[2023-06-30 12:42:04,561] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:42:04,568] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:42:04,568] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c91eb4e-e59f-406a-a5b5-9e6962ef2bea/dqc_reference
[2023-06-30 12:42:05,839] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:42:05,840] [INFO] Task started: Prodigal
[2023-06-30 12:42:05,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg22f21509-e2c0-4405-ac66-0f9cc10251c3/GCA_016708575.1_ASM1670857v1_genomic.fna.gz | prodigal -d GCA_016708575.1_ASM1670857v1_genomic.fna/cds.fna -a GCA_016708575.1_ASM1670857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:42:17,893] [INFO] Task succeeded: Prodigal
[2023-06-30 12:42:17,893] [INFO] Task started: HMMsearch
[2023-06-30 12:42:17,893] [INFO] Running command: hmmsearch --tblout GCA_016708575.1_ASM1670857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c91eb4e-e59f-406a-a5b5-9e6962ef2bea/dqc_reference/reference_markers.hmm GCA_016708575.1_ASM1670857v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:42:18,193] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:42:18,194] [INFO] Found 6/6 markers.
[2023-06-30 12:42:18,238] [INFO] Query marker FASTA was written to GCA_016708575.1_ASM1670857v1_genomic.fna/markers.fasta
[2023-06-30 12:42:18,238] [INFO] Task started: Blastn
[2023-06-30 12:42:18,239] [INFO] Running command: blastn -query GCA_016708575.1_ASM1670857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c91eb4e-e59f-406a-a5b5-9e6962ef2bea/dqc_reference/reference_markers.fasta -out GCA_016708575.1_ASM1670857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:42:19,183] [INFO] Task succeeded: Blastn
[2023-06-30 12:42:19,187] [INFO] Selected 24 target genomes.
[2023-06-30 12:42:19,187] [INFO] Target genome list was writen to GCA_016708575.1_ASM1670857v1_genomic.fna/target_genomes.txt
[2023-06-30 12:42:19,194] [INFO] Task started: fastANI
[2023-06-30 12:42:19,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg22f21509-e2c0-4405-ac66-0f9cc10251c3/GCA_016708575.1_ASM1670857v1_genomic.fna.gz --refList GCA_016708575.1_ASM1670857v1_genomic.fna/target_genomes.txt --output GCA_016708575.1_ASM1670857v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:42:36,633] [INFO] Task succeeded: fastANI
[2023-06-30 12:42:36,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c91eb4e-e59f-406a-a5b5-9e6962ef2bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:42:36,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c91eb4e-e59f-406a-a5b5-9e6962ef2bea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:42:36,653] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:42:36,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:42:36,653] [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
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	80.8772	712	1172	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	78.7222	424	1172	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	78.1906	415	1172	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	78.0492	315	1172	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	78.0429	311	1172	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.9624	354	1172	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	77.7117	288	1172	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	77.7104	279	1172	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.709	227	1172	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.6763	316	1172	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	77.6662	270	1172	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	77.6642	270	1172	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	77.6564	281	1172	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	77.6474	267	1172	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	77.6168	370	1172	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	77.5318	298	1172	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.5185	216	1172	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	77.4781	289	1172	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	77.4682	259	1172	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	77.448	275	1172	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	77.4437	247	1172	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.4014	297	1172	95	below_threshold
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	77.3818	244	1172	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	77.0604	233	1172	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:42:36,656] [INFO] DFAST Taxonomy check result was written to GCA_016708575.1_ASM1670857v1_genomic.fna/tc_result.tsv
[2023-06-30 12:42:36,656] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:42:36,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:42:36,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c91eb4e-e59f-406a-a5b5-9e6962ef2bea/dqc_reference/checkm_data
[2023-06-30 12:42:36,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:42:36,693] [INFO] Task started: CheckM
[2023-06-30 12:42:36,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708575.1_ASM1670857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708575.1_ASM1670857v1_genomic.fna/checkm_input GCA_016708575.1_ASM1670857v1_genomic.fna/checkm_result
[2023-06-30 12:43:25,047] [INFO] Task succeeded: CheckM
[2023-06-30 12:43:25,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:43:25,071] [INFO] ===== Completeness check finished =====
[2023-06-30 12:43:25,071] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:43:25,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708575.1_ASM1670857v1_genomic.fna/markers.fasta)
[2023-06-30 12:43:25,072] [INFO] Task started: Blastn
[2023-06-30 12:43:25,072] [INFO] Running command: blastn -query GCA_016708575.1_ASM1670857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c91eb4e-e59f-406a-a5b5-9e6962ef2bea/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708575.1_ASM1670857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:43:26,791] [INFO] Task succeeded: Blastn
[2023-06-30 12:43:26,796] [INFO] Selected 9 target genomes.
[2023-06-30 12:43:26,796] [INFO] Target genome list was writen to GCA_016708575.1_ASM1670857v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:43:26,804] [INFO] Task started: fastANI
[2023-06-30 12:43:26,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg22f21509-e2c0-4405-ac66-0f9cc10251c3/GCA_016708575.1_ASM1670857v1_genomic.fna.gz --refList GCA_016708575.1_ASM1670857v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708575.1_ASM1670857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:43:35,052] [INFO] Task succeeded: fastANI
[2023-06-30 12:43:35,063] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:43:35,064] [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
GCA_016707485.1	s__Dokdonella sp016707485	99.1804	1103	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	99.34	99.18	0.96	0.94	4	conclusive
GCA_001899855.1	s__Dokdonella sp001899855	93.4911	994	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721015.1	s__Dokdonella sp016721015	82.992	855	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115085.1	s__Dokdonella immobilis	80.923	707	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712865.1	s__Dokdonella sp016712865	79.4758	552	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	99.46	99.45	0.98	0.98	3	-
GCA_017302215.1	s__Dokdonella sp017302215	79.4641	485	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295005.1	s__Dokdonella sp004295005	79.3396	484	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	78.3996	458	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004143945.1	s__Dokdonella_A sp004143945	78.3537	362	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:43:35,066] [INFO] GTDB search result was written to GCA_016708575.1_ASM1670857v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:43:35,066] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:43:35,071] [INFO] DFAST_QC result json was written to GCA_016708575.1_ASM1670857v1_genomic.fna/dqc_result.json
[2023-06-30 12:43:35,071] [INFO] DFAST_QC completed!
[2023-06-30 12:43:35,071] [INFO] Total running time: 0h1m31s