[2024-01-24 12:53:55,126] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:55,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:55,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg159eaabe-58c9-4e37-b908-446ac76ee34c/dqc_reference
[2024-01-24 12:53:56,410] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:56,411] [INFO] Task started: Prodigal
[2024-01-24 12:53:56,411] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1f1d082-ae42-4d67-8d78-46dfd3086943/GCF_006539865.1_ASM653986v1_genomic.fna.gz | prodigal -d GCF_006539865.1_ASM653986v1_genomic.fna/cds.fna -a GCF_006539865.1_ASM653986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:09,821] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:09,822] [INFO] Task started: HMMsearch
[2024-01-24 12:54:09,822] [INFO] Running command: hmmsearch --tblout GCF_006539865.1_ASM653986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg159eaabe-58c9-4e37-b908-446ac76ee34c/dqc_reference/reference_markers.hmm GCF_006539865.1_ASM653986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:10,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:10,103] [INFO] Found 6/6 markers.
[2024-01-24 12:54:10,151] [INFO] Query marker FASTA was written to GCF_006539865.1_ASM653986v1_genomic.fna/markers.fasta
[2024-01-24 12:54:10,151] [INFO] Task started: Blastn
[2024-01-24 12:54:10,151] [INFO] Running command: blastn -query GCF_006539865.1_ASM653986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg159eaabe-58c9-4e37-b908-446ac76ee34c/dqc_reference/reference_markers.fasta -out GCF_006539865.1_ASM653986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:11,252] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:11,255] [INFO] Selected 18 target genomes.
[2024-01-24 12:54:11,256] [INFO] Target genome list was writen to GCF_006539865.1_ASM653986v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:11,283] [INFO] Task started: fastANI
[2024-01-24 12:54:11,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1f1d082-ae42-4d67-8d78-46dfd3086943/GCF_006539865.1_ASM653986v1_genomic.fna.gz --refList GCF_006539865.1_ASM653986v1_genomic.fna/target_genomes.txt --output GCF_006539865.1_ASM653986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:28,359] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:28,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg159eaabe-58c9-4e37-b908-446ac76ee34c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:28,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg159eaabe-58c9-4e37-b908-446ac76ee34c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:28,374] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:28,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:28,374] [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
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	100.0	1431	1439	95	conclusive
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	83.4963	864	1439	95	below_threshold
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	83.2319	874	1439	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	81.0089	558	1439	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	80.5156	567	1439	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	80.1199	521	1439	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	79.9782	573	1439	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	79.9084	522	1439	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	79.8043	462	1439	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	79.6332	556	1439	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.3696	507	1439	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.3146	519	1439	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	77.4856	302	1439	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	77.2131	307	1439	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.6996	355	1439	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.5717	187	1439	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	75.712	142	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:28,376] [INFO] DFAST Taxonomy check result was written to GCF_006539865.1_ASM653986v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:28,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:28,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:28,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg159eaabe-58c9-4e37-b908-446ac76ee34c/dqc_reference/checkm_data
[2024-01-24 12:54:28,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:28,423] [INFO] Task started: CheckM
[2024-01-24 12:54:28,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539865.1_ASM653986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539865.1_ASM653986v1_genomic.fna/checkm_input GCF_006539865.1_ASM653986v1_genomic.fna/checkm_result
[2024-01-24 12:55:08,869] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:08,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:08,888] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:08,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:08,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539865.1_ASM653986v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:08,889] [INFO] Task started: Blastn
[2024-01-24 12:55:08,889] [INFO] Running command: blastn -query GCF_006539865.1_ASM653986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg159eaabe-58c9-4e37-b908-446ac76ee34c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539865.1_ASM653986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:10,930] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:10,933] [INFO] Selected 14 target genomes.
[2024-01-24 12:55:10,933] [INFO] Target genome list was writen to GCF_006539865.1_ASM653986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:10,943] [INFO] Task started: fastANI
[2024-01-24 12:55:10,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1f1d082-ae42-4d67-8d78-46dfd3086943/GCF_006539865.1_ASM653986v1_genomic.fna.gz --refList GCF_006539865.1_ASM653986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539865.1_ASM653986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:25,463] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:25,474] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:25,474] [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_006539865.1	s__Zoogloea ramigera	100.0	1431	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	99.03	99.03	0.93	0.93	2	conclusive
GCA_016789125.1	s__Zoogloea sp016789125	91.8337	856	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	85.1498	965	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657735.1	s__Zoogloea sp015657735	84.7202	626	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720685.1	s__Zoogloea sp016720685	84.1063	832	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026175.1	s__Zoogloea sp009026175	83.4863	788	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927165.1	s__Zoogloea sp012927165	83.4568	867	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241665.1	s__Zoogloea sp018241665	83.4139	831	1439	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	83.368	822	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241685.1	s__Zoogloea sp018241685	83.2297	814	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309145.1	s__Zoogloea sp017309145	82.9213	707	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241725.1	s__Zoogloea sp018241725	82.8999	805	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	79.9935	491	1439	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_008501585.1	s__Denitromonas sp008501585	79.5375	534	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:25,476] [INFO] GTDB search result was written to GCF_006539865.1_ASM653986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:25,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:25,480] [INFO] DFAST_QC result json was written to GCF_006539865.1_ASM653986v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:25,480] [INFO] DFAST_QC completed!
[2024-01-24 12:55:25,480] [INFO] Total running time: 0h1m30s