[2024-01-24 12:30:05,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg09a12cf7-69ee-43ae-9bb3-ab7c62e42fad/dqc_reference
[2024-01-24 12:30:07,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,246] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,246] [INFO] Running command: gunzip -c /var/lib/cwl/stg36bbb894-b1eb-4167-b945-008cf2d80e23/GCF_901538355.1_ASM90153835v1_genomic.fna.gz | prodigal -d GCF_901538355.1_ASM90153835v1_genomic.fna/cds.fna -a GCF_901538355.1_ASM90153835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:48,456] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:48,457] [INFO] Task started: HMMsearch
[2024-01-24 12:30:48,457] [INFO] Running command: hmmsearch --tblout GCF_901538355.1_ASM90153835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09a12cf7-69ee-43ae-9bb3-ab7c62e42fad/dqc_reference/reference_markers.hmm GCF_901538355.1_ASM90153835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:48,844] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:48,845] [INFO] Found 6/6 markers.
[2024-01-24 12:30:48,896] [INFO] Query marker FASTA was written to GCF_901538355.1_ASM90153835v1_genomic.fna/markers.fasta
[2024-01-24 12:30:48,896] [INFO] Task started: Blastn
[2024-01-24 12:30:48,896] [INFO] Running command: blastn -query GCF_901538355.1_ASM90153835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a12cf7-69ee-43ae-9bb3-ab7c62e42fad/dqc_reference/reference_markers.fasta -out GCF_901538355.1_ASM90153835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:49,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:49,509] [INFO] Selected 22 target genomes.
[2024-01-24 12:30:49,509] [INFO] Target genome list was writen to GCF_901538355.1_ASM90153835v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:49,526] [INFO] Task started: fastANI
[2024-01-24 12:30:49,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg36bbb894-b1eb-4167-b945-008cf2d80e23/GCF_901538355.1_ASM90153835v1_genomic.fna.gz --refList GCF_901538355.1_ASM90153835v1_genomic.fna/target_genomes.txt --output GCF_901538355.1_ASM90153835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:11,308] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:11,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09a12cf7-69ee-43ae-9bb3-ab7c62e42fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:11,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09a12cf7-69ee-43ae-9bb3-ab7c62e42fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:11,315] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:11,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:11,316] [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
Tuwongella immobilis		GCA_901538355.1	692036	692036	type	True	100.0	2230	2230	95	conclusive
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	76.4328	75	2230	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	76.3191	71	2230	95	below_threshold
Telmatocola sphagniphila	strain=SP2T	GCA_018398935.1	1123043	1123043	type	True	76.1354	63	2230	95	below_threshold
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	75.7956	80	2230	95	below_threshold
Zavarzinella formosa	strain=DSM 19928	GCA_000255705.1	360055	360055	type	True	75.7117	99	2230	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.0705	52	2230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:11,322] [INFO] DFAST Taxonomy check result was written to GCF_901538355.1_ASM90153835v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:11,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:11,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:11,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09a12cf7-69ee-43ae-9bb3-ab7c62e42fad/dqc_reference/checkm_data
[2024-01-24 12:31:11,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:11,387] [INFO] Task started: CheckM
[2024-01-24 12:31:11,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_901538355.1_ASM90153835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_901538355.1_ASM90153835v1_genomic.fna/checkm_input GCF_901538355.1_ASM90153835v1_genomic.fna/checkm_result
[2024-01-24 12:33:31,859] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:31,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:31,879] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:31,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:31,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_901538355.1_ASM90153835v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:31,880] [INFO] Task started: Blastn
[2024-01-24 12:33:31,880] [INFO] Running command: blastn -query GCF_901538355.1_ASM90153835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09a12cf7-69ee-43ae-9bb3-ab7c62e42fad/dqc_reference/reference_markers_gtdb.fasta -out GCF_901538355.1_ASM90153835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:32,618] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:32,620] [INFO] Selected 27 target genomes.
[2024-01-24 12:33:32,620] [INFO] Target genome list was writen to GCF_901538355.1_ASM90153835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:32,652] [INFO] Task started: fastANI
[2024-01-24 12:33:32,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg36bbb894-b1eb-4167-b945-008cf2d80e23/GCF_901538355.1_ASM90153835v1_genomic.fna.gz --refList GCF_901538355.1_ASM90153835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_901538355.1_ASM90153835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:57,129] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:57,135] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:57,135] [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_901538355.1	s__Tuwongella immobilis	100.0	2230	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Tuwongella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001610895.1	s__Paludisphaera sp001610895	76.0524	55	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255705.1	s__Zavarzinella formosa	75.7128	99	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Zavarzinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823135.1	s__Gemmata sp013823135	75.4942	67	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000531095.1	s__Gemmata massiliana	75.4278	69	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCA_016873095.1	s__VGYC01 sp016873095	75.127	77	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__VGYC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	75.063	53	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697105.1	s__SIAQ01 sp009697105	74.756	52	2230	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:57,136] [INFO] GTDB search result was written to GCF_901538355.1_ASM90153835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:57,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:57,139] [INFO] DFAST_QC result json was written to GCF_901538355.1_ASM90153835v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:57,139] [INFO] DFAST_QC completed!
[2024-01-24 12:33:57,139] [INFO] Total running time: 0h3m52s