[2024-01-24 12:31:51,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,076] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,077] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2b9a044-d442-4520-8152-413c1c335d9a/dqc_reference
[2024-01-24 12:31:52,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,380] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg77f653fa-ed63-4404-ab98-9c0e0ff66756/GCF_009674665.1_ASM967466v1_genomic.fna.gz | prodigal -d GCF_009674665.1_ASM967466v1_genomic.fna/cds.fna -a GCF_009674665.1_ASM967466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:02,553] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:02,553] [INFO] Task started: HMMsearch
[2024-01-24 12:32:02,553] [INFO] Running command: hmmsearch --tblout GCF_009674665.1_ASM967466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2b9a044-d442-4520-8152-413c1c335d9a/dqc_reference/reference_markers.hmm GCF_009674665.1_ASM967466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:02,818] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:02,819] [INFO] Found 6/6 markers.
[2024-01-24 12:32:02,855] [INFO] Query marker FASTA was written to GCF_009674665.1_ASM967466v1_genomic.fna/markers.fasta
[2024-01-24 12:32:02,856] [INFO] Task started: Blastn
[2024-01-24 12:32:02,856] [INFO] Running command: blastn -query GCF_009674665.1_ASM967466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2b9a044-d442-4520-8152-413c1c335d9a/dqc_reference/reference_markers.fasta -out GCF_009674665.1_ASM967466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:04,200] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:04,204] [INFO] Selected 11 target genomes.
[2024-01-24 12:32:04,205] [INFO] Target genome list was writen to GCF_009674665.1_ASM967466v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:04,210] [INFO] Task started: fastANI
[2024-01-24 12:32:04,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f653fa-ed63-4404-ab98-9c0e0ff66756/GCF_009674665.1_ASM967466v1_genomic.fna.gz --refList GCF_009674665.1_ASM967466v1_genomic.fna/target_genomes.txt --output GCF_009674665.1_ASM967466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:14,835] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:14,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2b9a044-d442-4520-8152-413c1c335d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:14,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2b9a044-d442-4520-8152-413c1c335d9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:14,853] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:14,853] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:14,853] [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 kandeliae	strain=Q22	GCA_009674665.1	2666141	2666141	type	True	100.0	1249	1249	95	conclusive
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	92.9207	704	1249	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	90.054	1065	1249	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	89.5223	1047	1249	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	85.2319	853	1249	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	85.2041	917	1249	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	84.4455	881	1249	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	84.3927	876	1249	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.1206	819	1249	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.0577	740	1249	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.6623	578	1249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:14,855] [INFO] DFAST Taxonomy check result was written to GCF_009674665.1_ASM967466v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:14,856] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:14,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:14,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2b9a044-d442-4520-8152-413c1c335d9a/dqc_reference/checkm_data
[2024-01-24 12:32:14,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:14,899] [INFO] Task started: CheckM
[2024-01-24 12:32:14,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674665.1_ASM967466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674665.1_ASM967466v1_genomic.fna/checkm_input GCF_009674665.1_ASM967466v1_genomic.fna/checkm_result
[2024-01-24 12:33:08,252] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:08,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:08,275] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:08,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:08,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674665.1_ASM967466v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:08,276] [INFO] Task started: Blastn
[2024-01-24 12:33:08,276] [INFO] Running command: blastn -query GCF_009674665.1_ASM967466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2b9a044-d442-4520-8152-413c1c335d9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674665.1_ASM967466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:10,277] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:10,282] [INFO] Selected 7 target genomes.
[2024-01-24 12:33:10,282] [INFO] Target genome list was writen to GCF_009674665.1_ASM967466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:10,291] [INFO] Task started: fastANI
[2024-01-24 12:33:10,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f653fa-ed63-4404-ab98-9c0e0ff66756/GCF_009674665.1_ASM967466v1_genomic.fna.gz --refList GCF_009674665.1_ASM967466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674665.1_ASM967466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:17,925] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:17,938] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:17,939] [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_009674665.1	s__Agromyces kandeliae	100.0	1249	1249	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_004135055.1	s__Agromyces binzhouensis	92.9207	704	1249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	90.0791	1063	1249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	89.5223	1047	1249	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	85.2447	913	1249	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	84.9539	782	1249	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	84.4168	893	1249	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 12:33:17,941] [INFO] GTDB search result was written to GCF_009674665.1_ASM967466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:17,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:17,946] [INFO] DFAST_QC result json was written to GCF_009674665.1_ASM967466v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:17,947] [INFO] DFAST_QC completed!
[2024-01-24 12:33:17,947] [INFO] Total running time: 0h1m27s