[2024-01-24 12:23:04,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:04,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:04,181] [INFO] DQC Reference Directory: /var/lib/cwl/stgd44e6a87-5b33-4d69-8ac8-826904f534c6/dqc_reference
[2024-01-24 12:23:05,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,456] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg716d960b-76a9-4235-9f0b-72f14b939281/GCF_027922085.1_ASM2792208v1_genomic.fna.gz | prodigal -d GCF_027922085.1_ASM2792208v1_genomic.fna/cds.fna -a GCF_027922085.1_ASM2792208v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:16,427] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:16,427] [INFO] Task started: HMMsearch
[2024-01-24 12:23:16,427] [INFO] Running command: hmmsearch --tblout GCF_027922085.1_ASM2792208v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd44e6a87-5b33-4d69-8ac8-826904f534c6/dqc_reference/reference_markers.hmm GCF_027922085.1_ASM2792208v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:16,709] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:16,710] [INFO] Found 6/6 markers.
[2024-01-24 12:23:16,755] [INFO] Query marker FASTA was written to GCF_027922085.1_ASM2792208v1_genomic.fna/markers.fasta
[2024-01-24 12:23:16,755] [INFO] Task started: Blastn
[2024-01-24 12:23:16,755] [INFO] Running command: blastn -query GCF_027922085.1_ASM2792208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd44e6a87-5b33-4d69-8ac8-826904f534c6/dqc_reference/reference_markers.fasta -out GCF_027922085.1_ASM2792208v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:18,093] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:18,097] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:18,097] [INFO] Target genome list was writen to GCF_027922085.1_ASM2792208v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:18,101] [INFO] Task started: fastANI
[2024-01-24 12:23:18,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg716d960b-76a9-4235-9f0b-72f14b939281/GCF_027922085.1_ASM2792208v1_genomic.fna.gz --refList GCF_027922085.1_ASM2792208v1_genomic.fna/target_genomes.txt --output GCF_027922085.1_ASM2792208v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:29,437] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:29,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd44e6a87-5b33-4d69-8ac8-826904f534c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:29,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd44e6a87-5b33-4d69-8ac8-826904f534c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:29,451] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:29,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:29,452] [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
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	99.9937	1272	1286	95	conclusive
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	91.7311	1084	1286	95	below_threshold
Agromyces kandeliae	strain=Q22	GCA_009674665.1	2666141	2666141	type	True	90.0553	1056	1286	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	89.9651	700	1286	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	85.7652	834	1286	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	85.5216	945	1286	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	84.978	885	1286	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	84.9741	882	1286	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.5457	864	1286	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.5983	747	1286	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.9324	604	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,453] [INFO] DFAST Taxonomy check result was written to GCF_027922085.1_ASM2792208v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:29,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:29,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:29,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd44e6a87-5b33-4d69-8ac8-826904f534c6/dqc_reference/checkm_data
[2024-01-24 12:23:29,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:29,498] [INFO] Task started: CheckM
[2024-01-24 12:23:29,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027922085.1_ASM2792208v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027922085.1_ASM2792208v1_genomic.fna/checkm_input GCF_027922085.1_ASM2792208v1_genomic.fna/checkm_result
[2024-01-24 12:24:20,847] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:20,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:20,868] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:20,868] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:20,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027922085.1_ASM2792208v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:20,869] [INFO] Task started: Blastn
[2024-01-24 12:24:20,869] [INFO] Running command: blastn -query GCF_027922085.1_ASM2792208v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd44e6a87-5b33-4d69-8ac8-826904f534c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_027922085.1_ASM2792208v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:23,018] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:23,022] [INFO] Selected 7 target genomes.
[2024-01-24 12:24:23,022] [INFO] Target genome list was writen to GCF_027922085.1_ASM2792208v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:23,027] [INFO] Task started: fastANI
[2024-01-24 12:24:23,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg716d960b-76a9-4235-9f0b-72f14b939281/GCF_027922085.1_ASM2792208v1_genomic.fna.gz --refList GCF_027922085.1_ASM2792208v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027922085.1_ASM2792208v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:30,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:30,738] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:30,739] [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_009729855.1	s__Agromyces luteolus	99.9937	1272	1286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009709675.1	s__Agromyces bracchium	91.7311	1084	1286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674665.1	s__Agromyces kandeliae	90.0519	1057	1286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135055.1	s__Agromyces binzhouensis	89.9795	698	1286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	85.4879	948	1286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620055.1	s__Agromyces sp001620055	85.1751	809	1286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104685.1	s__Agromyces flavus	84.949	896	1286	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:30,741] [INFO] GTDB search result was written to GCF_027922085.1_ASM2792208v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:30,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:30,746] [INFO] DFAST_QC result json was written to GCF_027922085.1_ASM2792208v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:30,746] [INFO] DFAST_QC completed!
[2024-01-24 12:24:30,747] [INFO] Total running time: 0h1m27s