[2023-06-30 14:11:40,849] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:11:40,851] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:11:40,851] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb7934cb-1390-43b5-87fa-8d9b1a2feee5/dqc_reference
[2023-06-30 14:11:42,073] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:11:42,074] [INFO] Task started: Prodigal
[2023-06-30 14:11:42,074] [INFO] Running command: gunzip -c /var/lib/cwl/stga641b3f2-848a-45ef-9f22-33b409bbba5d/GCA_016708725.1_ASM1670872v1_genomic.fna.gz | prodigal -d GCA_016708725.1_ASM1670872v1_genomic.fna/cds.fna -a GCA_016708725.1_ASM1670872v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:12:05,251] [INFO] Task succeeded: Prodigal
[2023-06-30 14:12:05,251] [INFO] Task started: HMMsearch
[2023-06-30 14:12:05,251] [INFO] Running command: hmmsearch --tblout GCA_016708725.1_ASM1670872v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb7934cb-1390-43b5-87fa-8d9b1a2feee5/dqc_reference/reference_markers.hmm GCA_016708725.1_ASM1670872v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:12:05,599] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:12:05,601] [INFO] Found 6/6 markers.
[2023-06-30 14:12:05,652] [INFO] Query marker FASTA was written to GCA_016708725.1_ASM1670872v1_genomic.fna/markers.fasta
[2023-06-30 14:12:05,653] [INFO] Task started: Blastn
[2023-06-30 14:12:05,653] [INFO] Running command: blastn -query GCA_016708725.1_ASM1670872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb7934cb-1390-43b5-87fa-8d9b1a2feee5/dqc_reference/reference_markers.fasta -out GCA_016708725.1_ASM1670872v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:12:06,299] [INFO] Task succeeded: Blastn
[2023-06-30 14:12:06,304] [INFO] Selected 27 target genomes.
[2023-06-30 14:12:06,305] [INFO] Target genome list was writen to GCA_016708725.1_ASM1670872v1_genomic.fna/target_genomes.txt
[2023-06-30 14:12:06,336] [INFO] Task started: fastANI
[2023-06-30 14:12:06,337] [INFO] Running command: fastANI --query /var/lib/cwl/stga641b3f2-848a-45ef-9f22-33b409bbba5d/GCA_016708725.1_ASM1670872v1_genomic.fna.gz --refList GCA_016708725.1_ASM1670872v1_genomic.fna/target_genomes.txt --output GCA_016708725.1_ASM1670872v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:12:24,873] [INFO] Task succeeded: fastANI
[2023-06-30 14:12:24,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb7934cb-1390-43b5-87fa-8d9b1a2feee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:12:24,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb7934cb-1390-43b5-87fa-8d9b1a2feee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:12:24,898] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:12:24,898] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:12:24,899] [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
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.6758	309	2009	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	77.5929	263	2009	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	77.5624	206	2009	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	77.5355	183	2009	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.5175	262	2009	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.5155	231	2009	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.5003	160	2009	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	77.3825	225	2009	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	77.3268	242	2009	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	77.2839	200	2009	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	77.2807	184	2009	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.255	220	2009	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.252	169	2009	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	77.2489	236	2009	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	77.1556	204	2009	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	77.153	187	2009	95	below_threshold
Ottowia oryzae	strain=KADR8-3	GCA_003008535.1	2109914	2109914	type	True	77.0939	179	2009	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	76.9816	188	2009	95	below_threshold
Extensimonas vulgaris	strain=DSM 100911	GCA_003337425.1	1031594	1031594	type	True	76.9262	173	2009	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	76.8874	189	2009	95	below_threshold
Extensimonas vulgaris	strain=CGMCC 1.10977	GCA_007830535.1	1031594	1031594	type	True	76.8872	176	2009	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.8797	167	2009	95	below_threshold
Extensimonas vulgaris	strain=S4	GCA_007996985.1	1031594	1031594	type	True	76.8795	176	2009	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.8746	239	2009	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	76.7051	165	2009	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	76.6903	203	2009	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	76.1713	128	2009	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:12:24,901] [INFO] DFAST Taxonomy check result was written to GCA_016708725.1_ASM1670872v1_genomic.fna/tc_result.tsv
[2023-06-30 14:12:24,901] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:12:24,902] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:12:24,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb7934cb-1390-43b5-87fa-8d9b1a2feee5/dqc_reference/checkm_data
[2023-06-30 14:12:24,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:12:24,959] [INFO] Task started: CheckM
[2023-06-30 14:12:24,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708725.1_ASM1670872v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708725.1_ASM1670872v1_genomic.fna/checkm_input GCA_016708725.1_ASM1670872v1_genomic.fna/checkm_result
[2023-06-30 14:13:30,552] [INFO] Task succeeded: CheckM
[2023-06-30 14:13:30,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:13:30,579] [INFO] ===== Completeness check finished =====
[2023-06-30 14:13:30,579] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:13:30,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708725.1_ASM1670872v1_genomic.fna/markers.fasta)
[2023-06-30 14:13:30,580] [INFO] Task started: Blastn
[2023-06-30 14:13:30,580] [INFO] Running command: blastn -query GCA_016708725.1_ASM1670872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb7934cb-1390-43b5-87fa-8d9b1a2feee5/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708725.1_ASM1670872v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:13:31,618] [INFO] Task succeeded: Blastn
[2023-06-30 14:13:31,624] [INFO] Selected 21 target genomes.
