[2024-01-24 15:35:23,518] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:35:23,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:35:23,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7cf5371-dd36-4e36-a56f-208a68e14fec/dqc_reference
[2024-01-24 15:35:26,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:35:26,929] [INFO] Task started: Prodigal
[2024-01-24 15:35:26,931] [INFO] Running command: gunzip -c /var/lib/cwl/stgff54ed39-fcc3-4d6e-9287-52e5752671ea/GCF_012972705.2_ASM1297270v2_genomic.fna.gz | prodigal -d GCF_012972705.2_ASM1297270v2_genomic.fna/cds.fna -a GCF_012972705.2_ASM1297270v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:35:40,575] [INFO] Task succeeded: Prodigal
[2024-01-24 15:35:40,576] [INFO] Task started: HMMsearch
[2024-01-24 15:35:40,576] [INFO] Running command: hmmsearch --tblout GCF_012972705.2_ASM1297270v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7cf5371-dd36-4e36-a56f-208a68e14fec/dqc_reference/reference_markers.hmm GCF_012972705.2_ASM1297270v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:35:40,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:35:40,924] [INFO] Found 6/6 markers.
[2024-01-24 15:35:40,980] [INFO] Query marker FASTA was written to GCF_012972705.2_ASM1297270v2_genomic.fna/markers.fasta
[2024-01-24 15:35:40,980] [INFO] Task started: Blastn
[2024-01-24 15:35:40,981] [INFO] Running command: blastn -query GCF_012972705.2_ASM1297270v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7cf5371-dd36-4e36-a56f-208a68e14fec/dqc_reference/reference_markers.fasta -out GCF_012972705.2_ASM1297270v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:35:41,949] [INFO] Task succeeded: Blastn
[2024-01-24 15:35:41,952] [INFO] Selected 23 target genomes.
[2024-01-24 15:35:41,953] [INFO] Target genome list was writen to GCF_012972705.2_ASM1297270v2_genomic.fna/target_genomes.txt
[2024-01-24 15:35:41,998] [INFO] Task started: fastANI
[2024-01-24 15:35:41,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgff54ed39-fcc3-4d6e-9287-52e5752671ea/GCF_012972705.2_ASM1297270v2_genomic.fna.gz --refList GCF_012972705.2_ASM1297270v2_genomic.fna/target_genomes.txt --output GCF_012972705.2_ASM1297270v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:36:03,078] [INFO] Task succeeded: fastANI
[2024-01-24 15:36:03,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7cf5371-dd36-4e36-a56f-208a68e14fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:36:03,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7cf5371-dd36-4e36-a56f-208a68e14fec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:36:03,098] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:36:03,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:36:03,098] [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
Uliginosibacterium aquaticum	strain=IMCC34675	GCA_012972705.2	2731212	2731212	type	True	100.0	1358	1358	95	conclusive
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.0052	253	1358	95	below_threshold
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	77.991	267	1358	95	below_threshold
Niveibacterium microcysteis	strain=HC41	GCA_017161445.1	2811415	2811415	type	True	77.9111	305	1358	95	below_threshold
Uliginosibacterium gangwonense	strain=DSM 18521	GCA_000373965.1	392736	392736	type	True	77.8799	321	1358	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	77.748	258	1358	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	77.7425	255	1358	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	77.6506	319	1358	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	77.6495	313	1358	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.6411	231	1358	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.6249	311	1358	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.6224	234	1358	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	77.6018	240	1358	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	77.5737	291	1358	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	77.4688	262	1358	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_012910815.1	41977	41977	type	True	77.4201	205	1358	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	77.286	157	1358	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	76.8718	155	1358	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.8585	190	1358	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	76.6093	175	1358	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	76.0995	151	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:36:03,101] [INFO] DFAST Taxonomy check result was written to GCF_012972705.2_ASM1297270v2_genomic.fna/tc_result.tsv
[2024-01-24 15:36:03,102] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:36:03,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:36:03,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7cf5371-dd36-4e36-a56f-208a68e14fec/dqc_reference/checkm_data
[2024-01-24 15:36:03,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:36:03,144] [INFO] Task started: CheckM
[2024-01-24 15:36:03,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012972705.2_ASM1297270v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012972705.2_ASM1297270v2_genomic.fna/checkm_input GCF_012972705.2_ASM1297270v2_genomic.fna/checkm_result
[2024-01-24 15:36:44,843] [INFO] Task succeeded: CheckM
[2024-01-24 15:36:44,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:36:44,870] [INFO] ===== Completeness check finished =====
[2024-01-24 15:36:44,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:36:44,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012972705.2_ASM1297270v2_genomic.fna/markers.fasta)
[2024-01-24 15:36:44,871] [INFO] Task started: Blastn
[2024-01-24 15:36:44,871] [INFO] Running command: blastn -query GCF_012972705.2_ASM1297270v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7cf5371-dd36-4e36-a56f-208a68e14fec/dqc_reference/reference_markers_gtdb.fasta -out GCF_012972705.2_ASM1297270v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:36:46,403] [INFO] Task succeeded: Blastn
[2024-01-24 15:36:46,406] [INFO] Selected 18 target genomes.
