[2023-06-28 10:47:17,258] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:47:17,264] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:47:17,265] [INFO] DQC Reference Directory: /var/lib/cwl/stgd33e0e11-87c0-4f19-a5c6-ad1dbf0de6c6/dqc_reference
[2023-06-28 10:47:19,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:47:19,436] [INFO] Task started: Prodigal
[2023-06-28 10:47:19,437] [INFO] Running command: gunzip -c /var/lib/cwl/stg58a36836-32f4-4dbd-8b78-fc1d04dd97aa/GCA_027310665.1_ASM2731066v1_genomic.fna.gz | prodigal -d GCA_027310665.1_ASM2731066v1_genomic.fna/cds.fna -a GCA_027310665.1_ASM2731066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:47:29,344] [INFO] Task succeeded: Prodigal
[2023-06-28 10:47:29,345] [INFO] Task started: HMMsearch
[2023-06-28 10:47:29,345] [INFO] Running command: hmmsearch --tblout GCA_027310665.1_ASM2731066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd33e0e11-87c0-4f19-a5c6-ad1dbf0de6c6/dqc_reference/reference_markers.hmm GCA_027310665.1_ASM2731066v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:47:29,617] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:47:29,619] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg58a36836-32f4-4dbd-8b78-fc1d04dd97aa/GCA_027310665.1_ASM2731066v1_genomic.fna.gz]
[2023-06-28 10:47:29,652] [INFO] Query marker FASTA was written to GCA_027310665.1_ASM2731066v1_genomic.fna/markers.fasta
[2023-06-28 10:47:29,652] [INFO] Task started: Blastn
[2023-06-28 10:47:29,652] [INFO] Running command: blastn -query GCA_027310665.1_ASM2731066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd33e0e11-87c0-4f19-a5c6-ad1dbf0de6c6/dqc_reference/reference_markers.fasta -out GCA_027310665.1_ASM2731066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:30,494] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:30,499] [INFO] Selected 29 target genomes.
[2023-06-28 10:47:30,499] [INFO] Target genome list was writen to GCA_027310665.1_ASM2731066v1_genomic.fna/target_genomes.txt
[2023-06-28 10:47:30,507] [INFO] Task started: fastANI
[2023-06-28 10:47:30,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg58a36836-32f4-4dbd-8b78-fc1d04dd97aa/GCA_027310665.1_ASM2731066v1_genomic.fna.gz --refList GCA_027310665.1_ASM2731066v1_genomic.fna/target_genomes.txt --output GCA_027310665.1_ASM2731066v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:47:49,154] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:49,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd33e0e11-87c0-4f19-a5c6-ad1dbf0de6c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:47:49,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd33e0e11-87c0-4f19-a5c6-ad1dbf0de6c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:47:49,183] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:47:49,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:47:49,183] [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
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	79.8106	332	998	95	below_threshold
Ferriphaselus amnicola	strain=OYT1	GCA_000974685.2	1188319	1188319	type	True	77.798	201	998	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	77.1912	122	998	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.0892	127	998	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.0645	150	998	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	77.0059	130	998	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	76.9694	119	998	95	below_threshold
Gallionella capsiferriformans	strain=ES-2	GCA_000145255.1	370405	370405	type	True	76.8526	126	998	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	76.8449	111	998	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	76.8263	140	998	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	76.793	127	998	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	76.7858	142	998	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.7746	110	998	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	76.7382	110	998	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.7319	183	998	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.7199	112	998	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	76.6593	110	998	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.6305	120	998	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	76.6172	139	998	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	76.5934	141	998	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.4807	135	998	95	below_threshold
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	76.4209	90	998	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.3781	96	998	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.2705	94	998	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	76.2194	105	998	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	76.2083	103	998	95	below_threshold
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	76.1981	97	998	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	76.0343	63	998	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:47:49,185] [INFO] DFAST Taxonomy check result was written to GCA_027310665.1_ASM2731066v1_genomic.fna/tc_result.tsv
[2023-06-28 10:47:49,186] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:47:49,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:47:49,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd33e0e11-87c0-4f19-a5c6-ad1dbf0de6c6/dqc_reference/checkm_data
[2023-06-28 10:47:49,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:47:49,225] [INFO] Task started: CheckM
[2023-06-28 10:47:49,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310665.1_ASM2731066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310665.1_ASM2731066v1_genomic.fna/checkm_input GCA_027310665.1_ASM2731066v1_genomic.fna/checkm_result
[2023-06-28 10:48:22,042] [INFO] Task succeeded: CheckM
[2023-06-28 10:48:22,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:48:22,069] [INFO] ===== Completeness check finished =====
[2023-06-28 10:48:22,069] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:48:22,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310665.1_ASM2731066v1_genomic.fna/markers.fasta)
[2023-06-28 10:48:22,070] [INFO] Task started: Blastn
[2023-06-28 10:48:22,070] [INFO] Running command: blastn -query GCA_027310665.1_ASM2731066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd33e0e11-87c0-4f19-a5c6-ad1dbf0de6c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310665.1_ASM2731066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:48:23,556] [INFO] Task succeeded: Blastn
[2023-06-28 10:48:23,562] [INFO] Selected 9 target genomes.
[2023-06-28 10:48:23,562] [INFO] Target genome list was writen to GCA_027310665.1_ASM2731066v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:48:23,577] [INFO] Task started: fastANI
[2023-06-28 10:48:23,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg58a36836-32f4-4dbd-8b78-fc1d04dd97aa/GCA_027310665.1_ASM2731066v1_genomic.fna.gz --refList GCA_027310665.1_ASM2731066v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310665.1_ASM2731066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:48:29,001] [INFO] Task succeeded: fastANI
[2023-06-28 10:48:29,014] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:48:29,014] [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_000025705.1	s__Sideroxydans lithotrophicus	82.3624	586	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214695.1	s__Sideroxydans sp016214695	81.9303	477	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208015.1	s__Sideroxydans sp016208015	81.8788	513	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235045.1	s__Sideroxydans sp016235045	81.8631	518	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813765.1	s__Sideroxydans sp018813765	81.4569	481	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.93	99.86	0.97	0.93	3	-
GCA_003445795.1	s__Sideroxydans sp003445795	81.3404	479	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820925.1	s__Sideroxydans sp018820925	81.2346	535	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.99	99.99	0.96	0.96	2	-
GCA_903847155.1	s__Sideroxydans sp903847155	79.8937	414	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297065.1	s__PALSA-1006 sp004297065	79.3168	343	998	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__PALSA-1006	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:48:29,017] [INFO] GTDB search result was written to GCA_027310665.1_ASM2731066v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:48:29,017] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:48:29,022] [INFO] DFAST_QC result json was written to GCA_027310665.1_ASM2731066v1_genomic.fna/dqc_result.json
[2023-06-28 10:48:29,022] [INFO] DFAST_QC completed!
[2023-06-28 10:48:29,022] [INFO] Total running time: 0h1m12s