[2024-01-24 12:29:52,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:52,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:52,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg237e8ca9-c49e-49ca-85d3-e29a7a1bfb20/dqc_reference
[2024-01-24 12:29:53,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:53,852] [INFO] Task started: Prodigal
[2024-01-24 12:29:53,852] [INFO] Running command: gunzip -c /var/lib/cwl/stg9786c2d1-e8dd-44bb-825c-d5222888a97f/GCF_016653295.1_ASM1665329v1_genomic.fna.gz | prodigal -d GCF_016653295.1_ASM1665329v1_genomic.fna/cds.fna -a GCF_016653295.1_ASM1665329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:04,795] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:04,795] [INFO] Task started: HMMsearch
[2024-01-24 12:30:04,795] [INFO] Running command: hmmsearch --tblout GCF_016653295.1_ASM1665329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg237e8ca9-c49e-49ca-85d3-e29a7a1bfb20/dqc_reference/reference_markers.hmm GCF_016653295.1_ASM1665329v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:05,092] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:05,093] [INFO] Found 6/6 markers.
[2024-01-24 12:30:05,128] [INFO] Query marker FASTA was written to GCF_016653295.1_ASM1665329v1_genomic.fna/markers.fasta
[2024-01-24 12:30:05,128] [INFO] Task started: Blastn
[2024-01-24 12:30:05,128] [INFO] Running command: blastn -query GCF_016653295.1_ASM1665329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237e8ca9-c49e-49ca-85d3-e29a7a1bfb20/dqc_reference/reference_markers.fasta -out GCF_016653295.1_ASM1665329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:05,916] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:05,920] [INFO] Selected 20 target genomes.
[2024-01-24 12:30:05,920] [INFO] Target genome list was writen to GCF_016653295.1_ASM1665329v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:05,928] [INFO] Task started: fastANI
[2024-01-24 12:30:05,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg9786c2d1-e8dd-44bb-825c-d5222888a97f/GCF_016653295.1_ASM1665329v1_genomic.fna.gz --refList GCF_016653295.1_ASM1665329v1_genomic.fna/target_genomes.txt --output GCF_016653295.1_ASM1665329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:21,893] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:21,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg237e8ca9-c49e-49ca-85d3-e29a7a1bfb20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:21,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg237e8ca9-c49e-49ca-85d3-e29a7a1bfb20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:21,911] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:21,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:21,912] [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
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	100.0	1223	1227	95	conclusive
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	83.0074	798	1227	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	81.8505	749	1227	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	78.933	418	1227	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	78.5645	340	1227	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	78.5494	475	1227	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	78.4881	345	1227	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	78.3851	351	1227	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	77.7545	317	1227	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	77.5623	264	1227	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	76.9366	124	1227	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	76.4711	142	1227	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.4438	117	1227	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.3976	147	1227	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	76.3735	85	1227	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	76.356	136	1227	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.2872	116	1227	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	76.2048	82	1227	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.184	146	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:21,913] [INFO] DFAST Taxonomy check result was written to GCF_016653295.1_ASM1665329v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:21,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:21,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:21,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg237e8ca9-c49e-49ca-85d3-e29a7a1bfb20/dqc_reference/checkm_data
[2024-01-24 12:30:21,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:21,953] [INFO] Task started: CheckM
[2024-01-24 12:30:21,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016653295.1_ASM1665329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016653295.1_ASM1665329v1_genomic.fna/checkm_input GCF_016653295.1_ASM1665329v1_genomic.fna/checkm_result
[2024-01-24 12:30:57,443] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:57,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:57,468] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:57,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:57,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016653295.1_ASM1665329v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:57,470] [INFO] Task started: Blastn
[2024-01-24 12:30:57,470] [INFO] Running command: blastn -query GCF_016653295.1_ASM1665329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237e8ca9-c49e-49ca-85d3-e29a7a1bfb20/dqc_reference/reference_markers_gtdb.fasta -out GCF_016653295.1_ASM1665329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:58,802] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:58,807] [INFO] Selected 11 target genomes.
[2024-01-24 12:30:58,807] [INFO] Target genome list was writen to GCF_016653295.1_ASM1665329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:58,816] [INFO] Task started: fastANI
[2024-01-24 12:30:58,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg9786c2d1-e8dd-44bb-825c-d5222888a97f/GCF_016653295.1_ASM1665329v1_genomic.fna.gz --refList GCF_016653295.1_ASM1665329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016653295.1_ASM1665329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:07,966] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:07,986] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:07,987] [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_016653295.1	s__Halochromatium salexigens	100.0	1223	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003562815.1	s__Halochromatium sp003562815	88.6534	684	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCF_016583905.1	s__Halochromatium modestohalophilus	83.5325	816	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653315.1	s__Halochromatium roseum	82.9857	801	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010912705.1	s__Halochromatium sp010912705	81.8836	635	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584085.1	s__Halochromatium glycolicum	81.8619	747	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908845.1	s__Halochromatium sp009908845	81.4751	595	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901955.1	s__Halomonas icarae	76.315	88	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.73	97.73	0.87	0.87	2	-
GCF_011742875.1	s__Luteibacter yeojuensis	76.1851	83	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	76.1567	106	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003560175.1	s__Halomonas sp003560175	75.7927	71	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:07,989] [INFO] GTDB search result was written to GCF_016653295.1_ASM1665329v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:07,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:07,996] [INFO] DFAST_QC result json was written to GCF_016653295.1_ASM1665329v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:07,997] [INFO] DFAST_QC completed!
[2024-01-24 12:31:07,997] [INFO] Total running time: 0h1m15s