[2024-01-24 12:06:33,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,818] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcd4bde5-73ec-4dd0-bf0a-3aaf04e580f9/dqc_reference
[2024-01-24 12:06:35,197] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,198] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,198] [INFO] Running command: gunzip -c /var/lib/cwl/stgd12cf7c8-594a-4a7c-8ea3-2ba64d814b38/GCF_012910885.1_ASM1291088v1_genomic.fna.gz | prodigal -d GCF_012910885.1_ASM1291088v1_genomic.fna/cds.fna -a GCF_012910885.1_ASM1291088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:47,783] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:47,783] [INFO] Task started: HMMsearch
[2024-01-24 12:06:47,784] [INFO] Running command: hmmsearch --tblout GCF_012910885.1_ASM1291088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcd4bde5-73ec-4dd0-bf0a-3aaf04e580f9/dqc_reference/reference_markers.hmm GCF_012910885.1_ASM1291088v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:48,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:48,090] [INFO] Found 6/6 markers.
[2024-01-24 12:06:48,128] [INFO] Query marker FASTA was written to GCF_012910885.1_ASM1291088v1_genomic.fna/markers.fasta
[2024-01-24 12:06:48,128] [INFO] Task started: Blastn
[2024-01-24 12:06:48,128] [INFO] Running command: blastn -query GCF_012910885.1_ASM1291088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd4bde5-73ec-4dd0-bf0a-3aaf04e580f9/dqc_reference/reference_markers.fasta -out GCF_012910885.1_ASM1291088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:49,161] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:49,165] [INFO] Selected 26 target genomes.
[2024-01-24 12:06:49,165] [INFO] Target genome list was writen to GCF_012910885.1_ASM1291088v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:49,175] [INFO] Task started: fastANI
[2024-01-24 12:06:49,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgd12cf7c8-594a-4a7c-8ea3-2ba64d814b38/GCF_012910885.1_ASM1291088v1_genomic.fna.gz --refList GCF_012910885.1_ASM1291088v1_genomic.fna/target_genomes.txt --output GCF_012910885.1_ASM1291088v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:08,132] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:08,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcd4bde5-73ec-4dd0-bf0a-3aaf04e580f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:08,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcd4bde5-73ec-4dd0-bf0a-3aaf04e580f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:08,152] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:08,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:08,153] [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
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	80.0114	415	1258	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.994	416	1258	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.7806	420	1258	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	79.6462	368	1258	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	79.4989	397	1258	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	79.4782	383	1258	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	79.4477	393	1258	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	79.4196	375	1258	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	79.3239	395	1258	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	79.2663	419	1258	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	79.257	359	1258	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	79.1166	356	1258	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	79.0341	375	1258	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.9093	404	1258	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.7522	375	1258	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	78.734	366	1258	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	78.6907	369	1258	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	78.6766	343	1258	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.6149	330	1258	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	78.6065	331	1258	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.5185	304	1258	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.4737	310	1258	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.047	219	1258	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	77.9343	256	1258	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	77.4301	159	1258	95	below_threshold
Uliginosibacterium aquaticum	strain=IMCC34675	GCA_012972705.2	2731212	2731212	type	True	76.8318	159	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:08,155] [INFO] DFAST Taxonomy check result was written to GCF_012910885.1_ASM1291088v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:08,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:08,156] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:08,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcd4bde5-73ec-4dd0-bf0a-3aaf04e580f9/dqc_reference/checkm_data
[2024-01-24 12:07:08,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:08,199] [INFO] Task started: CheckM
[2024-01-24 12:07:08,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012910885.1_ASM1291088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012910885.1_ASM1291088v1_genomic.fna/checkm_input GCF_012910885.1_ASM1291088v1_genomic.fna/checkm_result
[2024-01-24 12:07:48,162] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:48,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:48,190] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:48,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:48,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012910885.1_ASM1291088v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:48,191] [INFO] Task started: Blastn
[2024-01-24 12:07:48,191] [INFO] Running command: blastn -query GCF_012910885.1_ASM1291088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd4bde5-73ec-4dd0-bf0a-3aaf04e580f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_012910885.1_ASM1291088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:50,122] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:50,126] [INFO] Selected 24 target genomes.
[2024-01-24 12:07:50,126] [INFO] Target genome list was writen to GCF_012910885.1_ASM1291088v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:50,155] [INFO] Task started: fastANI
[2024-01-24 12:07:50,155] [INFO] Running command: fastANI --query /var/lib/cwl/stgd12cf7c8-594a-4a7c-8ea3-2ba64d814b38/GCF_012910885.1_ASM1291088v1_genomic.fna.gz --refList GCF_012910885.1_ASM1291088v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012910885.1_ASM1291088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:09,760] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:09,782] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:09,783] [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_012910885.1	s__Azoarcus_F taiwanensis	100.0	1247	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000310225.1	s__Thauera phenylacetica	80.0024	415	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	79.9623	418	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCF_001591165.1	s__Thauera butanivorans	79.7648	420	1258	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	79.7478	439	1258	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_018240785.1	s__Thauera sp018240785	79.7409	422	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006496635.1	s__Azoarcus sp006496635	79.6585	418	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696715.1	s__Thauera phenolivorans	79.631	372	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCF_003034845.1	s__Thauera_A sp003034845	79.4619	403	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	79.4252	412	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801295.1	s__Thauera_A nasutitermitis	79.2614	419	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628555.1	s__Aromatoleum sp003628555	79.1341	383	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310205.1	s__Thauera linaloolentis	79.0781	360	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003446655.1	s__Thauera sp003446655	79.0636	302	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_002872475.1	s__Azoarcus_D pumilus	78.9383	339	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	78.9183	403	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910805.1	s__Aromatoleum evansii	78.8982	378	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190925.1	s__Aromatoleum sp001190925	78.8278	393	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910905.1	s__Aromatoleum toluvorans	78.746	375	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017894385.1	s__Aromatoleum petrolei	78.686	370	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000025965.1	s__Aromatoleum aromaticum	78.6823	342	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	98.48	98.48	0.91	0.91	2	-
GCA_013911595.1	s__Azoarcus_D sp013911595	78.5843	258	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111645.1	s__Azoarcus_C communis_A	78.4024	333	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_C	95.0	97.65	97.63	0.87	0.87	3	-
GCF_001274695.1	s__Aromatoleum sp001274695	78.3828	326	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:09,785] [INFO] GTDB search result was written to GCF_012910885.1_ASM1291088v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:09,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:09,790] [INFO] DFAST_QC result json was written to GCF_012910885.1_ASM1291088v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:09,790] [INFO] DFAST_QC completed!
[2024-01-24 12:08:09,790] [INFO] Total running time: 0h1m36s