[2023-06-30 17:16:39,087] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:16:39,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:16:39,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg875133ae-b889-493d-821e-db36d91df5ce/dqc_reference
[2023-06-30 17:16:40,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:16:40,333] [INFO] Task started: Prodigal
[2023-06-30 17:16:40,333] [INFO] Running command: gunzip -c /var/lib/cwl/stgd982b56b-12b9-4d68-9dbc-62b5d40e99d2/GCA_016708665.1_ASM1670866v1_genomic.fna.gz | prodigal -d GCA_016708665.1_ASM1670866v1_genomic.fna/cds.fna -a GCA_016708665.1_ASM1670866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:16:54,185] [INFO] Task succeeded: Prodigal
[2023-06-30 17:16:54,186] [INFO] Task started: HMMsearch
[2023-06-30 17:16:54,186] [INFO] Running command: hmmsearch --tblout GCA_016708665.1_ASM1670866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg875133ae-b889-493d-821e-db36d91df5ce/dqc_reference/reference_markers.hmm GCA_016708665.1_ASM1670866v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:16:54,417] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:16:54,418] [INFO] Found 6/6 markers.
[2023-06-30 17:16:54,452] [INFO] Query marker FASTA was written to GCA_016708665.1_ASM1670866v1_genomic.fna/markers.fasta
[2023-06-30 17:16:54,453] [INFO] Task started: Blastn
[2023-06-30 17:16:54,453] [INFO] Running command: blastn -query GCA_016708665.1_ASM1670866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875133ae-b889-493d-821e-db36d91df5ce/dqc_reference/reference_markers.fasta -out GCA_016708665.1_ASM1670866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:16:55,289] [INFO] Task succeeded: Blastn
[2023-06-30 17:16:55,294] [INFO] Selected 26 target genomes.
[2023-06-30 17:16:55,294] [INFO] Target genome list was writen to GCA_016708665.1_ASM1670866v1_genomic.fna/target_genomes.txt
[2023-06-30 17:16:55,296] [INFO] Task started: fastANI
[2023-06-30 17:16:55,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgd982b56b-12b9-4d68-9dbc-62b5d40e99d2/GCA_016708665.1_ASM1670866v1_genomic.fna.gz --refList GCA_016708665.1_ASM1670866v1_genomic.fna/target_genomes.txt --output GCA_016708665.1_ASM1670866v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:17:15,038] [INFO] Task succeeded: fastANI
[2023-06-30 17:17:15,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg875133ae-b889-493d-821e-db36d91df5ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:17:15,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg875133ae-b889-493d-821e-db36d91df5ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:17:15,058] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:17:15,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:17:15,058] [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=BSN1	GCA_003865015.1	1381557	1381557	type	True	80.71	531	1450	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	80.6586	529	1450	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	78.8677	387	1450	95	below_threshold
Sterolibacterium denitrificans	strain=DSM 13999	GCA_001586935.1	157592	157592	type	True	78.8639	117	1450	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	78.8439	352	1450	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.8317	411	1450	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.7885	377	1450	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	78.7724	386	1450	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.7623	383	1450	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	78.5966	354	1450	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.5785	400	1450	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	78.4975	316	1450	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.1578	402	1450	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.0839	396	1450	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	77.9281	327	1450	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	77.9176	378	1450	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.8477	313	1450	95	below_threshold
Niveibacterium umoris	strain=DSM 106739	GCA_014197015.1	1193620	1193620	type	True	77.5881	259	1450	95	below_threshold
Niveibacterium umoris	strain=KACC 17062	GCA_017311475.1	1193620	1193620	type	True	77.4542	262	1450	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	77.2921	333	1450	95	below_threshold
Cupriavidus oxalaticus	strain=NBRC 13593	GCA_001592245.1	96344	96344	type	True	77.1226	324	1450	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.0149	224	1450	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7389	309	1450	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	76.55	250	1450	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	76.4166	263	1450	95	below_threshold
Caballeronia concitans		GCA_001544615.2	1777133	1777133	type	True	75.9559	153	1450	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:17:15,061] [INFO] DFAST Taxonomy check result was written to GCA_016708665.1_ASM1670866v1_genomic.fna/tc_result.tsv
[2023-06-30 17:17:15,061] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:17:15,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:17:15,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg875133ae-b889-493d-821e-db36d91df5ce/dqc_reference/checkm_data
[2023-06-30 17:17:15,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:17:15,103] [INFO] Task started: CheckM
[2023-06-30 17:17:15,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708665.1_ASM1670866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708665.1_ASM1670866v1_genomic.fna/checkm_input GCA_016708665.1_ASM1670866v1_genomic.fna/checkm_result
[2023-06-30 17:17:59,715] [INFO] Task succeeded: CheckM
[2023-06-30 17:17:59,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:17:59,734] [INFO] ===== Completeness check finished =====
[2023-06-30 17:17:59,734] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:17:59,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708665.1_ASM1670866v1_genomic.fna/markers.fasta)
[2023-06-30 17:17:59,735] [INFO] Task started: Blastn
[2023-06-30 17:17:59,735] [INFO] Running command: blastn -query GCA_016708665.1_ASM1670866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg875133ae-b889-493d-821e-db36d91df5ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708665.1_ASM1670866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:18:01,205] [INFO] Task succeeded: Blastn
[2023-06-30 17:18:01,209] [INFO] Selected 22 target genomes.
