[2024-01-24 13:40:55,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d5a6c2a-664a-4119-9bd0-6bb0c5790cc6/dqc_reference
[2024-01-24 13:40:57,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:57,129] [INFO] Task started: Prodigal
[2024-01-24 13:40:57,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg96b7bd25-ede4-441d-b460-30ad1fabb242/GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna.gz | prodigal -d GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/cds.fna -a GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:18,896] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:18,896] [INFO] Task started: HMMsearch
[2024-01-24 13:41:18,896] [INFO] Running command: hmmsearch --tblout GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d5a6c2a-664a-4119-9bd0-6bb0c5790cc6/dqc_reference/reference_markers.hmm GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:19,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:19,318] [INFO] Found 6/6 markers.
[2024-01-24 13:41:19,385] [INFO] Query marker FASTA was written to GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/markers.fasta
[2024-01-24 13:41:19,386] [INFO] Task started: Blastn
[2024-01-24 13:41:19,386] [INFO] Running command: blastn -query GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d5a6c2a-664a-4119-9bd0-6bb0c5790cc6/dqc_reference/reference_markers.fasta -out GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:20,185] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:20,188] [INFO] Selected 26 target genomes.
[2024-01-24 13:41:20,188] [INFO] Target genome list was writen to GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/target_genomes.txt
[2024-01-24 13:41:20,194] [INFO] Task started: fastANI
[2024-01-24 13:41:20,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b7bd25-ede4-441d-b460-30ad1fabb242/GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna.gz --refList GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/target_genomes.txt --output GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:47,913] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:47,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d5a6c2a-664a-4119-9bd0-6bb0c5790cc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:47,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d5a6c2a-664a-4119-9bd0-6bb0c5790cc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:47,928] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:47,929] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:47,929] [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
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	100.0	2465	2470	95	conclusive
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.294	337	2470	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	78.2806	684	2470	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	78.062	251	2470	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.8694	554	2470	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.7212	376	2470	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	77.6769	400	2470	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	77.6563	505	2470	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	77.6315	533	2470	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	77.5228	618	2470	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	77.4942	523	2470	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	77.4751	318	2470	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	77.4058	592	2470	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	77.3803	602	2470	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.3331	440	2470	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.3057	650	2470	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.2483	429	2470	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	77.2003	524	2470	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	77.1796	590	2470	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.9598	481	2470	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.8975	506	2470	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	76.7757	192	2470	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	75.8634	316	2470	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	75.4152	201	2470	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	75.3871	203	2470	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	75.3845	204	2470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,930] [INFO] DFAST Taxonomy check result was written to GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/tc_result.tsv
[2024-01-24 13:41:47,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:47,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:47,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d5a6c2a-664a-4119-9bd0-6bb0c5790cc6/dqc_reference/checkm_data
[2024-01-24 13:41:47,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:47,998] [INFO] Task started: CheckM
[2024-01-24 13:41:47,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/checkm_input GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/checkm_result
[2024-01-24 13:43:55,834] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:55,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:55,849] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:55,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:55,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/markers.fasta)
[2024-01-24 13:43:55,850] [INFO] Task started: Blastn
[2024-01-24 13:43:55,850] [INFO] Running command: blastn -query GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d5a6c2a-664a-4119-9bd0-6bb0c5790cc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:57,154] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:57,156] [INFO] Selected 18 target genomes.
[2024-01-24 13:43:57,156] [INFO] Target genome list was writen to GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:57,220] [INFO] Task started: fastANI
[2024-01-24 13:43:57,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b7bd25-ede4-441d-b460-30ad1fabb242/GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna.gz --refList GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/target_genomes_gtdb.txt --output GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:17,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:17,181] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:17,181] [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_008630155.1	s__Rhodovastum atsumiense	99.9362	2257	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903907955.1	s__BOG-930 sp903907955	80.5719	767	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCA_903918195.1	s__BOG-930 sp903918195	80.3537	779	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCA_001899585.1	s__70-18 sp001899585	79.3895	732	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_903839965.1	s__BOG-930 sp903839965	79.338	539	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971455.1	s__REEB85 sp018971455	79.0424	341	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164455.1	s__BOG-930 sp003164455	78.9736	486	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	78.4066	625	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307285.1	s__JAFKFI01 sp017307285	78.3137	522	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898425.1	s__69-11 sp001898425	78.247	621	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCA_019240395.1	s__JAFAYA01 sp019240395	78.2224	515	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864895.1	s__CAIPHQ01 sp903864895	77.8671	465	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIPHQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928895.1	s__CAIYPH01 sp903928895	77.5889	533	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	99.93	99.91	0.97	0.97	4	-
GCA_903845065.1	s__CAIYPH01 sp903845065	77.2651	554	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114375.1	s__Methylobacterium salsuginis	76.0731	348	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386575.1	s__BN140002 sp008386575	75.8898	309	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__BN140002	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007000325.1	s__Rhizobium sp007000325	75.7128	166	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.07	97.10	0.92	0.88	7	-
GCF_008728195.1	s__Roseovarius indicus	75.4109	199	2470	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:17,182] [INFO] GTDB search result was written to GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:17,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:17,189] [INFO] DFAST_QC result json was written to GCF_937425535.1_Rhodovastum_atsumiense_G2-11_genomic.fna/dqc_result.json
[2024-01-24 13:44:17,189] [INFO] DFAST_QC completed!
[2024-01-24 13:44:17,189] [INFO] Total running time: 0h3m21s