[2024-01-24 11:26:36,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:36,206] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:36,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg28a7a656-dd36-46d8-9121-2be0716df4f5/dqc_reference
[2024-01-24 11:26:37,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:37,487] [INFO] Task started: Prodigal
[2024-01-24 11:26:37,487] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9401fc1-599d-4753-bcb2-92d0e0e14b7e/GCF_007625205.1_ASM762520v1_genomic.fna.gz | prodigal -d GCF_007625205.1_ASM762520v1_genomic.fna/cds.fna -a GCF_007625205.1_ASM762520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:51,860] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:51,861] [INFO] Task started: HMMsearch
[2024-01-24 11:26:51,861] [INFO] Running command: hmmsearch --tblout GCF_007625205.1_ASM762520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28a7a656-dd36-46d8-9121-2be0716df4f5/dqc_reference/reference_markers.hmm GCF_007625205.1_ASM762520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:52,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:52,182] [INFO] Found 6/6 markers.
[2024-01-24 11:26:52,222] [INFO] Query marker FASTA was written to GCF_007625205.1_ASM762520v1_genomic.fna/markers.fasta
[2024-01-24 11:26:52,223] [INFO] Task started: Blastn
[2024-01-24 11:26:52,223] [INFO] Running command: blastn -query GCF_007625205.1_ASM762520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28a7a656-dd36-46d8-9121-2be0716df4f5/dqc_reference/reference_markers.fasta -out GCF_007625205.1_ASM762520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:53,192] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:53,195] [INFO] Selected 21 target genomes.
[2024-01-24 11:26:53,196] [INFO] Target genome list was writen to GCF_007625205.1_ASM762520v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:53,204] [INFO] Task started: fastANI
[2024-01-24 11:26:53,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9401fc1-599d-4753-bcb2-92d0e0e14b7e/GCF_007625205.1_ASM762520v1_genomic.fna.gz --refList GCF_007625205.1_ASM762520v1_genomic.fna/target_genomes.txt --output GCF_007625205.1_ASM762520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:10,355] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:10,356] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28a7a656-dd36-46d8-9121-2be0716df4f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:10,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28a7a656-dd36-46d8-9121-2be0716df4f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:10,376] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:10,376] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:10,377] [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
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	80.4232	681	1451	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.4575	452	1451	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	79.2951	535	1451	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.2644	467	1451	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.1217	465	1451	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	79.0838	447	1451	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.9839	475	1451	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.8292	479	1451	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.8286	468	1451	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	78.8233	429	1451	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.8088	425	1451	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.7725	487	1451	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	78.7491	421	1451	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.5872	403	1451	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.5352	421	1451	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	78.5234	463	1451	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	78.4951	394	1451	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_003226565.1	41977	41977	type	True	78.3487	369	1451	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.2844	322	1451	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.2832	363	1451	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_012910815.1	41977	41977	type	True	78.2707	371	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:10,379] [INFO] DFAST Taxonomy check result was written to GCF_007625205.1_ASM762520v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:10,379] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:10,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:10,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28a7a656-dd36-46d8-9121-2be0716df4f5/dqc_reference/checkm_data
[2024-01-24 11:27:10,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:10,424] [INFO] Task started: CheckM
[2024-01-24 11:27:10,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007625205.1_ASM762520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007625205.1_ASM762520v1_genomic.fna/checkm_input GCF_007625205.1_ASM762520v1_genomic.fna/checkm_result
[2024-01-24 11:27:58,887] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:58,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:58,916] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:58,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:58,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007625205.1_ASM762520v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:58,917] [INFO] Task started: Blastn
[2024-01-24 11:27:58,917] [INFO] Running command: blastn -query GCF_007625205.1_ASM762520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28a7a656-dd36-46d8-9121-2be0716df4f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_007625205.1_ASM762520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:00,803] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:00,807] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:00,807] [INFO] Target genome list was writen to GCF_007625205.1_ASM762520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:00,817] [INFO] Task started: fastANI
[2024-01-24 11:28:00,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9401fc1-599d-4753-bcb2-92d0e0e14b7e/GCF_007625205.1_ASM762520v1_genomic.fna.gz --refList GCF_007625205.1_ASM762520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007625205.1_ASM762520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:10,562] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:10,577] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:10,578] [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_007625205.1	s__Denitromonas halophilus	100.0	1448	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.77	98.30	0.95	0.94	5	conclusive
GCF_007625155.1	s__Denitromonas halophilus_A	94.4713	1223	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501585.1	s__Denitromonas sp008501585	85.9421	1090	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018524365.1	s__Denitromonas sp018524365	85.2184	1064	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010983895.1	s__Denitromonas sp010983895	80.4096	683	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378245.1	s__Aromatoleum toluclasticum	79.0732	448	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030465.1	s__Thauera aromatica	78.715	425	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910955.1	s__Aromatoleum diolicum	78.5061	393	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302315.1	s__Zoogloea sp017302315	77.7873	346	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791005.1	s__JAEUNX01 sp016791005	77.2338	231	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAEUNX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:10,579] [INFO] GTDB search result was written to GCF_007625205.1_ASM762520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:10,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:10,583] [INFO] DFAST_QC result json was written to GCF_007625205.1_ASM762520v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:10,583] [INFO] DFAST_QC completed!
[2024-01-24 11:28:10,584] [INFO] Total running time: 0h1m34s