[2024-01-24 12:13:06,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:06,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:06,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg526ef157-c900-422a-ad08-36995caf5af9/dqc_reference
[2024-01-24 12:13:07,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:07,584] [INFO] Task started: Prodigal
[2024-01-24 12:13:07,584] [INFO] Running command: gunzip -c /var/lib/cwl/stg08b045e3-cc63-4a9e-83f6-a5752f10bfd3/GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/cds.fna -a GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:22,235] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:22,236] [INFO] Task started: HMMsearch
[2024-01-24 12:13:22,236] [INFO] Running command: hmmsearch --tblout GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg526ef157-c900-422a-ad08-36995caf5af9/dqc_reference/reference_markers.hmm GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:22,493] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:22,495] [INFO] Found 6/6 markers.
[2024-01-24 12:13:22,537] [INFO] Query marker FASTA was written to GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:22,538] [INFO] Task started: Blastn
[2024-01-24 12:13:22,538] [INFO] Running command: blastn -query GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg526ef157-c900-422a-ad08-36995caf5af9/dqc_reference/reference_markers.fasta -out GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:23,549] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:23,553] [INFO] Selected 11 target genomes.
[2024-01-24 12:13:23,554] [INFO] Target genome list was writen to GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:23,559] [INFO] Task started: fastANI
[2024-01-24 12:13:23,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b045e3-cc63-4a9e-83f6-a5752f10bfd3/GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna.gz --refList GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:36,066] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:36,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg526ef157-c900-422a-ad08-36995caf5af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:36,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg526ef157-c900-422a-ad08-36995caf5af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:36,076] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:36,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:36,076] [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
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	100.0	1683	1684	95	conclusive
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	93.2478	1345	1684	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	90.2622	1336	1684	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	89.4306	1259	1684	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	88.9712	1170	1684	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	88.8942	1238	1684	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	87.6204	1116	1684	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	82.4631	771	1684	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	82.3409	736	1684	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.9517	515	1684	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.936	333	1684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:36,078] [INFO] DFAST Taxonomy check result was written to GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:36,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:36,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:36,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg526ef157-c900-422a-ad08-36995caf5af9/dqc_reference/checkm_data
[2024-01-24 12:13:36,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:36,125] [INFO] Task started: CheckM
[2024-01-24 12:13:36,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/checkm_input GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:23,209] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:23,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:23,228] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:23,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:23,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:23,229] [INFO] Task started: Blastn
[2024-01-24 12:14:23,230] [INFO] Running command: blastn -query GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg526ef157-c900-422a-ad08-36995caf5af9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:25,276] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:25,283] [INFO] Selected 7 target genomes.
[2024-01-24 12:14:25,283] [INFO] Target genome list was writen to GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:25,289] [INFO] Task started: fastANI
[2024-01-24 12:14:25,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b045e3-cc63-4a9e-83f6-a5752f10bfd3/GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna.gz --refList GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:34,773] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:34,780] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:34,780] [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_900156155.1	s__Aromatoleum tolulyticum	100.0	1683	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012911005.1	s__Aromatoleum toluolicum	93.2619	1344	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014822185.1	s__Aromatoleum sp014822185	92.7295	1333	1684	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	92.6624	1365	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378245.1	s__Aromatoleum toluclasticum	90.2493	1337	1684	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	89.4449	1256	1684	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	88.8829	1239	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:34,781] [INFO] GTDB search result was written to GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:34,782] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:34,785] [INFO] DFAST_QC result json was written to GCF_900156155.1_IMG-taxon_2681812808_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:14:34,785] [INFO] DFAST_QC completed!
[2024-01-24 12:14:34,785] [INFO] Total running time: 0h1m28s