[2024-01-24 13:32:42,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f255747-ab9f-4619-8cc9-a5e8842f710e/dqc_reference
[2024-01-24 13:32:43,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,665] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f2b39f2-1b4e-4291-8c53-27ac4d4f23cd/GCF_003345255.1_ASM334525v1_genomic.fna.gz | prodigal -d GCF_003345255.1_ASM334525v1_genomic.fna/cds.fna -a GCF_003345255.1_ASM334525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:54,755] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:54,756] [INFO] Task started: HMMsearch
[2024-01-24 13:32:54,756] [INFO] Running command: hmmsearch --tblout GCF_003345255.1_ASM334525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f255747-ab9f-4619-8cc9-a5e8842f710e/dqc_reference/reference_markers.hmm GCF_003345255.1_ASM334525v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:55,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:55,039] [INFO] Found 6/6 markers.
[2024-01-24 13:32:55,083] [INFO] Query marker FASTA was written to GCF_003345255.1_ASM334525v1_genomic.fna/markers.fasta
[2024-01-24 13:32:55,083] [INFO] Task started: Blastn
[2024-01-24 13:32:55,083] [INFO] Running command: blastn -query GCF_003345255.1_ASM334525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f255747-ab9f-4619-8cc9-a5e8842f710e/dqc_reference/reference_markers.fasta -out GCF_003345255.1_ASM334525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:55,963] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:55,968] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:55,968] [INFO] Target genome list was writen to GCF_003345255.1_ASM334525v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:55,974] [INFO] Task started: fastANI
[2024-01-24 13:32:55,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f2b39f2-1b4e-4291-8c53-27ac4d4f23cd/GCF_003345255.1_ASM334525v1_genomic.fna.gz --refList GCF_003345255.1_ASM334525v1_genomic.fna/target_genomes.txt --output GCF_003345255.1_ASM334525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:11,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f255747-ab9f-4619-8cc9-a5e8842f710e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:11,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f255747-ab9f-4619-8cc9-a5e8842f710e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:11,996] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:11,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:11,997] [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 hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	100.0	1018	1019	95	conclusive
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	81.0431	644	1019	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	80.7895	622	1019	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.4979	427	1019	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	79.3973	418	1019	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	79.3282	406	1019	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	79.139	436	1019	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.0906	428	1019	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	79.0886	428	1019	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.0744	437	1019	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	78.8032	454	1019	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	78.7523	462	1019	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.3918	365	1019	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.3005	382	1019	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.269	365	1019	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.0501	322	1019	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	77.8959	331	1019	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.7809	255	1019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,999] [INFO] DFAST Taxonomy check result was written to GCF_003345255.1_ASM334525v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:12,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:12,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:12,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f255747-ab9f-4619-8cc9-a5e8842f710e/dqc_reference/checkm_data
[2024-01-24 13:33:12,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:12,034] [INFO] Task started: CheckM
[2024-01-24 13:33:12,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003345255.1_ASM334525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003345255.1_ASM334525v1_genomic.fna/checkm_input GCF_003345255.1_ASM334525v1_genomic.fna/checkm_result
[2024-01-24 13:33:47,348] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:47,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:47,367] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:47,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:47,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003345255.1_ASM334525v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:47,368] [INFO] Task started: Blastn
[2024-01-24 13:33:47,368] [INFO] Running command: blastn -query GCF_003345255.1_ASM334525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f255747-ab9f-4619-8cc9-a5e8842f710e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003345255.1_ASM334525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:48,965] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:48,968] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:48,968] [INFO] Target genome list was writen to GCF_003345255.1_ASM334525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:48,981] [INFO] Task started: fastANI
[2024-01-24 13:33:48,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f2b39f2-1b4e-4291-8c53-27ac4d4f23cd/GCF_003345255.1_ASM334525v1_genomic.fna.gz --refList GCF_003345255.1_ASM334525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003345255.1_ASM334525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:58,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:58,028] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:58,028] [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_003345255.1	s__Thauera_A hydrothermalis	100.0	1018	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	98.04	97.85	0.92	0.92	3	conclusive
GCF_014489115.1	s__Thauera_A sp014489115	85.0488	812	1019	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_003034845.1	s__Thauera_A sp003034845	81.0929	590	1019	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_004801305.1	s__Thauera_A rhizosphaerae	81.0106	648	1019	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_004801295.1	s__Thauera_A nasutitermitis	80.7962	621	1019	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	79.5218	425	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001051995.2	s__Thauera humireducens	79.188	433	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCF_001591165.1	s__Thauera butanivorans	79.1018	434	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245655.1	s__Thauera propionica	79.0687	431	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.06	98.06	0.86	0.86	2	-
GCA_003963015.1	s__Thauera sp003963015	79.0107	437	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911025.1	s__Azoarcus sp012911025	78.7778	458	1019	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:58,030] [INFO] GTDB search result was written to GCF_003345255.1_ASM334525v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:58,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:58,034] [INFO] DFAST_QC result json was written to GCF_003345255.1_ASM334525v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:58,034] [INFO] DFAST_QC completed!
[2024-01-24 13:33:58,034] [INFO] Total running time: 0h1m16s