[2023-06-30 17:18:01,209] [INFO] Target genome list was writen to GCA_016708665.1_ASM1670866v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:18:01,221] [INFO] Task started: fastANI
[2023-06-30 17:18:01,221] [INFO] Running command: fastANI --query /var/lib/cwl/stgd982b56b-12b9-4d68-9dbc-62b5d40e99d2/GCA_016708665.1_ASM1670866v1_genomic.fna.gz --refList GCA_016708665.1_ASM1670866v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708665.1_ASM1670866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:18:21,223] [INFO] Task succeeded: fastANI
[2023-06-30 17:18:21,241] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:18:21,241] [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_016710465.1	s__Sulfuritalea sp016710465	97.3719	1211	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	97.35	97.30	0.83	0.82	3	conclusive
GCA_017302275.1	s__Sulfuritalea sp017302275	85.9406	904	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215645.1	s__Sulfuritalea sp016215645	85.4879	802	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235165.1	s__Sulfuritalea sp016235165	85.1737	945	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959855.1	s__Sulfuritalea sp903959855	85.0768	847	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.57	99.34	0.90	0.90	4	-
GCA_016708585.1	s__Sulfuritalea sp016708585	84.6555	768	1450	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	84.5042	873	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.89	99.84	0.95	0.93	5	-
GCA_016716965.1	s__Sulfuritalea sp016716965	84.3838	849	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828635.1	s__Sulfuritalea hydrogenivorans	83.3123	793	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192435.1	s__Sulfuritalea sp016192435	83.1036	680	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026675.1	s__Sulfuritalea sp012026675	82.3592	598	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828935.1	s__Sulfuritalea sp001828935	81.9832	713	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903932755.1	s__Sulfuritalea sp903932755	81.8058	375	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	98.78	98.78	0.75	0.75	2	-
GCA_003105015.1	s__Desulfobacillus sp003105015	79.8121	535	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.07	97.07	0.88	0.88	2	-
GCA_008933825.1	s__Desulfobacillus sp008933825	79.6888	440	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	99.14	98.51	0.86	0.84	3	-
GCA_013821865.1	s__PNJM01 sp013821865	79.4869	317	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__PNJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262775.1	s__Desulfobacillus sp018262775	78.8231	405	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	78.6443	327	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197015.1	s__Niveibacterium umoris	77.5413	262	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Niveibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905339295.1	s__VBCG01 sp905339295	76.6929	236	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830455.1	s__Pseudoduganella lurida	76.508	256	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001184395.1	s__Caballeronia calva	75.9672	118	1450	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:18:21,243] [INFO] GTDB search result was written to GCA_016708665.1_ASM1670866v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:18:21,243] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:18:21,248] [INFO] DFAST_QC result json was written to GCA_016708665.1_ASM1670866v1_genomic.fna/dqc_result.json
[2023-06-30 17:18:21,248] [INFO] DFAST_QC completed!
[2023-06-30 17:18:21,249] [INFO] Total running time: 0h1m42s