[2024-01-25 18:59:35,893] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:35,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:35,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b02eb69-8248-4baa-8e90-91a2bc221106/dqc_reference
[2024-01-25 18:59:37,023] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:37,024] [INFO] Task started: Prodigal
[2024-01-25 18:59:37,024] [INFO] Running command: gunzip -c /var/lib/cwl/stga395870c-1ff8-48fe-8af1-e5522022bb3f/GCF_023078495.1_ASM2307849v1_genomic.fna.gz | prodigal -d GCF_023078495.1_ASM2307849v1_genomic.fna/cds.fna -a GCF_023078495.1_ASM2307849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:57,547] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:57,547] [INFO] Task started: HMMsearch
[2024-01-25 18:59:57,547] [INFO] Running command: hmmsearch --tblout GCF_023078495.1_ASM2307849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b02eb69-8248-4baa-8e90-91a2bc221106/dqc_reference/reference_markers.hmm GCF_023078495.1_ASM2307849v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:57,779] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:57,780] [INFO] Found 6/6 markers.
[2024-01-25 18:59:57,818] [INFO] Query marker FASTA was written to GCF_023078495.1_ASM2307849v1_genomic.fna/markers.fasta
[2024-01-25 18:59:57,818] [INFO] Task started: Blastn
[2024-01-25 18:59:57,818] [INFO] Running command: blastn -query GCF_023078495.1_ASM2307849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b02eb69-8248-4baa-8e90-91a2bc221106/dqc_reference/reference_markers.fasta -out GCF_023078495.1_ASM2307849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:58,723] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:58,725] [INFO] Selected 11 target genomes.
[2024-01-25 18:59:58,726] [INFO] Target genome list was writen to GCF_023078495.1_ASM2307849v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:58,728] [INFO] Task started: fastANI
[2024-01-25 18:59:58,728] [INFO] Running command: fastANI --query /var/lib/cwl/stga395870c-1ff8-48fe-8af1-e5522022bb3f/GCF_023078495.1_ASM2307849v1_genomic.fna.gz --refList GCF_023078495.1_ASM2307849v1_genomic.fna/target_genomes.txt --output GCF_023078495.1_ASM2307849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:08,648] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:08,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b02eb69-8248-4baa-8e90-91a2bc221106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:08,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b02eb69-8248-4baa-8e90-91a2bc221106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:08,657] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:00:08,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:00:08,657] [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	84.9585	1187	1664	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	82.0226	884	1664	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	81.8687	835	1664	95	below_threshold
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	81.4894	913	1664	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	81.4455	821	1664	95	below_threshold
Luteibacter rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	81.4224	794	1664	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.5201	580	1664	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.4661	440	1664	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.1985	454	1664	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.578	464	1664	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	78.0201	247	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:08,659] [INFO] DFAST Taxonomy check result was written to GCF_023078495.1_ASM2307849v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:08,659] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:08,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:08,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b02eb69-8248-4baa-8e90-91a2bc221106/dqc_reference/checkm_data
[2024-01-25 19:00:08,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:08,707] [INFO] Task started: CheckM
[2024-01-25 19:00:08,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023078495.1_ASM2307849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023078495.1_ASM2307849v1_genomic.fna/checkm_input GCF_023078495.1_ASM2307849v1_genomic.fna/checkm_result
[2024-01-25 19:01:10,432] [INFO] Task succeeded: CheckM
[2024-01-25 19:01:10,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:01:10,449] [INFO] ===== Completeness check finished =====
[2024-01-25 19:01:10,449] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:01:10,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023078495.1_ASM2307849v1_genomic.fna/markers.fasta)
[2024-01-25 19:01:10,450] [INFO] Task started: Blastn
[2024-01-25 19:01:10,450] [INFO] Running command: blastn -query GCF_023078495.1_ASM2307849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b02eb69-8248-4baa-8e90-91a2bc221106/dqc_reference/reference_markers_gtdb.fasta -out GCF_023078495.1_ASM2307849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:12,218] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:12,221] [INFO] Selected 11 target genomes.
[2024-01-25 19:01:12,221] [INFO] Target genome list was writen to GCF_023078495.1_ASM2307849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:01:12,236] [INFO] Task started: fastANI
[2024-01-25 19:01:12,237] [INFO] Running command: fastANI --query /var/lib/cwl/stga395870c-1ff8-48fe-8af1-e5522022bb3f/GCF_023078495.1_ASM2307849v1_genomic.fna.gz --refList GCF_023078495.1_ASM2307849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023078495.1_ASM2307849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:01:24,167] [INFO] Task succeeded: fastANI
[2024-01-25 19:01:24,175] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:01:24,175] [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	84.9585	1187	1664	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	84.5416	1056	1664	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	83.9789	1086	1664	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	82.141	870	1664	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	81.9914	888	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110505.1	s__Luteibacter sp900110505	81.9052	870	1664	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	81.8509	837	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109915.1	s__Luteibacter sp900109915	81.8119	838	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001887595.1	s__Luteibacter rhizovicinus	81.4836	913	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018449605.1	s__Luteibacter sp018449605	81.2863	874	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119235.1	s__Luteibacter sp900119235	81.2359	807	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:01:24,176] [INFO] GTDB search result was written to GCF_023078495.1_ASM2307849v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:01:24,177] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:01:24,180] [INFO] DFAST_QC result json was written to GCF_023078495.1_ASM2307849v1_genomic.fna/dqc_result.json
[2024-01-25 19:01:24,180] [INFO] DFAST_QC completed!
[2024-01-25 19:01:24,180] [INFO] Total running time: 0h1m48s