[2023-06-29 18:53:04,902] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:53:04,908] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:53:04,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgf76caa81-be7e-4030-ba3f-ad1ca0e5633a/dqc_reference
[2023-06-29 18:53:06,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:53:06,223] [INFO] Task started: Prodigal
[2023-06-29 18:53:06,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fb67fde-a828-41ad-be99-b2105b9994ca/GCA_023390155.1_ASM2339015v1_genomic.fna.gz | prodigal -d GCA_023390155.1_ASM2339015v1_genomic.fna/cds.fna -a GCA_023390155.1_ASM2339015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:53:13,333] [INFO] Task succeeded: Prodigal
[2023-06-29 18:53:13,335] [INFO] Task started: HMMsearch
[2023-06-29 18:53:13,335] [INFO] Running command: hmmsearch --tblout GCA_023390155.1_ASM2339015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf76caa81-be7e-4030-ba3f-ad1ca0e5633a/dqc_reference/reference_markers.hmm GCA_023390155.1_ASM2339015v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:53:13,577] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:53:13,579] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6fb67fde-a828-41ad-be99-b2105b9994ca/GCA_023390155.1_ASM2339015v1_genomic.fna.gz]
[2023-06-29 18:53:13,626] [INFO] Query marker FASTA was written to GCA_023390155.1_ASM2339015v1_genomic.fna/markers.fasta
[2023-06-29 18:53:13,626] [INFO] Task started: Blastn
[2023-06-29 18:53:13,626] [INFO] Running command: blastn -query GCA_023390155.1_ASM2339015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf76caa81-be7e-4030-ba3f-ad1ca0e5633a/dqc_reference/reference_markers.fasta -out GCA_023390155.1_ASM2339015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:53:14,779] [INFO] Task succeeded: Blastn
[2023-06-29 18:53:14,784] [INFO] Selected 10 target genomes.
[2023-06-29 18:53:14,784] [INFO] Target genome list was writen to GCA_023390155.1_ASM2339015v1_genomic.fna/target_genomes.txt
[2023-06-29 18:53:14,788] [INFO] Task started: fastANI
[2023-06-29 18:53:14,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb67fde-a828-41ad-be99-b2105b9994ca/GCA_023390155.1_ASM2339015v1_genomic.fna.gz --refList GCA_023390155.1_ASM2339015v1_genomic.fna/target_genomes.txt --output GCA_023390155.1_ASM2339015v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:53:22,564] [INFO] Task succeeded: fastANI
[2023-06-29 18:53:22,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf76caa81-be7e-4030-ba3f-ad1ca0e5633a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:53:22,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf76caa81-be7e-4030-ba3f-ad1ca0e5633a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:53:22,578] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:53:22,578] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 18:53:22,578] [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
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	87.3656	607	826	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	87.3445	510	826	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	87.3442	611	826	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	84.2766	565	826	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	83.6733	546	826	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.8365	382	826	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.5976	361	826	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.2732	342	826	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.1876	346	826	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	79.1529	329	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 18:53:22,580] [INFO] DFAST Taxonomy check result was written to GCA_023390155.1_ASM2339015v1_genomic.fna/tc_result.tsv
[2023-06-29 18:53:22,582] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:53:22,582] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:53:22,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf76caa81-be7e-4030-ba3f-ad1ca0e5633a/dqc_reference/checkm_data
[2023-06-29 18:53:22,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:53:22,625] [INFO] Task started: CheckM
[2023-06-29 18:53:22,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023390155.1_ASM2339015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023390155.1_ASM2339015v1_genomic.fna/checkm_input GCA_023390155.1_ASM2339015v1_genomic.fna/checkm_result
[2023-06-29 18:53:48,859] [INFO] Task succeeded: CheckM
[2023-06-29 18:53:48,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.15%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:53:48,886] [INFO] ===== Completeness check finished =====
[2023-06-29 18:53:48,887] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:53:48,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023390155.1_ASM2339015v1_genomic.fna/markers.fasta)
[2023-06-29 18:53:48,888] [INFO] Task started: Blastn
[2023-06-29 18:53:48,888] [INFO] Running command: blastn -query GCA_023390155.1_ASM2339015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf76caa81-be7e-4030-ba3f-ad1ca0e5633a/dqc_reference/reference_markers_gtdb.fasta -out GCA_023390155.1_ASM2339015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:53:50,846] [INFO] Task succeeded: Blastn
[2023-06-29 18:53:50,851] [INFO] Selected 9 target genomes.
[2023-06-29 18:53:50,851] [INFO] Target genome list was writen to GCA_023390155.1_ASM2339015v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:53:50,858] [INFO] Task started: fastANI
[2023-06-29 18:53:50,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb67fde-a828-41ad-be99-b2105b9994ca/GCA_023390155.1_ASM2339015v1_genomic.fna.gz --refList GCA_023390155.1_ASM2339015v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023390155.1_ASM2339015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:53:58,860] [INFO] Task succeeded: fastANI
[2023-06-29 18:53:58,874] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 18:53:58,875] [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
GCA_001898805.1	s__Leifsonia sp001898805	87.3636	634	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	87.2811	614	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCF_000633535.1	s__Leifsonia aquatica_A	86.7183	602	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	84.4702	561	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410375.1	s__Leifsonia shinshuensis	84.2766	565	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003367665.1	s__Leifsonia sp003367665	84.1806	557	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359685.1	s__Leifsonia sp013359685	84.1059	539	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647635.1	s__Leifsonia xyli_A	84.1009	522	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408745.1	s__Leifsonia soli	83.7011	544	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.25	98.25	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-29 18:53:58,877] [INFO] GTDB search result was written to GCA_023390155.1_ASM2339015v1_genomic.fna/result_gtdb.tsv
[2023-06-29 18:53:58,877] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:53:58,881] [INFO] DFAST_QC result json was written to GCA_023390155.1_ASM2339015v1_genomic.fna/dqc_result.json
[2023-06-29 18:53:58,881] [INFO] DFAST_QC completed!
[2023-06-29 18:53:58,881] [INFO] Total running time: 0h0m54s