[2023-06-30 14:13:31,624] [INFO] Target genome list was writen to GCA_016708725.1_ASM1670872v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:13:31,635] [INFO] Task started: fastANI
[2023-06-30 14:13:31,635] [INFO] Running command: fastANI --query /var/lib/cwl/stga641b3f2-848a-45ef-9f22-33b409bbba5d/GCA_016708725.1_ASM1670872v1_genomic.fna.gz --refList GCA_016708725.1_ASM1670872v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708725.1_ASM1670872v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:13:49,212] [INFO] Task succeeded: fastANI
[2023-06-30 14:13:49,236] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:13:49,236] [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_016708725.1	s__Rhodoferax sp016708725	100.0	2003	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016719405.1	s__Rhodoferax sp016719405	79.9606	387	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.38	98.38	0.86	0.86	2	-
GCA_903863395.1	s__Rhodoferax sp903863395	77.9497	257	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.94	98.87	0.83	0.81	5	-
GCF_002163715.1	s__Rhodoferax sp002163715	77.7156	188	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	97.64	97.64	0.97	0.97	2	-
GCF_000282655.1	s__Polaromonas sp000282655	77.6852	182	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003415675.1	s__Rhodoferax sp003415675	77.6722	311	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015235.1	s__Rhodoferax sp008015235	77.6334	250	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786915.1	s__Rhodoferax sp002786915	77.6282	224	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.98	0.98	2	-
GCA_903960915.1	s__Rhodoferax sp903960915	77.6017	194	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCA_001770935.1	s__Rhodoferax sp001770935	77.5505	301	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798165.1	s__Rhodoferax sp017798165	77.5249	319	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017988075.1	s__Ramlibacter sp017988075	77.4788	158	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828665.1	s__Rhodoferax sp903828665	77.4114	199	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.74	99.58	0.91	0.86	28	-
GCA_903945325.1	s__Rhodoferax sp903945325	77.3342	262	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.68	99.56	0.89	0.88	4	-
GCA_010365055.1	s__Rhodoferax sp010365055	77.3242	247	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853895.1	s__Rhodoferax sp903853895	77.1707	285	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.86	99.86	0.86	0.86	2	-
GCF_016428875.1	s__Xylophilus sp016428875	76.9901	184	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823505.1	s__Hydrogenophaga sp013823505	76.9681	157	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434305.1	s__Pulveribacter sp002434305	76.9271	177	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCA_002255935.1	s__Limnohabitans_A sp002255935	76.6285	157	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780385.1	s__Hydrogenophaga sp018780385	76.62	178	2009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:13:49,240] [INFO] GTDB search result was written to GCA_016708725.1_ASM1670872v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:13:49,241] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:13:49,246] [INFO] DFAST_QC result json was written to GCA_016708725.1_ASM1670872v1_genomic.fna/dqc_result.json
[2023-06-30 14:13:49,247] [INFO] DFAST_QC completed!
[2023-06-30 14:13:49,247] [INFO] Total running time: 0h2m8s