[2024-01-24 14:23:03,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:03,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:03,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg1af82849-ee12-47c4-8e94-0498d355be40/dqc_reference
[2024-01-24 14:23:05,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:05,244] [INFO] Task started: Prodigal
[2024-01-24 14:23:05,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg52ff32c2-6820-4516-a73e-705bbd322605/GCF_003990045.1_ASM399004v1_genomic.fna.gz | prodigal -d GCF_003990045.1_ASM399004v1_genomic.fna/cds.fna -a GCF_003990045.1_ASM399004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:15,535] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:15,536] [INFO] Task started: HMMsearch
[2024-01-24 14:23:15,536] [INFO] Running command: hmmsearch --tblout GCF_003990045.1_ASM399004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1af82849-ee12-47c4-8e94-0498d355be40/dqc_reference/reference_markers.hmm GCF_003990045.1_ASM399004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:15,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:15,887] [INFO] Found 6/6 markers.
[2024-01-24 14:23:15,923] [INFO] Query marker FASTA was written to GCF_003990045.1_ASM399004v1_genomic.fna/markers.fasta
[2024-01-24 14:23:15,923] [INFO] Task started: Blastn
[2024-01-24 14:23:15,923] [INFO] Running command: blastn -query GCF_003990045.1_ASM399004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af82849-ee12-47c4-8e94-0498d355be40/dqc_reference/reference_markers.fasta -out GCF_003990045.1_ASM399004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:17,159] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:17,163] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:17,163] [INFO] Target genome list was writen to GCF_003990045.1_ASM399004v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:17,167] [INFO] Task started: fastANI
[2024-01-24 14:23:17,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg52ff32c2-6820-4516-a73e-705bbd322605/GCF_003990045.1_ASM399004v1_genomic.fna.gz --refList GCF_003990045.1_ASM399004v1_genomic.fna/target_genomes.txt --output GCF_003990045.1_ASM399004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:26,140] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:26,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1af82849-ee12-47c4-8e94-0498d355be40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:26,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1af82849-ee12-47c4-8e94-0498d355be40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:26,151] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:26,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:26,152] [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
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	100.0	1214	1215	95	conclusive
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	84.518	916	1215	95	below_threshold
Labedella gwakjiensis	strain=DSM 21548	GCA_003014675.1	390269	390269	type	True	84.4619	927	1215	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	82.8366	801	1215	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	82.5195	790	1215	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.0064	424	1215	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.7628	419	1215	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.7079	410	1215	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.5584	398	1215	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.4911	434	1215	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.3564	395	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:26,154] [INFO] DFAST Taxonomy check result was written to GCF_003990045.1_ASM399004v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:26,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:26,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:26,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1af82849-ee12-47c4-8e94-0498d355be40/dqc_reference/checkm_data
[2024-01-24 14:23:26,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:26,207] [INFO] Task started: CheckM
[2024-01-24 14:23:26,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990045.1_ASM399004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990045.1_ASM399004v1_genomic.fna/checkm_input GCF_003990045.1_ASM399004v1_genomic.fna/checkm_result
[2024-01-24 14:24:16,531] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:16,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:16,555] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:16,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:16,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990045.1_ASM399004v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:16,557] [INFO] Task started: Blastn
[2024-01-24 14:24:16,557] [INFO] Running command: blastn -query GCF_003990045.1_ASM399004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af82849-ee12-47c4-8e94-0498d355be40/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990045.1_ASM399004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:18,455] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:18,459] [INFO] Selected 12 target genomes.
[2024-01-24 14:24:18,460] [INFO] Target genome list was writen to GCF_003990045.1_ASM399004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:18,477] [INFO] Task started: fastANI
[2024-01-24 14:24:18,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg52ff32c2-6820-4516-a73e-705bbd322605/GCF_003990045.1_ASM399004v1_genomic.fna.gz --refList GCF_003990045.1_ASM399004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990045.1_ASM399004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:27,869] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:27,883] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:27,884] [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_003990045.1	s__Labedella endophytica	100.0	1214	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003014675.1	s__Labedella gwakjiensis	84.4832	925	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004078635.1	s__Labedella phragmitis	82.8261	802	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004078655.1	s__Labedella populi	82.506	791	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834225.1	s__Rathayibacter sp009834225	78.8315	450	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	78.8255	422	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422325.1	s__Leifsonia_A sp001422325	78.7156	401	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	96.12	96.12	0.77	0.77	2	-
GCF_014190775.1	s__Leifsonia aquatica	78.6662	426	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_001425085.1	s__Microterricola sp001425085	78.5523	342	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365295.1	s__Agromyces intestinalis	78.5208	393	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809835.1	s__Agromyces sp902809835	78.4252	343	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	78.4165	321	1215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:27,885] [INFO] GTDB search result was written to GCF_003990045.1_ASM399004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:27,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:27,890] [INFO] DFAST_QC result json was written to GCF_003990045.1_ASM399004v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:27,890] [INFO] DFAST_QC completed!
[2024-01-24 14:24:27,890] [INFO] Total running time: 0h1m24s