[2024-01-24 15:36:46,406] [INFO] Target genome list was writen to GCF_012972705.2_ASM1297270v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:36:46,781] [INFO] Task started: fastANI
[2024-01-24 15:36:46,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgff54ed39-fcc3-4d6e-9287-52e5752671ea/GCF_012972705.2_ASM1297270v2_genomic.fna.gz --refList GCF_012972705.2_ASM1297270v2_genomic.fna/target_genomes_gtdb.txt --output GCF_012972705.2_ASM1297270v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:37:03,661] [INFO] Task succeeded: fastANI
[2024-01-24 15:37:03,694] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:37:03,695] [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_002855595.1	s__Dactylopiibacterium sp002855595	95.4828	1244	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Dactylopiibacterium	95.0	95.50	95.50	0.92	0.92	2	conclusive
GCA_018262235.1	s__Dactylopiibacterium sp018262235	79.7859	516	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Dactylopiibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014736495.1	s__Dactylopiibacterium carminicum	79.2523	474	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Dactylopiibacterium	95.0	99.96	99.89	0.99	0.97	4	-
GCA_016718265.1	s__Uliginosibacterium sp016718265	79.0435	382	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Uliginosibacterium	95.0	98.20	98.02	0.86	0.86	3	-
GCA_002307175.1	s__Dactylopiibacterium sp002307175	78.0087	377	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Dactylopiibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	78.0052	253	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107625.1	s__Zoogloea oleivorans	77.9749	266	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373965.1	s__Uliginosibacterium gangwonense	77.8905	320	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Uliginosibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006496635.1	s__Azoarcus sp006496635	77.7675	314	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527135.1	s__Methyloversatilis discipulorum	77.7563	254	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	97.77	95.54	0.94	0.88	3	-
GCF_012911025.1	s__Azoarcus sp012911025	77.6949	290	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026175.1	s__Zoogloea sp009026175	77.5695	288	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295105.1	s__Thauera sp004295105	77.5368	231	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789125.1	s__Zoogloea sp016789125	77.4223	221	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105015.1	s__Desulfobacillus sp003105015	77.2213	211	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.07	97.07	0.88	0.88	2	-
GCA_011526165.1	s__Desulfobacillus sp011526165	76.9267	183	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.84	98.84	0.79	0.79	2	-
GCF_001274695.1	s__Aromatoleum sp001274695	76.9201	179	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_907163075.1	s__Propionivibrio sp907163075	76.597	157	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:37:03,699] [INFO] GTDB search result was written to GCF_012972705.2_ASM1297270v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:37:03,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:37:03,714] [INFO] DFAST_QC result json was written to GCF_012972705.2_ASM1297270v2_genomic.fna/dqc_result.json
[2024-01-24 15:37:03,714] [INFO] DFAST_QC completed!
[2024-01-24 15:37:03,714] [INFO] Total running time: 0h1m40s