[2023-06-29 05:14:18,901] [INFO] DFAST_QC pipeline started.
[2023-06-29 05:14:18,904] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 05:14:18,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg8990c078-6ec4-4527-861c-8b931572e7a6/dqc_reference
[2023-06-29 05:14:20,241] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 05:14:20,242] [INFO] Task started: Prodigal
[2023-06-29 05:14:20,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg58716572-9f64-4eaf-9035-8d87e4ce051e/GCA_020249465.1_ASM2024946v1_genomic.fna.gz | prodigal -d GCA_020249465.1_ASM2024946v1_genomic.fna/cds.fna -a GCA_020249465.1_ASM2024946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 05:14:33,040] [INFO] Task succeeded: Prodigal
[2023-06-29 05:14:33,040] [INFO] Task started: HMMsearch
[2023-06-29 05:14:33,041] [INFO] Running command: hmmsearch --tblout GCA_020249465.1_ASM2024946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8990c078-6ec4-4527-861c-8b931572e7a6/dqc_reference/reference_markers.hmm GCA_020249465.1_ASM2024946v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 05:14:33,251] [INFO] Task succeeded: HMMsearch
[2023-06-29 05:14:33,253] [INFO] Found 6/6 markers.
[2023-06-29 05:14:33,285] [INFO] Query marker FASTA was written to GCA_020249465.1_ASM2024946v1_genomic.fna/markers.fasta
[2023-06-29 05:14:33,286] [INFO] Task started: Blastn
[2023-06-29 05:14:33,286] [INFO] Running command: blastn -query GCA_020249465.1_ASM2024946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8990c078-6ec4-4527-861c-8b931572e7a6/dqc_reference/reference_markers.fasta -out GCA_020249465.1_ASM2024946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:14:33,972] [INFO] Task succeeded: Blastn
[2023-06-29 05:14:33,976] [INFO] Selected 22 target genomes.
[2023-06-29 05:14:33,976] [INFO] Target genome list was writen to GCA_020249465.1_ASM2024946v1_genomic.fna/target_genomes.txt
[2023-06-29 05:14:33,977] [INFO] Task started: fastANI
[2023-06-29 05:14:33,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg58716572-9f64-4eaf-9035-8d87e4ce051e/GCA_020249465.1_ASM2024946v1_genomic.fna.gz --refList GCA_020249465.1_ASM2024946v1_genomic.fna/target_genomes.txt --output GCA_020249465.1_ASM2024946v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 05:14:50,561] [INFO] Task succeeded: fastANI
[2023-06-29 05:14:50,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8990c078-6ec4-4527-861c-8b931572e7a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 05:14:50,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8990c078-6ec4-4527-861c-8b931572e7a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 05:14:50,577] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 05:14:50,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 05:14:50,577] [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
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.9488	351	1279	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.9209	361	1279	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	76.9183	371	1279	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	76.8765	355	1279	95	below_threshold
Falsiroseomonas tokyonensis	strain=K-20	GCA_019024325.1	430521	430521	type	True	76.6398	328	1279	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.5578	235	1279	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.54	289	1279	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	76.5324	256	1279	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	76.4401	191	1279	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.4363	257	1279	95	below_threshold
Falsiroseomonas selenitidurans	strain=BU-1	GCA_012103215.1	2716335	2716335	type	True	76.3966	308	1279	95	below_threshold
Roseomonas vastitatis	strain=CPCC 101021	GCA_003604215.1	2307076	2307076	type	True	76.3505	188	1279	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	76.286	155	1279	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	76.2331	189	1279	95	below_threshold
Acidisoma cellulosilyticum	strain=HW T5.17	GCA_020621385.1	2802395	2802395	type	True	76.1969	98	1279	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	76.1196	151	1279	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.1106	179	1279	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.0719	206	1279	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	75.9626	65	1279	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	75.9336	83	1279	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.6937	104	1279	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 05:14:50,579] [INFO] DFAST Taxonomy check result was written to GCA_020249465.1_ASM2024946v1_genomic.fna/tc_result.tsv
[2023-06-29 05:14:50,580] [INFO] ===== Taxonomy check completed =====
[2023-06-29 05:14:50,580] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 05:14:50,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8990c078-6ec4-4527-861c-8b931572e7a6/dqc_reference/checkm_data
[2023-06-29 05:14:50,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 05:14:50,620] [INFO] Task started: CheckM
[2023-06-29 05:14:50,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020249465.1_ASM2024946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020249465.1_ASM2024946v1_genomic.fna/checkm_input GCA_020249465.1_ASM2024946v1_genomic.fna/checkm_result
[2023-06-29 05:15:30,748] [INFO] Task succeeded: CheckM
[2023-06-29 05:15:30,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 05:15:30,765] [INFO] ===== Completeness check finished =====
[2023-06-29 05:15:30,765] [INFO] ===== Start GTDB Search =====
[2023-06-29 05:15:30,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020249465.1_ASM2024946v1_genomic.fna/markers.fasta)
[2023-06-29 05:15:30,766] [INFO] Task started: Blastn
[2023-06-29 05:15:30,766] [INFO] Running command: blastn -query GCA_020249465.1_ASM2024946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8990c078-6ec4-4527-861c-8b931572e7a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_020249465.1_ASM2024946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:15:31,922] [INFO] Task succeeded: Blastn
[2023-06-29 05:15:31,926] [INFO] Selected 12 target genomes.
[2023-06-29 05:15:31,926] [INFO] Target genome list was writen to GCA_020249465.1_ASM2024946v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 05:15:31,927] [INFO] Task started: fastANI
[2023-06-29 05:15:31,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg58716572-9f64-4eaf-9035-8d87e4ce051e/GCA_020249465.1_ASM2024946v1_genomic.fna.gz --refList GCA_020249465.1_ASM2024946v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020249465.1_ASM2024946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 05:15:42,127] [INFO] Task succeeded: fastANI
[2023-06-29 05:15:42,137] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 05:15:42,138] [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_016869715.1	s__Roseomonas_B sp016869715	89.5084	907	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869735.1	s__Roseomonas_B sp016869735	88.4789	890	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927465.1	s__Roseomonas_B sp903927465	86.646	913	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	95.83	95.83	0.91	0.91	2	-
GCA_903844785.1	s__Roseomonas_B sp903844785	85.3518	723	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813355.1	s__Roseomonas_B sp017813355	77.1394	399	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	77.0986	359	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	76.9882	346	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	76.947	379	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	76.9349	352	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_005222755.1	s__Roseomonas_B sp005222755	76.8196	365	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129025.1	s__Roseomonas_B terrae	76.7377	333	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927745.1	s__Roseomonas_B sp012927745	76.7327	346	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 05:15:42,139] [INFO] GTDB search result was written to GCA_020249465.1_ASM2024946v1_genomic.fna/result_gtdb.tsv
[2023-06-29 05:15:42,140] [INFO] ===== GTDB Search completed =====
[2023-06-29 05:15:42,143] [INFO] DFAST_QC result json was written to GCA_020249465.1_ASM2024946v1_genomic.fna/dqc_result.json
[2023-06-29 05:15:42,143] [INFO] DFAST_QC completed!
[2023-06-29 05:15:42,143] [INFO] Total running time: 0h1m23s