[2024-01-24 14:20:15,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:15,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:15,718] [INFO] DQC Reference Directory: /var/lib/cwl/stgd894e3da-cc62-4977-a5cc-1ae7a17d19bf/dqc_reference
[2024-01-24 14:20:17,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:17,691] [INFO] Task started: Prodigal
[2024-01-24 14:20:17,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg22e0ed31-830d-4f74-8d8b-e99fbf2bc4fd/GCF_001010405.1_ASM101040v1_genomic.fna.gz | prodigal -d GCF_001010405.1_ASM101040v1_genomic.fna/cds.fna -a GCF_001010405.1_ASM101040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:32,756] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:32,757] [INFO] Task started: HMMsearch
[2024-01-24 14:20:32,757] [INFO] Running command: hmmsearch --tblout GCF_001010405.1_ASM101040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd894e3da-cc62-4977-a5cc-1ae7a17d19bf/dqc_reference/reference_markers.hmm GCF_001010405.1_ASM101040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:33,081] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:33,083] [INFO] Found 6/6 markers.
[2024-01-24 14:20:33,124] [INFO] Query marker FASTA was written to GCF_001010405.1_ASM101040v1_genomic.fna/markers.fasta
[2024-01-24 14:20:33,125] [INFO] Task started: Blastn
[2024-01-24 14:20:33,125] [INFO] Running command: blastn -query GCF_001010405.1_ASM101040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd894e3da-cc62-4977-a5cc-1ae7a17d19bf/dqc_reference/reference_markers.fasta -out GCF_001010405.1_ASM101040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:35,107] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:35,111] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:35,111] [INFO] Target genome list was writen to GCF_001010405.1_ASM101040v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:35,116] [INFO] Task started: fastANI
[2024-01-24 14:20:35,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e0ed31-830d-4f74-8d8b-e99fbf2bc4fd/GCF_001010405.1_ASM101040v1_genomic.fna.gz --refList GCF_001010405.1_ASM101040v1_genomic.fna/target_genomes.txt --output GCF_001010405.1_ASM101040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:48,736] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:48,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd894e3da-cc62-4977-a5cc-1ae7a17d19bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:48,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd894e3da-cc62-4977-a5cc-1ae7a17d19bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:48,797] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:48,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:48,797] [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 rhizovicinus	strain=DSM 16549	GCA_001010405.1	242606	242606	type	True	100.0	1420	1426	95	conclusive
Luteibacter rhizovicinus	strain=LJ96	GCA_001887595.1	242606	242606	type	True	99.9898	1426	1426	95	conclusive
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	82.2124	788	1426	95	below_threshold
Luteibacter pinisoli	strain=MAH-14	GCA_006385595.1	2589080	2589080	type	True	82.2015	826	1426	95	below_threshold
Luteibacter anthropi	strain=CCUG 25036	GCA_011759365.1	564369	564369	type	True	81.8416	744	1426	95	below_threshold
Luteibacter jiangsuensis	strain=CGMCC 1.10133	GCA_011742555.1	637577	637577	type	True	81.7912	764	1426	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.3884	397	1426	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	79.3085	491	1426	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.1732	491	1426	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.9004	427	1426	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.4336	425	1426	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.9634	285	1426	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	77.7733	234	1426	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.2412	99	1426	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.2036	100	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:48,799] [INFO] DFAST Taxonomy check result was written to GCF_001010405.1_ASM101040v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:48,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:48,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:48,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd894e3da-cc62-4977-a5cc-1ae7a17d19bf/dqc_reference/checkm_data
[2024-01-24 14:20:48,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:48,851] [INFO] Task started: CheckM
[2024-01-24 14:20:48,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001010405.1_ASM101040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001010405.1_ASM101040v1_genomic.fna/checkm_input GCF_001010405.1_ASM101040v1_genomic.fna/checkm_result
[2024-01-24 14:21:34,951] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:34,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:34,972] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:34,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:34,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001010405.1_ASM101040v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:34,973] [INFO] Task started: Blastn
[2024-01-24 14:21:34,973] [INFO] Running command: blastn -query GCF_001010405.1_ASM101040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd894e3da-cc62-4977-a5cc-1ae7a17d19bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_001010405.1_ASM101040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:37,919] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:37,926] [INFO] Selected 11 target genomes.
[2024-01-24 14:21:37,926] [INFO] Target genome list was writen to GCF_001010405.1_ASM101040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:37,935] [INFO] Task started: fastANI
[2024-01-24 14:21:37,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e0ed31-830d-4f74-8d8b-e99fbf2bc4fd/GCF_001010405.1_ASM101040v1_genomic.fna.gz --refList GCF_001010405.1_ASM101040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001010405.1_ASM101040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:49,575] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:49,633] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:49,633] [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_001887595.1	s__Luteibacter rhizovicinus	99.9898	1426	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003050935.1	s__Luteibacter sp003050935	86.7493	1127	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449605.1	s__Luteibacter sp018449605	86.7443	1142	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745005.1	s__Luteibacter sp000745005	82.7082	790	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745055.1	s__Luteibacter sp000745055	82.7002	842	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	98.38	97.45	0.94	0.90	5	-
GCF_900110505.1	s__Luteibacter sp900110505	82.6736	816	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	97.58	97.58	0.93	0.93	2	-
GCF_900109915.1	s__Luteibacter sp900109915	82.5867	780	1426	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	82.2229	835	1426	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	82.0885	802	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759605.1	s__Luteibacter sp011759605	82.0125	744	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742555.1	s__Luteibacter jiangsuensis	81.7906	764	1426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:49,635] [INFO] GTDB search result was written to GCF_001010405.1_ASM101040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:49,636] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:49,640] [INFO] DFAST_QC result json was written to GCF_001010405.1_ASM101040v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:49,640] [INFO] DFAST_QC completed!
[2024-01-24 14:21:49,640] [INFO] Total running time: 0h1m34s