[2024-01-25 20:14:35,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:35,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:35,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg3215f78f-0ea1-49ad-940b-d2020006a7d5/dqc_reference
[2024-01-25 20:14:36,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:36,722] [INFO] Task started: Prodigal
[2024-01-25 20:14:36,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg6af32479-eb87-4fb2-9564-609beb5caf91/GCF_000215975.1_ASM21597v1_genomic.fna.gz | prodigal -d GCF_000215975.1_ASM21597v1_genomic.fna/cds.fna -a GCF_000215975.1_ASM21597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:38,963] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:38,963] [INFO] Task started: HMMsearch
[2024-01-25 20:14:38,963] [INFO] Running command: hmmsearch --tblout GCF_000215975.1_ASM21597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3215f78f-0ea1-49ad-940b-d2020006a7d5/dqc_reference/reference_markers.hmm GCF_000215975.1_ASM21597v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:39,197] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:39,198] [INFO] Found 6/6 markers.
[2024-01-25 20:14:39,219] [INFO] Query marker FASTA was written to GCF_000215975.1_ASM21597v1_genomic.fna/markers.fasta
[2024-01-25 20:14:39,219] [INFO] Task started: Blastn
[2024-01-25 20:14:39,219] [INFO] Running command: blastn -query GCF_000215975.1_ASM21597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3215f78f-0ea1-49ad-940b-d2020006a7d5/dqc_reference/reference_markers.fasta -out GCF_000215975.1_ASM21597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:39,743] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:39,748] [INFO] Selected 12 target genomes.
[2024-01-25 20:14:39,749] [INFO] Target genome list was writen to GCF_000215975.1_ASM21597v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:39,756] [INFO] Task started: fastANI
[2024-01-25 20:14:39,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg6af32479-eb87-4fb2-9564-609beb5caf91/GCF_000215975.1_ASM21597v1_genomic.fna.gz --refList GCF_000215975.1_ASM21597v1_genomic.fna/target_genomes.txt --output GCF_000215975.1_ASM21597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:45,239] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:45,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3215f78f-0ea1-49ad-940b-d2020006a7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:45,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3215f78f-0ea1-49ad-940b-d2020006a7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:45,245] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:45,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:45,245] [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 geofontis	strain=OPF15	GCA_000215975.1	1295609	1295609	type	True	100.0	544	544	95	conclusive
Thermodesulfobacterium hydrogeniphilum	strain=DSM 14290	GCA_000746255.1	161156	161156	type	True	77.8988	243	544	95	below_threshold
Thermodesulfobacterium thermophilum	strain=DSM 1276	GCA_000421605.1	886	886	type	True	77.2561	79	544	95	below_threshold
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000746435.1	1741	1741	type	True	77.0199	92	544	95	below_threshold
Thermodesulfobacterium commune	strain=DSM 2178	GCA_000734015.1	1741	1741	type	True	77.0063	93	544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:45,246] [INFO] DFAST Taxonomy check result was written to GCF_000215975.1_ASM21597v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:45,247] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:45,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:45,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3215f78f-0ea1-49ad-940b-d2020006a7d5/dqc_reference/checkm_data
[2024-01-25 20:14:45,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:45,267] [INFO] Task started: CheckM
[2024-01-25 20:14:45,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000215975.1_ASM21597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000215975.1_ASM21597v1_genomic.fna/checkm_input GCF_000215975.1_ASM21597v1_genomic.fna/checkm_result
[2024-01-25 20:14:58,804] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:58,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:58,822] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:58,822] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:58,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000215975.1_ASM21597v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:58,823] [INFO] Task started: Blastn
[2024-01-25 20:14:58,823] [INFO] Running command: blastn -query GCF_000215975.1_ASM21597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3215f78f-0ea1-49ad-940b-d2020006a7d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000215975.1_ASM21597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:59,538] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:59,542] [INFO] Selected 8 target genomes.
[2024-01-25 20:14:59,543] [INFO] Target genome list was writen to GCF_000215975.1_ASM21597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:59,550] [INFO] Task started: fastANI
[2024-01-25 20:14:59,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg6af32479-eb87-4fb2-9564-609beb5caf91/GCF_000215975.1_ASM21597v1_genomic.fna.gz --refList GCF_000215975.1_ASM21597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000215975.1_ASM21597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:02,826] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:02,831] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:02,831] [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_000215975.1	s__Thermodesulfobacterium geofontis	100.0	544	544	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	96.03	96.03	0.85	0.85	2	conclusive
GCA_011361985.1	s__Thermodesulfobacterium geofontis_D	88.88	350	544	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011380535.1	s__Thermodesulfobacterium geofontis_C	88.7856	412	544	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	99.32	99.32	0.91	0.91	2	-
GCA_002877985.1	s__Thermodesulfobacterium geofontis_A	81.7689	335	544	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003641645.1	s__Thermodesulfobacterium sp003641645	81.653	188	544	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	80.0655	344	544	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:02,833] [INFO] GTDB search result was written to GCF_000215975.1_ASM21597v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:02,833] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:02,835] [INFO] DFAST_QC result json was written to GCF_000215975.1_ASM21597v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:02,836] [INFO] DFAST_QC completed!
[2024-01-25 20:15:02,836] [INFO] Total running time: 0h0m27s