[2024-01-24 15:02:18,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg61dedd62-0f97-44a6-a9c0-88175e144ac0/dqc_reference
[2024-01-24 15:02:20,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,833] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg30911d62-5c3c-4421-890a-2c7df7aafebc/GCF_000423845.1_ASM42384v1_genomic.fna.gz | prodigal -d GCF_000423845.1_ASM42384v1_genomic.fna/cds.fna -a GCF_000423845.1_ASM42384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:23,929] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:23,929] [INFO] Task started: HMMsearch
[2024-01-24 15:02:23,930] [INFO] Running command: hmmsearch --tblout GCF_000423845.1_ASM42384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61dedd62-0f97-44a6-a9c0-88175e144ac0/dqc_reference/reference_markers.hmm GCF_000423845.1_ASM42384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:24,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:24,232] [INFO] Found 6/6 markers.
[2024-01-24 15:02:24,252] [INFO] Query marker FASTA was written to GCF_000423845.1_ASM42384v1_genomic.fna/markers.fasta
[2024-01-24 15:02:24,252] [INFO] Task started: Blastn
[2024-01-24 15:02:24,253] [INFO] Running command: blastn -query GCF_000423845.1_ASM42384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61dedd62-0f97-44a6-a9c0-88175e144ac0/dqc_reference/reference_markers.fasta -out GCF_000423845.1_ASM42384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:27,961] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:27,969] [INFO] Selected 8 target genomes.
[2024-01-24 15:02:27,970] [INFO] Target genome list was writen to GCF_000423845.1_ASM42384v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:28,017] [INFO] Task started: fastANI
[2024-01-24 15:02:28,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg30911d62-5c3c-4421-890a-2c7df7aafebc/GCF_000423845.1_ASM42384v1_genomic.fna.gz --refList GCF_000423845.1_ASM42384v1_genomic.fna/target_genomes.txt --output GCF_000423845.1_ASM42384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:32,009] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:32,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61dedd62-0f97-44a6-a9c0-88175e144ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:32,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61dedd62-0f97-44a6-a9c0-88175e144ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:32,019] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:32,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:32,019] [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 hveragerdense	strain=DSM 12571	GCA_000423845.1	53424	53424	type	True	100.0	554	556	95	conclusive
Thermodesulfobacterium thermophilum	strain=DSM 1276	GCA_000421605.1	886	886	type	True	94.6591	512	556	95	below_threshold
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000746435.1	1741	1741	type	True	93.93	509	556	95	below_threshold
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000734015.1	1741	1741	type	True	93.8203	522	556	95	below_threshold
Thermodesulfobacterium hydrogeniphilum	strain=DSM 14290	GCA_000746255.1	161156	161156	type	True	77.1901	102	556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:32,022] [INFO] DFAST Taxonomy check result was written to GCF_000423845.1_ASM42384v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:32,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:32,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:32,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61dedd62-0f97-44a6-a9c0-88175e144ac0/dqc_reference/checkm_data
[2024-01-24 15:02:32,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:32,053] [INFO] Task started: CheckM
[2024-01-24 15:02:32,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423845.1_ASM42384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423845.1_ASM42384v1_genomic.fna/checkm_input GCF_000423845.1_ASM42384v1_genomic.fna/checkm_result
[2024-01-24 15:02:52,462] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:52,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:52,483] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:52,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:52,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423845.1_ASM42384v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:52,487] [INFO] Task started: Blastn
[2024-01-24 15:02:52,488] [INFO] Running command: blastn -query GCF_000423845.1_ASM42384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61dedd62-0f97-44a6-a9c0-88175e144ac0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423845.1_ASM42384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:53,791] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:53,795] [INFO] Selected 10 target genomes.
[2024-01-24 15:02:53,796] [INFO] Target genome list was writen to GCF_000423845.1_ASM42384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:53,824] [INFO] Task started: fastANI
[2024-01-24 15:02:53,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg30911d62-5c3c-4421-890a-2c7df7aafebc/GCF_000423845.1_ASM42384v1_genomic.fna.gz --refList GCF_000423845.1_ASM42384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423845.1_ASM42384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:57,975] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:57,981] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:57,982] [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_000423845.1	s__Thermodesulfobacterium hveragerdense	100.0	554	556	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000421605.1	s__Thermodesulfobacterium thermophilum	94.6876	511	556	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.9677	N/A	N/A	N/A	N/A	1	-
GCF_000734015.1	s__Thermodesulfobacterium commune	93.826	522	556	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.9677	99.11	98.83	0.97	0.93	10	-
GCF_008630935.1	s__Thermodesulfobacterium sp008630935	80.1567	402	556	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746255.1	s__Thermodesulfobacterium hydrogeniphilum	77.1632	103	556	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002877985.1	s__Thermodesulfobacterium geofontis_A	75.9323	54	556	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 15:02:57,986] [INFO] GTDB search result was written to GCF_000423845.1_ASM42384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:57,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:57,989] [INFO] DFAST_QC result json was written to GCF_000423845.1_ASM42384v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:57,989] [INFO] DFAST_QC completed!
[2024-01-24 15:02:57,989] [INFO] Total running time: 0h0m40s