[2024-01-24 12:31:04,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f88d80b-66e9-4bdf-a5a4-cc17cb8785b9/dqc_reference
[2024-01-24 12:31:05,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,806] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg65796d82-7470-46f1-a00f-4b5a025b70d5/GCF_004801305.1_ASM480130v1_genomic.fna.gz | prodigal -d GCF_004801305.1_ASM480130v1_genomic.fna/cds.fna -a GCF_004801305.1_ASM480130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:20,928] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:20,929] [INFO] Task started: HMMsearch
[2024-01-24 12:31:20,929] [INFO] Running command: hmmsearch --tblout GCF_004801305.1_ASM480130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f88d80b-66e9-4bdf-a5a4-cc17cb8785b9/dqc_reference/reference_markers.hmm GCF_004801305.1_ASM480130v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:21,215] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:21,217] [INFO] Found 6/6 markers.
[2024-01-24 12:31:21,257] [INFO] Query marker FASTA was written to GCF_004801305.1_ASM480130v1_genomic.fna/markers.fasta
[2024-01-24 12:31:21,257] [INFO] Task started: Blastn
[2024-01-24 12:31:21,258] [INFO] Running command: blastn -query GCF_004801305.1_ASM480130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f88d80b-66e9-4bdf-a5a4-cc17cb8785b9/dqc_reference/reference_markers.fasta -out GCF_004801305.1_ASM480130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:22,307] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:22,310] [INFO] Selected 19 target genomes.
[2024-01-24 12:31:22,310] [INFO] Target genome list was writen to GCF_004801305.1_ASM480130v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:22,320] [INFO] Task started: fastANI
[2024-01-24 12:31:22,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg65796d82-7470-46f1-a00f-4b5a025b70d5/GCF_004801305.1_ASM480130v1_genomic.fna.gz --refList GCF_004801305.1_ASM480130v1_genomic.fna/target_genomes.txt --output GCF_004801305.1_ASM480130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:41,528] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:41,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f88d80b-66e9-4bdf-a5a4-cc17cb8785b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:41,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f88d80b-66e9-4bdf-a5a4-cc17cb8785b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:41,548] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:41,548] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:41,548] [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
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	100.0	1509	1512	95	conclusive
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	85.3472	954	1512	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	82.3208	604	1512	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	81.9165	704	1512	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	81.909	622	1512	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	81.609	786	1512	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	81.5864	665	1512	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	81.5786	796	1512	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	81.558	708	1512	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	81.3234	594	1512	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	81.0918	632	1512	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	80.6378	625	1512	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	80.5438	646	1512	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.5359	641	1512	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	80.3274	641	1512	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	80.301	587	1512	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.6506	546	1512	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.5776	496	1512	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.907	402	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:41,550] [INFO] DFAST Taxonomy check result was written to GCF_004801305.1_ASM480130v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:41,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:41,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:41,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f88d80b-66e9-4bdf-a5a4-cc17cb8785b9/dqc_reference/checkm_data
[2024-01-24 12:31:41,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:41,599] [INFO] Task started: CheckM
[2024-01-24 12:31:41,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801305.1_ASM480130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801305.1_ASM480130v1_genomic.fna/checkm_input GCF_004801305.1_ASM480130v1_genomic.fna/checkm_result
[2024-01-24 12:32:33,886] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:33,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:33,912] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:33,912] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:33,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801305.1_ASM480130v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:33,913] [INFO] Task started: Blastn
[2024-01-24 12:32:33,913] [INFO] Running command: blastn -query GCF_004801305.1_ASM480130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f88d80b-66e9-4bdf-a5a4-cc17cb8785b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801305.1_ASM480130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:36,000] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:36,003] [INFO] Selected 13 target genomes.
[2024-01-24 12:32:36,003] [INFO] Target genome list was writen to GCF_004801305.1_ASM480130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:36,024] [INFO] Task started: fastANI
[2024-01-24 12:32:36,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg65796d82-7470-46f1-a00f-4b5a025b70d5/GCF_004801305.1_ASM480130v1_genomic.fna.gz --refList GCF_004801305.1_ASM480130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801305.1_ASM480130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:49,565] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:49,582] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:49,583] [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_004801305.1	s__Thauera_A rhizosphaerae	100.0	1509	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014489115.1	s__Thauera_A sp014489115	86.0268	889	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004801295.1	s__Thauera_A nasutitermitis	85.3089	958	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	83.8515	776	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	82.2848	607	1512	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	81.9124	705	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682385.1	s__Azoarcus olearius	81.8218	738	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	98.77	98.77	0.96	0.96	2	-
GCF_006496635.1	s__Azoarcus sp006496635	81.6535	780	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361735.1	s__Azoarcus indigens	81.6181	792	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012911025.1	s__Azoarcus sp012911025	81.5717	762	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345255.1	s__Thauera_A hydrothermalis	81.1239	629	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	98.04	97.85	0.92	0.92	3	-
GCF_012910905.1	s__Aromatoleum toluvorans	80.6163	626	1512	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	80.533	648	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:49,584] [INFO] GTDB search result was written to GCF_004801305.1_ASM480130v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:49,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:49,589] [INFO] DFAST_QC result json was written to GCF_004801305.1_ASM480130v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:49,589] [INFO] DFAST_QC completed!
[2024-01-24 12:32:49,589] [INFO] Total running time: 0h1m45s