[2023-06-29 19:25:22,541] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:25:22,545] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:25:22,546] [INFO] DQC Reference Directory: /var/lib/cwl/stgd03ae6c1-38d1-46c1-a04b-f8887f937dab/dqc_reference
[2023-06-29 19:25:23,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:25:23,967] [INFO] Task started: Prodigal
[2023-06-29 19:25:23,967] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb724411-c728-4bbf-9666-af8ff8ec871c/GCA_024710625.1_ASM2471062v1_genomic.fna.gz | prodigal -d GCA_024710625.1_ASM2471062v1_genomic.fna/cds.fna -a GCA_024710625.1_ASM2471062v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:25:32,639] [INFO] Task succeeded: Prodigal
[2023-06-29 19:25:32,640] [INFO] Task started: HMMsearch
[2023-06-29 19:25:32,640] [INFO] Running command: hmmsearch --tblout GCA_024710625.1_ASM2471062v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd03ae6c1-38d1-46c1-a04b-f8887f937dab/dqc_reference/reference_markers.hmm GCA_024710625.1_ASM2471062v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:25:32,890] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:25:32,892] [INFO] Found 6/6 markers.
[2023-06-29 19:25:32,930] [INFO] Query marker FASTA was written to GCA_024710625.1_ASM2471062v1_genomic.fna/markers.fasta
[2023-06-29 19:25:32,931] [INFO] Task started: Blastn
[2023-06-29 19:25:32,931] [INFO] Running command: blastn -query GCA_024710625.1_ASM2471062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03ae6c1-38d1-46c1-a04b-f8887f937dab/dqc_reference/reference_markers.fasta -out GCA_024710625.1_ASM2471062v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:25:33,910] [INFO] Task succeeded: Blastn
[2023-06-29 19:25:33,915] [INFO] Selected 15 target genomes.
[2023-06-29 19:25:33,915] [INFO] Target genome list was writen to GCA_024710625.1_ASM2471062v1_genomic.fna/target_genomes.txt
[2023-06-29 19:25:33,919] [INFO] Task started: fastANI
[2023-06-29 19:25:33,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb724411-c728-4bbf-9666-af8ff8ec871c/GCA_024710625.1_ASM2471062v1_genomic.fna.gz --refList GCA_024710625.1_ASM2471062v1_genomic.fna/target_genomes.txt --output GCA_024710625.1_ASM2471062v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:25:48,183] [INFO] Task succeeded: fastANI
[2023-06-29 19:25:48,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd03ae6c1-38d1-46c1-a04b-f8887f937dab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:25:48,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd03ae6c1-38d1-46c1-a04b-f8887f937dab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:25:48,209] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 19:25:48,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 19:25:48,210] [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 aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	95.2067	774	960	95	conclusive
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	94.0321	769	960	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	94.0089	766	960	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	84.3135	542	960	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	83.8618	544	960	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	82.978	510	960	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	82.9104	525	960	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	82.6304	513	960	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	82.543	488	960	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	82.533	464	960	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.5006	471	960	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	80.3072	443	960	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.9858	428	960	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.0241	356	960	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.0105	217	960	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:25:48,227] [INFO] DFAST Taxonomy check result was written to GCA_024710625.1_ASM2471062v1_genomic.fna/tc_result.tsv
[2023-06-29 19:25:48,228] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:25:48,228] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:25:48,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd03ae6c1-38d1-46c1-a04b-f8887f937dab/dqc_reference/checkm_data
[2023-06-29 19:25:48,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:25:48,355] [INFO] Task started: CheckM
[2023-06-29 19:25:48,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024710625.1_ASM2471062v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024710625.1_ASM2471062v1_genomic.fna/checkm_input GCA_024710625.1_ASM2471062v1_genomic.fna/checkm_result
[2023-06-29 19:26:21,158] [INFO] Task succeeded: CheckM
[2023-06-29 19:26:21,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.95%
Contamintation: 13.02%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 19:26:21,193] [INFO] ===== Completeness check finished =====
[2023-06-29 19:26:21,194] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:26:21,194] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024710625.1_ASM2471062v1_genomic.fna/markers.fasta)
[2023-06-29 19:26:21,195] [INFO] Task started: Blastn
[2023-06-29 19:26:21,195] [INFO] Running command: blastn -query GCA_024710625.1_ASM2471062v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03ae6c1-38d1-46c1-a04b-f8887f937dab/dqc_reference/reference_markers_gtdb.fasta -out GCA_024710625.1_ASM2471062v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:26:23,021] [INFO] Task succeeded: Blastn
[2023-06-29 19:26:23,026] [INFO] Selected 14 target genomes.
[2023-06-29 19:26:23,026] [INFO] Target genome list was writen to GCA_024710625.1_ASM2471062v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:26:23,036] [INFO] Task started: fastANI
[2023-06-29 19:26:23,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb724411-c728-4bbf-9666-af8ff8ec871c/GCA_024710625.1_ASM2471062v1_genomic.fna.gz --refList GCA_024710625.1_ASM2471062v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024710625.1_ASM2471062v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:26:33,785] [INFO] Task succeeded: fastANI
[2023-06-29 19:26:33,800] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:26:33,800] [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_003030465.1	s__Thauera aromatica	95.2067	774	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001922305.1	s__Thauera chlorobenzoica	94.0068	770	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCF_000310225.1	s__Thauera phenylacetica	84.3534	540	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	84.099	521	960	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	83.8576	544	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_017997795.1	s__Thauera sp017997795	83.7514	409	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	83.3866	487	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790365.1	s__Thauera sp016790365	83.0447	393	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	83.0307	507	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	82.9284	405	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_001696715.1	s__Thauera phenolivorans	82.6623	511	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCF_009469595.1	s__Thauera sp009469595	82.349	465	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	82.2233	494	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	81.9562	459	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:26:33,802] [INFO] GTDB search result was written to GCA_024710625.1_ASM2471062v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:26:33,803] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:26:33,806] [INFO] DFAST_QC result json was written to GCA_024710625.1_ASM2471062v1_genomic.fna/dqc_result.json
[2023-06-29 19:26:33,807] [INFO] DFAST_QC completed!
[2023-06-29 19:26:33,807] [INFO] Total running time: 0h1m11s