_000746435.1_ASM74643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:40,860] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:40,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd930d79c-00d0-4772-9666-e812765d8a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:40,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd930d79c-00d0-4772-9666-e812765d8a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:40,867] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:57:40,868] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:57:40,868] [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
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000746435.1	1741	1741	type	True	100.0	562	563	95	inconclusive
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000734015.1	1741	1741	type	True	99.9902	562	563	95	inconclusive
Thermodesulfobacterium thermophilum	strain=DSM 1276	GCA_000421605.1	886	886	type	True	95.9674	510	563	95	inconclusive
Thermodesulfobacterium hveragerdense	strain=DSM 12571	GCA_000423845.1	53424	53424	type	True	93.908	500	563	95	below_threshold
Thermodesulfobacterium geofontis	strain=OPF15	GCA_000215975.1	1295609	1295609	type	True	77.3669	91	563	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:40,869] [INFO] DFAST Taxonomy check result was written to GCF_000746435.1_ASM74643v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:40,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:40,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:40,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd930d79c-00d0-4772-9666-e812765d8a76/dqc_reference/checkm_data
[2024-01-24 13:57:40,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:40,890] [INFO] Task started: CheckM
[2024-01-24 13:57:40,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000746435.1_ASM74643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000746435.1_ASM74643v1_genomic.fna/checkm_input GCF_000746435.1_ASM74643v1_genomic.fna/checkm_result
[2024-01-24 13:57:57,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:57,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:57,372] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:57,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:57,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000746435.1_ASM74643v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:57,373] [INFO] Task started: Blastn
[2024-01-24 13:57:57,374] [INFO] Running command: blastn -query GCF_000746435.1_ASM74643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd930d79c-00d0-4772-9666-e812765d8a76/dqc_reference/reference_markers_gtdb.fasta -out GCF_000746435.1_ASM74643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,177] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,181] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:58,181] [INFO] Target genome list was writen to GCF_000746435.1_ASM74643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:58,190] [INFO] Task started: fastANI
[2024-01-24 13:57:58,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f1bcb7-ed30-4207-aff9-106b11a9e108/GCF_000746435.1_ASM74643v1_genomic.fna.gz --refList GCF_000746435.1_ASM74643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000746435.1_ASM74643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:02,237] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:02,245] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:02,245] [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_000734015.1	s__Thermodesulfobacterium commune	99.9902	562	563	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.9677	99.11	98.83	0.97	0.93	10	conclusive
GCF_000421605.1	s__Thermodesulfobacterium thermophilum	95.9674	510	563	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.9677	N/A	N/A	N/A	N/A	1	-
GCF_000423845.1	s__Thermodesulfobacterium hveragerdense	93.908	500	563	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630935.1	s__Thermodesulfobacterium sp008630935	80.0589	395	563	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215975.1	s__Thermodesulfobacterium geofontis	77.3669	91	563	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	96.03	96.03	0.85	0.85	2	-
GCA_011361985.1	s__Thermodesulfobacterium geofontis_D	76.7178	76	563	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656385.1	s__Thermodesulfobacterium sp017656385	76.7153	67	563	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:02,247] [INFO] GTDB search result was written to GCF_000746435.1_ASM74643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:02,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:02,250] [INFO] DFAST_QC result json was written to GCF_000746435.1_ASM74643v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:02,250] [INFO] DFAST_QC completed!
[2024-01-24 13:58:02,251] [INFO] Total running time: 0h0m31s