[2024-01-25 18:15:35,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg46a42ba7-c0ea-4d47-8d41-37e646ec5e3a/dqc_reference
[2024-01-25 18:15:36,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,691] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,691] [INFO] Running command: gunzip -c /var/lib/cwl/stga9db4a32-6495-429d-bc00-5ea42b0ae325/GCF_009800965.1_ASM980096v1_genomic.fna.gz | prodigal -d GCF_009800965.1_ASM980096v1_genomic.fna/cds.fna -a GCF_009800965.1_ASM980096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:54,136] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:54,137] [INFO] Task started: HMMsearch
[2024-01-25 18:15:54,137] [INFO] Running command: hmmsearch --tblout GCF_009800965.1_ASM980096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46a42ba7-c0ea-4d47-8d41-37e646ec5e3a/dqc_reference/reference_markers.hmm GCF_009800965.1_ASM980096v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:54,465] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:54,466] [INFO] Found 6/6 markers.
[2024-01-25 18:15:54,517] [INFO] Query marker FASTA was written to GCF_009800965.1_ASM980096v1_genomic.fna/markers.fasta
[2024-01-25 18:15:54,518] [INFO] Task started: Blastn
[2024-01-25 18:15:54,518] [INFO] Running command: blastn -query GCF_009800965.1_ASM980096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a42ba7-c0ea-4d47-8d41-37e646ec5e3a/dqc_reference/reference_markers.fasta -out GCF_009800965.1_ASM980096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:55,367] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:55,374] [INFO] Selected 24 target genomes.
[2024-01-25 18:15:55,374] [INFO] Target genome list was writen to GCF_009800965.1_ASM980096v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:55,402] [INFO] Task started: fastANI
[2024-01-25 18:15:55,402] [INFO] Running command: fastANI --query /var/lib/cwl/stga9db4a32-6495-429d-bc00-5ea42b0ae325/GCF_009800965.1_ASM980096v1_genomic.fna.gz --refList GCF_009800965.1_ASM980096v1_genomic.fna/target_genomes.txt --output GCF_009800965.1_ASM980096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:17,023] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:17,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46a42ba7-c0ea-4d47-8d41-37e646ec5e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:17,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46a42ba7-c0ea-4d47-8d41-37e646ec5e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:17,038] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:17,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:17,038] [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
Cognatazoarcus halotolerans	strain=HKLI-1	GCA_009800965.1	2686016	2686016	type	True	100.0	1620	1625	95	conclusive
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.836	463	1625	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.5404	431	1625	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	79.1808	406	1625	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	79.1171	402	1625	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	78.9246	365	1625	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.8719	437	1625	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.8672	370	1625	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	78.8539	408	1625	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	78.7078	384	1625	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.689	471	1625	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	78.6855	423	1625	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.6823	379	1625	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.6766	389	1625	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.6656	449	1625	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	78.6228	363	1625	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	78.5401	380	1625	95	below_threshold
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	78.5017	374	1625	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.2334	345	1625	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.2224	367	1625	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.9853	349	1625	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.4788	150	1625	95	below_threshold
Paraburkholderia oxyphila	strain=NBRC 105797	GCA_000685075.1	614212	614212	type	True	76.3687	185	1625	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	75.9994	181	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:17,040] [INFO] DFAST Taxonomy check result was written to GCF_009800965.1_ASM980096v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:17,040] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:17,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:17,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46a42ba7-c0ea-4d47-8d41-37e646ec5e3a/dqc_reference/checkm_data
[2024-01-25 18:16:17,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:17,089] [INFO] Task started: CheckM
[2024-01-25 18:16:17,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009800965.1_ASM980096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009800965.1_ASM980096v1_genomic.fna/checkm_input GCF_009800965.1_ASM980096v1_genomic.fna/checkm_result
[2024-01-25 18:17:11,404] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:11,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:11,427] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:11,428] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:11,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009800965.1_ASM980096v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:11,429] [INFO] Task started: Blastn
[2024-01-25 18:17:11,429] [INFO] Running command: blastn -query GCF_009800965.1_ASM980096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a42ba7-c0ea-4d47-8d41-37e646ec5e3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009800965.1_ASM980096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:12,895] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:12,898] [INFO] Selected 27 target genomes.
[2024-01-25 18:17:12,898] [INFO] Target genome list was writen to GCF_009800965.1_ASM980096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:12,924] [INFO] Task started: fastANI
[2024-01-25 18:17:12,925] [INFO] Running command: fastANI --query /var/lib/cwl/stga9db4a32-6495-429d-bc00-5ea42b0ae325/GCF_009800965.1_ASM980096v1_genomic.fna.gz --refList GCF_009800965.1_ASM980096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009800965.1_ASM980096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:35,898] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:35,914] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:35,914] [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_009800965.1	s__Azoarcus_E halotolerans	100.0	1620	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_E	95.0	97.94	97.94	0.86	0.86	2	conclusive
GCF_001591165.1	s__Thauera butanivorans	79.8226	464	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489115.1	s__Thauera_A sp014489115	79.3368	445	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_008501585.1	s__Denitromonas sp008501585	79.1669	495	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001051995.2	s__Thauera humireducens	79.0996	403	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCA_003963015.1	s__Thauera sp003963015	79.0962	435	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997795.1	s__Thauera sp017997795	79.0616	282	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	79.0023	440	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	78.9503	312	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCA_017302295.1	s__Thauera sp017302295	78.9491	413	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310145.2	s__Thauera sp000310145	78.8737	397	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.71	98.54	0.88	0.86	4	-
GCF_001922305.1	s__Thauera chlorobenzoica	78.8703	371	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCA_002422685.1	s__Thauera sp002422685	78.8168	355	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240585.1	s__Thauera sp018240585	78.6985	363	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030465.1	s__Thauera aromatica	78.6967	385	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927165.1	s__Zoogloea sp012927165	78.6661	425	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310205.1	s__Thauera linaloolentis	78.6658	381	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900156155.1	s__Aromatoleum tolulyticum	78.6561	450	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017894365.1	s__Aromatoleum bremense	78.5092	383	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	99.97	99.97	1.00	1.00	2	-
GCF_008107625.1	s__Zoogloea oleivorans	78.4908	375	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002028455.1	s__Zoogloea sp002028455	78.4699	424	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910705.1	s__Aromatoleum anaerobium	78.2677	358	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790365.1	s__Thauera sp016790365	78.1625	273	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274695.1	s__Aromatoleum sp001274695	77.9949	342	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685075.1	s__Paraburkholderia oxyphila	76.3587	186	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	95.32	95.32	0.74	0.74	2	-
GCF_000785435.2	s__Paraburkholderia sacchari	76.1056	161	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.05	96.11	0.93	0.86	3	-
GCF_004353915.1	s__Paraburkholderia sp004353915	76.0032	179	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:35,915] [INFO] GTDB search result was written to GCF_009800965.1_ASM980096v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:35,916] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:35,921] [INFO] DFAST_QC result json was written to GCF_009800965.1_ASM980096v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:35,921] [INFO] DFAST_QC completed!
[2024-01-25 18:17:35,921] [INFO] Total running time: 0h2m0s