[2024-01-25 19:06:05,629] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:05,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:05,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg21902665-dd4f-4bfe-a2ce-a671a4def799/dqc_reference
[2024-01-25 19:06:06,777] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:06,777] [INFO] Task started: Prodigal
[2024-01-25 19:06:06,777] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bda7126-f403-4be7-905a-b27de5a01c58/GCF_003053845.1_ASM305384v1_genomic.fna.gz | prodigal -d GCF_003053845.1_ASM305384v1_genomic.fna/cds.fna -a GCF_003053845.1_ASM305384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:21,188] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:21,188] [INFO] Task started: HMMsearch
[2024-01-25 19:06:21,188] [INFO] Running command: hmmsearch --tblout GCF_003053845.1_ASM305384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21902665-dd4f-4bfe-a2ce-a671a4def799/dqc_reference/reference_markers.hmm GCF_003053845.1_ASM305384v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:21,586] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:21,587] [INFO] Found 6/6 markers.
[2024-01-25 19:06:21,629] [INFO] Query marker FASTA was written to GCF_003053845.1_ASM305384v1_genomic.fna/markers.fasta
[2024-01-25 19:06:21,629] [INFO] Task started: Blastn
[2024-01-25 19:06:21,630] [INFO] Running command: blastn -query GCF_003053845.1_ASM305384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21902665-dd4f-4bfe-a2ce-a671a4def799/dqc_reference/reference_markers.fasta -out GCF_003053845.1_ASM305384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:22,588] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:22,591] [INFO] Selected 24 target genomes.
[2024-01-25 19:06:22,591] [INFO] Target genome list was writen to GCF_003053845.1_ASM305384v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:22,621] [INFO] Task started: fastANI
[2024-01-25 19:06:22,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bda7126-f403-4be7-905a-b27de5a01c58/GCF_003053845.1_ASM305384v1_genomic.fna.gz --refList GCF_003053845.1_ASM305384v1_genomic.fna/target_genomes.txt --output GCF_003053845.1_ASM305384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:43,713] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:43,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21902665-dd4f-4bfe-a2ce-a671a4def799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:43,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21902665-dd4f-4bfe-a2ce-a671a4def799/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:43,728] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:06:43,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:43,728] [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
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	100.0	1765	1766	95	conclusive
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	78.2078	416	1766	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	78.174	407	1766	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	78.0146	359	1766	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	78.0053	360	1766	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	77.9937	380	1766	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	77.9846	460	1766	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.9717	453	1766	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.9696	459	1766	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	77.8641	421	1766	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	77.7926	421	1766	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	77.5565	358	1766	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.5221	362	1766	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.4726	305	1766	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.2286	336	1766	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.16	325	1766	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	77.0558	289	1766	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.0548	301	1766	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.9887	302	1766	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	76.983	216	1766	95	below_threshold
Phyllobacterium salinisoli	strain=LLAN61	GCA_003335045.1	1899321	1899321	type	True	76.9624	228	1766	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	76.5827	329	1766	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.5074	233	1766	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	75.938	119	1766	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:43,729] [INFO] DFAST Taxonomy check result was written to GCF_003053845.1_ASM305384v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:43,730] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:43,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:43,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21902665-dd4f-4bfe-a2ce-a671a4def799/dqc_reference/checkm_data
[2024-01-25 19:06:43,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:43,786] [INFO] Task started: CheckM
[2024-01-25 19:06:43,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003053845.1_ASM305384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003053845.1_ASM305384v1_genomic.fna/checkm_input GCF_003053845.1_ASM305384v1_genomic.fna/checkm_result
[2024-01-25 19:07:29,850] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:29,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:29,867] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:29,867] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:29,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003053845.1_ASM305384v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:29,867] [INFO] Task started: Blastn
[2024-01-25 19:07:29,867] [INFO] Running command: blastn -query GCF_003053845.1_ASM305384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21902665-dd4f-4bfe-a2ce-a671a4def799/dqc_reference/reference_markers_gtdb.fasta -out GCF_003053845.1_ASM305384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:31,720] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:31,724] [INFO] Selected 22 target genomes.
[2024-01-25 19:07:31,724] [INFO] Target genome list was writen to GCF_003053845.1_ASM305384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:31,751] [INFO] Task started: fastANI
[2024-01-25 19:07:31,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bda7126-f403-4be7-905a-b27de5a01c58/GCF_003053845.1_ASM305384v1_genomic.fna.gz --refList GCF_003053845.1_ASM305384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003053845.1_ASM305384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:52,328] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:52,342] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:52,342] [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_003053845.1	s__Breoghania corrubedonensis	100.0	1765	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003432385.1	s__Breoghania sp003432385	79.0411	603	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	78.6536	496	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_009789575.1	s__Stappia indica_A	78.6214	507	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	78.5027	483	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	78.4892	505	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_001696535.1	s__Stappia indica	78.4333	507	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_009915765.1	s__Pannonibacter sp009915765	78.3591	411	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	98.76	98.76	0.96	0.96	2	-
GCF_014050225.1	s__Hongsoonwoonella albiluteola	78.2259	414	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423705.1	s__Stappia stellulata	78.1823	406	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709505.1	s__Stappia sp002709505	78.1045	365	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635285.1	s__Stappia taiwanensis	77.8716	420	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002722295.1	s__Stappia sp002722295	77.7945	401	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
GCF_009826895.1	s__Hongsoonwoonella sp009826895	77.5547	371	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869065.1	s__Rhodobium sp002869065	77.5497	384	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	77.5007	346	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289965.1	s__Mesorhizobium atlanticum	77.4927	303	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952425.1	s__Mesorhizobium sp003952425	77.3597	309	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.51	95.02	0.90	0.84	19	-
GCF_016629525.1	s__Kaistia sp016629525	77.3012	338	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335045.1	s__Paramesorhizobium salinisoli	76.9737	227	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013341275.1	s__Methyloligella sp013341275	76.8342	182	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloligella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901457705.2	s__RH-AL1 sp901457705	76.702	229	1766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__RH-AL1	95.0	99.94	99.94	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:52,343] [INFO] GTDB search result was written to GCF_003053845.1_ASM305384v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:52,344] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:52,348] [INFO] DFAST_QC result json was written to GCF_003053845.1_ASM305384v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:52,348] [INFO] DFAST_QC completed!
[2024-01-25 19:07:52,348] [INFO] Total running time: 0h1m47s