[2024-01-24 11:44:38,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,166] [INFO] DQC Reference Directory: /var/lib/cwl/stgad87c4e0-2e73-40c2-a0b5-0f6244250efe/dqc_reference
[2024-01-24 11:44:41,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,485] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,486] [INFO] Running command: gunzip -c /var/lib/cwl/stgec5553ef-8ca1-4dee-8b1c-9763814542f2/GCF_016583795.1_ASM1658379v1_genomic.fna.gz | prodigal -d GCF_016583795.1_ASM1658379v1_genomic.fna/cds.fna -a GCF_016583795.1_ASM1658379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:54,163] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:54,164] [INFO] Task started: HMMsearch
[2024-01-24 11:44:54,164] [INFO] Running command: hmmsearch --tblout GCF_016583795.1_ASM1658379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad87c4e0-2e73-40c2-a0b5-0f6244250efe/dqc_reference/reference_markers.hmm GCF_016583795.1_ASM1658379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:54,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:54,436] [INFO] Found 6/6 markers.
[2024-01-24 11:44:54,477] [INFO] Query marker FASTA was written to GCF_016583795.1_ASM1658379v1_genomic.fna/markers.fasta
[2024-01-24 11:44:54,478] [INFO] Task started: Blastn
[2024-01-24 11:44:54,478] [INFO] Running command: blastn -query GCF_016583795.1_ASM1658379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad87c4e0-2e73-40c2-a0b5-0f6244250efe/dqc_reference/reference_markers.fasta -out GCF_016583795.1_ASM1658379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:55,134] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:55,138] [INFO] Selected 26 target genomes.
[2024-01-24 11:44:55,139] [INFO] Target genome list was writen to GCF_016583795.1_ASM1658379v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:55,211] [INFO] Task started: fastANI
[2024-01-24 11:44:55,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5553ef-8ca1-4dee-8b1c-9763814542f2/GCF_016583795.1_ASM1658379v1_genomic.fna.gz --refList GCF_016583795.1_ASM1658379v1_genomic.fna/target_genomes.txt --output GCF_016583795.1_ASM1658379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:14,012] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:14,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad87c4e0-2e73-40c2-a0b5-0f6244250efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:14,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad87c4e0-2e73-40c2-a0b5-0f6244250efe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:14,026] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:14,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:14,027] [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
Rhabdochromatium marinum	strain=DSM 5261	GCA_016583795.1	48729	48729	type	True	100.0	1340	1353	95	conclusive
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	77.6297	223	1353	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	77.516	241	1353	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.4775	213	1353	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.4256	248	1353	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.3514	234	1353	95	below_threshold
Thiorhodococcus mannitoliphagus	strain=DSM 18266	GCA_010915725.1	329406	329406	type	True	77.3234	193	1353	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	77.3015	214	1353	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	77.1787	192	1353	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	77.0477	218	1353	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	77.0121	201	1353	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	76.8386	160	1353	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	76.7917	205	1353	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.5654	107	1353	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	75.7919	64	1353	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	75.5745	63	1353	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	75.42	53	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:14,041] [INFO] DFAST Taxonomy check result was written to GCF_016583795.1_ASM1658379v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:14,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:14,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:14,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad87c4e0-2e73-40c2-a0b5-0f6244250efe/dqc_reference/checkm_data
[2024-01-24 11:45:14,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:14,091] [INFO] Task started: CheckM
[2024-01-24 11:45:14,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016583795.1_ASM1658379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016583795.1_ASM1658379v1_genomic.fna/checkm_input GCF_016583795.1_ASM1658379v1_genomic.fna/checkm_result
[2024-01-24 11:45:54,009] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:54,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:54,029] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:54,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:54,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016583795.1_ASM1658379v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:54,031] [INFO] Task started: Blastn
[2024-01-24 11:45:54,031] [INFO] Running command: blastn -query GCF_016583795.1_ASM1658379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad87c4e0-2e73-40c2-a0b5-0f6244250efe/dqc_reference/reference_markers_gtdb.fasta -out GCF_016583795.1_ASM1658379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:54,981] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:54,985] [INFO] Selected 20 target genomes.
[2024-01-24 11:45:54,986] [INFO] Target genome list was writen to GCF_016583795.1_ASM1658379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:55,008] [INFO] Task started: fastANI
[2024-01-24 11:45:55,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5553ef-8ca1-4dee-8b1c-9763814542f2/GCF_016583795.1_ASM1658379v1_genomic.fna.gz --refList GCF_016583795.1_ASM1658379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016583795.1_ASM1658379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:09,560] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:09,578] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:09,578] [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_016583795.1	s__Rhabdochromatium marinum	100.0	1340	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Rhabdochromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016653415.1	s__Thiorhodovibrio winogradskyi	79.6061	597	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000228725.2	s__Thiorhodovibrio sp000228725	79.5177	608	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653295.1	s__Halochromatium salexigens	77.6194	223	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	77.4626	240	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_008632335.1	s__Thiohalocapsa marina	77.4174	248	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010912705.1	s__Halochromatium sp010912705	77.4097	181	1353	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	77.3786	225	1353	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	77.032	180	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003562815.1	s__Halochromatium sp003562815	77.0282	220	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCA_019136395.1	s__M0108 sp019136395	76.9111	101	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018435665.1	s__M0108 sp018435665	76.7706	117	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	99.16	99.16	0.79	0.79	2	-
GCA_006227775.1	s__M0108 sp006227775	76.7226	82	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015231665.1	s__JADGBD01 sp015231665	76.2321	72	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__JADGBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000397205.1	s__Pseudomonas_E protegens	75.793	62	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	-
GCF_000633395.1	s__Pseudomonas_E sp000633395	75.147	55	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:09,580] [INFO] GTDB search result was written to GCF_016583795.1_ASM1658379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:09,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:09,584] [INFO] DFAST_QC result json was written to GCF_016583795.1_ASM1658379v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:09,585] [INFO] DFAST_QC completed!
[2024-01-24 11:46:09,585] [INFO] Total running time: 0h1m31s