[2024-01-24 11:51:06,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg870fae6c-a6c9-40f4-8624-0ded1cf706ca/dqc_reference
[2024-01-24 11:51:08,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,230] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg74207196-d7a1-4648-85b6-3b926a50b94d/GCF_003663955.1_ASM366395v1_genomic.fna.gz | prodigal -d GCF_003663955.1_ASM366395v1_genomic.fna/cds.fna -a GCF_003663955.1_ASM366395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:17,198] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:17,199] [INFO] Task started: HMMsearch
[2024-01-24 11:51:17,199] [INFO] Running command: hmmsearch --tblout GCF_003663955.1_ASM366395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg870fae6c-a6c9-40f4-8624-0ded1cf706ca/dqc_reference/reference_markers.hmm GCF_003663955.1_ASM366395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:17,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:17,499] [INFO] Found 6/6 markers.
[2024-01-24 11:51:17,530] [INFO] Query marker FASTA was written to GCF_003663955.1_ASM366395v1_genomic.fna/markers.fasta
[2024-01-24 11:51:17,530] [INFO] Task started: Blastn
[2024-01-24 11:51:17,530] [INFO] Running command: blastn -query GCF_003663955.1_ASM366395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg870fae6c-a6c9-40f4-8624-0ded1cf706ca/dqc_reference/reference_markers.fasta -out GCF_003663955.1_ASM366395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:18,626] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:18,630] [INFO] Selected 20 target genomes.
[2024-01-24 11:51:18,630] [INFO] Target genome list was writen to GCF_003663955.1_ASM366395v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:18,689] [INFO] Task started: fastANI
[2024-01-24 11:51:18,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg74207196-d7a1-4648-85b6-3b926a50b94d/GCF_003663955.1_ASM366395v1_genomic.fna.gz --refList GCF_003663955.1_ASM366395v1_genomic.fna/target_genomes.txt --output GCF_003663955.1_ASM366395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:33,140] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:33,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg870fae6c-a6c9-40f4-8624-0ded1cf706ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:33,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg870fae6c-a6c9-40f4-8624-0ded1cf706ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:33,162] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:33,163] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:33,163] [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	100.0	994	994	95	conclusive
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	99.9876	988	994	95	conclusive
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.7663	393	994	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	79.5184	391	994	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	79.2549	367	994	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	79.2463	378	994	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	79.0985	414	994	95	below_threshold
Sterolibacterium denitrificans	strain=DSM 13999	GCA_001586935.1	157592	157592	type	True	79.0185	112	994	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.9752	373	994	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	78.7087	310	994	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.6515	380	994	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	78.5966	335	994	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	78.5684	352	994	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	78.5645	334	994	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.4759	337	994	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	78.1108	302	994	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.1047	334	994	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.0716	297	994	95	below_threshold
Niveibacterium microcysteis	strain=HC41	GCA_017161445.1	2811415	2811415	type	True	78.0361	264	994	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.3268	216	994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:33,165] [INFO] DFAST Taxonomy check result was written to GCF_003663955.1_ASM366395v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:33,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:33,166] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:33,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg870fae6c-a6c9-40f4-8624-0ded1cf706ca/dqc_reference/checkm_data
[2024-01-24 11:51:33,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:33,198] [INFO] Task started: CheckM
[2024-01-24 11:51:33,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003663955.1_ASM366395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003663955.1_ASM366395v1_genomic.fna/checkm_input GCF_003663955.1_ASM366395v1_genomic.fna/checkm_result
[2024-01-24 11:52:04,710] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:04,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:04,734] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:04,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:04,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003663955.1_ASM366395v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:04,735] [INFO] Task started: Blastn
[2024-01-24 11:52:04,735] [INFO] Running command: blastn -query GCF_003663955.1_ASM366395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg870fae6c-a6c9-40f4-8624-0ded1cf706ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_003663955.1_ASM366395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:06,912] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:06,920] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:06,920] [INFO] Target genome list was writen to GCF_003663955.1_ASM366395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:06,935] [INFO] Task started: fastANI
[2024-01-24 11:52:06,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg74207196-d7a1-4648-85b6-3b926a50b94d/GCF_003663955.1_ASM366395v1_genomic.fna.gz --refList GCF_003663955.1_ASM366395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003663955.1_ASM366395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:19,079] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:19,097] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:19,097] [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_003865015.1	s__Sulfurisoma sediminicola	99.9876	988	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_018825305.1	s__Sulfurisoma sp018825305	84.8263	666	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	100.00	99.99	1.00	1.00	3	-
GCA_002347285.1	s__UBA2250 sp002347285	82.098	503	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235765.1	s__Fen-999 sp016235765	81.0441	454	994	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_018333815.1	s__UBA2250 sp018333815	81.0294	332	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016880655.1	s__Fen-999 sp016880655	80.7051	388	994	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	80.6643	461	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Fen-999	95.0	99.37	98.34	0.95	0.91	6	-
GCA_017302275.1	s__Sulfuritalea sp017302275	80.3668	517	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908065.1	s__Sulfuritalea sp903908065	80.291	473	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.89	99.84	0.95	0.93	5	-
GCA_016214175.1	s__JACRPB01 sp016214175	80.1848	413	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRPB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330945.1	s__UBA2250 sp011330945	80.1464	485	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	99.90	99.90	0.95	0.95	2	-
GCA_013821865.1	s__PNJM01 sp013821865	80.025	294	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__PNJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833355.1	s__Denitratisoma sp007833355	80.0201	402	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013426785.1	s__UBA2250 sp013426785	80.0077	400	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235805.1	s__Sulfuritalea sp016235805	79.9101	445	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819515.1	s__Fen-999 sp018819515	79.79	429	994	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_012026675.1	s__Sulfuritalea sp012026675	79.7108	394	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:19,099] [INFO] GTDB search result was written to GCF_003663955.1_ASM366395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:19,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:19,104] [INFO] DFAST_QC result json was written to GCF_003663955.1_ASM366395v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:19,105] [INFO] DFAST_QC completed!
[2024-01-24 11:52:19,105] [INFO] Total running time: 0h1m12s