[2023-06-16 19:11:43,936] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:11:43,940] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:11:43,940] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf141755-3f45-4be2-b40e-a1c40da0f2c7/dqc_reference
[2023-06-16 19:11:45,172] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:11:45,173] [INFO] Task started: Prodigal
[2023-06-16 19:11:45,173] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5b8dc7e-4f60-406f-a35c-008eb9e5154b/GCA_003152855.1_20120700_E3M_genomic.fna.gz | prodigal -d GCA_003152855.1_20120700_E3M_genomic.fna/cds.fna -a GCA_003152855.1_20120700_E3M_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:11:53,474] [INFO] Task succeeded: Prodigal
[2023-06-16 19:11:53,475] [INFO] Task started: HMMsearch
[2023-06-16 19:11:53,475] [INFO] Running command: hmmsearch --tblout GCA_003152855.1_20120700_E3M_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf141755-3f45-4be2-b40e-a1c40da0f2c7/dqc_reference/reference_markers.hmm GCA_003152855.1_20120700_E3M_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:11:53,665] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:11:53,666] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb5b8dc7e-4f60-406f-a35c-008eb9e5154b/GCA_003152855.1_20120700_E3M_genomic.fna.gz]
[2023-06-16 19:11:53,697] [INFO] Query marker FASTA was written to GCA_003152855.1_20120700_E3M_genomic.fna/markers.fasta
[2023-06-16 19:11:53,697] [INFO] Task started: Blastn
[2023-06-16 19:11:53,697] [INFO] Running command: blastn -query GCA_003152855.1_20120700_E3M_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf141755-3f45-4be2-b40e-a1c40da0f2c7/dqc_reference/reference_markers.fasta -out GCA_003152855.1_20120700_E3M_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:54,239] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:54,243] [INFO] Selected 15 target genomes.
[2023-06-16 19:11:54,243] [INFO] Target genome list was writen to GCA_003152855.1_20120700_E3M_genomic.fna/target_genomes.txt
[2023-06-16 19:11:54,248] [INFO] Task started: fastANI
[2023-06-16 19:11:54,248] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b8dc7e-4f60-406f-a35c-008eb9e5154b/GCA_003152855.1_20120700_E3M_genomic.fna.gz --refList GCA_003152855.1_20120700_E3M_genomic.fna/target_genomes.txt --output GCA_003152855.1_20120700_E3M_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:12:03,948] [INFO] Task succeeded: fastANI
[2023-06-16 19:12:03,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf141755-3f45-4be2-b40e-a1c40da0f2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:12:03,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf141755-3f45-4be2-b40e-a1c40da0f2c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:12:03,962] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:12:03,962] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:12:03,962] [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
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.7858	197	852	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.7812	198	852	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	76.6893	108	852	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	76.6046	103	852	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	76.5808	96	852	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	76.553	149	852	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	76.3316	110	852	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.2694	111	852	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.2642	104	852	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	76.0607	113	852	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	76.047	91	852	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	75.5528	70	852	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	75.4504	74	852	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	75.3152	65	852	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:12:03,964] [INFO] DFAST Taxonomy check result was written to GCA_003152855.1_20120700_E3M_genomic.fna/tc_result.tsv
[2023-06-16 19:12:03,965] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:12:03,965] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:12:03,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf141755-3f45-4be2-b40e-a1c40da0f2c7/dqc_reference/checkm_data
[2023-06-16 19:12:03,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:12:04,001] [INFO] Task started: CheckM
[2023-06-16 19:12:04,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003152855.1_20120700_E3M_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003152855.1_20120700_E3M_genomic.fna/checkm_input GCA_003152855.1_20120700_E3M_genomic.fna/checkm_result
[2023-06-16 19:12:32,300] [INFO] Task succeeded: CheckM
[2023-06-16 19:12:32,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:12:32,322] [INFO] ===== Completeness check finished =====
[2023-06-16 19:12:32,322] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:12:32,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003152855.1_20120700_E3M_genomic.fna/markers.fasta)
[2023-06-16 19:12:32,323] [INFO] Task started: Blastn
[2023-06-16 19:12:32,323] [INFO] Running command: blastn -query GCA_003152855.1_20120700_E3M_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf141755-3f45-4be2-b40e-a1c40da0f2c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_003152855.1_20120700_E3M_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:12:32,936] [INFO] Task succeeded: Blastn
[2023-06-16 19:12:32,939] [INFO] Selected 13 target genomes.
[2023-06-16 19:12:32,939] [INFO] Target genome list was writen to GCA_003152855.1_20120700_E3M_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:12:32,954] [INFO] Task started: fastANI
[2023-06-16 19:12:32,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b8dc7e-4f60-406f-a35c-008eb9e5154b/GCA_003152855.1_20120700_E3M_genomic.fna.gz --refList GCA_003152855.1_20120700_E3M_genomic.fna/target_genomes_gtdb.txt --output GCA_003152855.1_20120700_E3M_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:12:41,018] [INFO] Task succeeded: fastANI
[2023-06-16 19:12:41,031] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:12:41,031] [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_003157035.1	s__Fen-999 sp003157035	99.1767	740	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	99.18	99.18	0.87	0.87	2	conclusive
GCA_003158255.1	s__Fen-999 sp003158255	79.9284	266	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235765.1	s__Fen-999 sp016235765	79.0335	246	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819515.1	s__Fen-999 sp018819515	78.7222	233	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016880655.1	s__Fen-999 sp016880655	78.3911	195	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136545.1	s__Fen-999 sp019136545	78.2372	206	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704145.1	s__Fen-999 sp016704145	77.9156	217	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	99.37	98.34	0.95	0.91	6	-
GCF_003865015.1	s__Sulfurisoma sediminicola	77.7812	198	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002347285.1	s__UBA2250 sp002347285	77.7049	180	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214175.1	s__JACRPB01 sp016214175	77.345	202	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRPB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791145.1	s__JAEUNJ01 sp016791145	77.2547	131	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAEUNJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017347485.1	s__Desulfobacillus denitrificans	77.0387	162	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.90	98.32	0.92	0.90	5	-
GCF_000519045.1	s__Azonexus agitatus	76.532	105	852	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-16 19:12:41,034] [INFO] GTDB search result was written to GCA_003152855.1_20120700_E3M_genomic.fna/result_gtdb.tsv
[2023-06-16 19:12:41,034] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:12:41,038] [INFO] DFAST_QC result json was written to GCA_003152855.1_20120700_E3M_genomic.fna/dqc_result.json
[2023-06-16 19:12:41,038] [INFO] DFAST_QC completed!
[2023-06-16 19:12:41,038] [INFO] Total running time: 0h0m57s