[2024-01-25 20:14:50,322] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg589f33cb-8b87-4dcc-ba47-b0a7a14d4d08/dqc_reference
[2024-01-25 20:14:51,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,432] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,432] [INFO] Running command: gunzip -c /var/lib/cwl/stgac886ef9-5f65-4abf-9d9e-c475750b7933/GCF_023078475.1_ASM2307847v1_genomic.fna.gz | prodigal -d GCF_023078475.1_ASM2307847v1_genomic.fna/cds.fna -a GCF_023078475.1_ASM2307847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:09,698] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:09,698] [INFO] Task started: HMMsearch
[2024-01-25 20:15:09,698] [INFO] Running command: hmmsearch --tblout GCF_023078475.1_ASM2307847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg589f33cb-8b87-4dcc-ba47-b0a7a14d4d08/dqc_reference/reference_markers.hmm GCF_023078475.1_ASM2307847v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:10,006] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:10,007] [INFO] Found 6/6 markers.
[2024-01-25 20:15:10,047] [INFO] Query marker FASTA was written to GCF_023078475.1_ASM2307847v1_genomic.fna/markers.fasta
[2024-01-25 20:15:10,047] [INFO] Task started: Blastn
[2024-01-25 20:15:10,048] [INFO] Running command: blastn -query GCF_023078475.1_ASM2307847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg589f33cb-8b87-4dcc-ba47-b0a7a14d4d08/dqc_reference/reference_markers.fasta -out GCF_023078475.1_ASM2307847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:10,837] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:10,840] [INFO] Selected 16 target genomes.
[2024-01-25 20:15:10,840] [INFO] Target genome list was writen to GCF_023078475.1_ASM2307847v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:10,846] [INFO] Task started: fastANI
[2024-01-25 20:15:10,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgac886ef9-5f65-4abf-9d9e-c475750b7933/GCF_023078475.1_ASM2307847v1_genomic.fna.gz --refList GCF_023078475.1_ASM2307847v1_genomic.fna/target_genomes.txt --output GCF_023078475.1_ASM2307847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:25,183] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:25,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg589f33cb-8b87-4dcc-ba47-b0a7a14d4d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:25,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg589f33cb-8b87-4dcc-ba47-b0a7a14d4d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:25,193] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:15:25,193] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:15:25,194] [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
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	84.91	1158	1697	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	82.178	882	1697	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	82.0559	869	1697	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	81.6388	942	1697	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	81.5943	817	1697	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	81.5164	860	1697	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.6307	587	1697	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.4538	462	1697	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.0981	474	1697	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.7838	475	1697	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.4092	312	1697	95	below_threshold
Burkholderia territorii	strain=CCUG 65687	GCA_008802115.1	1503055	1503055	type	True	75.9407	127	1697	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	75.8837	172	1697	95	below_threshold
Burkholderia territorii		GCA_902499035.1	1503055	1503055	type	True	75.6998	163	1697	95	below_threshold
Burkholderia territorii	strain=LMG 28158	GCA_902833055.1	1503055	1503055	type	True	75.6752	164	1697	95	below_threshold
Chitinasiproducens palmae	strain=JS23	GCA_900095735.1	1770053	1770053	type	True	75.4598	131	1697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:25,196] [INFO] DFAST Taxonomy check result was written to GCF_023078475.1_ASM2307847v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:25,196] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:25,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:25,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg589f33cb-8b87-4dcc-ba47-b0a7a14d4d08/dqc_reference/checkm_data
[2024-01-25 20:15:25,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:25,243] [INFO] Task started: CheckM
[2024-01-25 20:15:25,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023078475.1_ASM2307847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023078475.1_ASM2307847v1_genomic.fna/checkm_input GCF_023078475.1_ASM2307847v1_genomic.fna/checkm_result
[2024-01-25 20:16:20,318] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:20,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:20,347] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:20,348] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:20,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023078475.1_ASM2307847v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:20,349] [INFO] Task started: Blastn
[2024-01-25 20:16:20,349] [INFO] Running command: blastn -query GCF_023078475.1_ASM2307847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg589f33cb-8b87-4dcc-ba47-b0a7a14d4d08/dqc_reference/reference_markers_gtdb.fasta -out GCF_023078475.1_ASM2307847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:21,753] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:21,756] [INFO] Selected 14 target genomes.
[2024-01-25 20:16:21,756] [INFO] Target genome list was writen to GCF_023078475.1_ASM2307847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:21,764] [INFO] Task started: fastANI
[2024-01-25 20:16:21,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgac886ef9-5f65-4abf-9d9e-c475750b7933/GCF_023078475.1_ASM2307847v1_genomic.fna.gz --refList GCF_023078475.1_ASM2307847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023078475.1_ASM2307847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:35,713] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:35,724] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:16:35,725] [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_006385595.1	s__Luteibacter pinisoli	84.901	1159	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964085.1	s__Luteibacter yeojuensis_A	84.8235	1089	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018889975.1	s__Luteibacter sp018889975	84.1511	1103	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009912395.1	s__Luteibacter sp009912395	82.2556	918	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759365.1	s__Luteibacter anthropi	82.2044	879	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829075.1	s__Luteibacter yeojuensis_B	82.2023	913	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900110505.1	s__Luteibacter sp900110505	82.1266	888	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	97.58	97.58	0.93	0.93	2	-
GCF_011742875.1	s__Luteibacter yeojuensis	82.0648	868	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050935.1	s__Luteibacter sp003050935	81.5494	918	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.3705	391	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716275.1	s__JADJWR01 sp016716275	76.1194	117	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JADJWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391285.1	s__Thiobacillus sp011391285	75.5523	75	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095735.1	s__Robbsia sp900095735	75.4677	130	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Robbsia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345025.1	s__Accumulibacter phosphatis_B	75.404	68	1697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.42	99.42	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:35,732] [INFO] GTDB search result was written to GCF_023078475.1_ASM2307847v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:35,732] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:35,736] [INFO] DFAST_QC result json was written to GCF_023078475.1_ASM2307847v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:35,736] [INFO] DFAST_QC completed!
[2024-01-25 20:16:35,736] [INFO] Total running time: 0h1m45s