[2024-01-24 13:17:14,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg71f68f83-178c-45db-a8eb-13aa151ded96/dqc_reference
[2024-01-24 13:17:15,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,395] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,395] [INFO] Running command: gunzip -c /var/lib/cwl/stg54baff59-28f9-42c0-a2f0-5da48f9476ec/GCF_004346085.1_ASM434608v1_genomic.fna.gz | prodigal -d GCF_004346085.1_ASM434608v1_genomic.fna/cds.fna -a GCF_004346085.1_ASM434608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:23,469] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:23,470] [INFO] Task started: HMMsearch
[2024-01-24 13:17:23,470] [INFO] Running command: hmmsearch --tblout GCF_004346085.1_ASM434608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71f68f83-178c-45db-a8eb-13aa151ded96/dqc_reference/reference_markers.hmm GCF_004346085.1_ASM434608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:23,729] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:23,730] [INFO] Found 6/6 markers.
[2024-01-24 13:17:23,765] [INFO] Query marker FASTA was written to GCF_004346085.1_ASM434608v1_genomic.fna/markers.fasta
[2024-01-24 13:17:23,765] [INFO] Task started: Blastn
[2024-01-24 13:17:23,766] [INFO] Running command: blastn -query GCF_004346085.1_ASM434608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71f68f83-178c-45db-a8eb-13aa151ded96/dqc_reference/reference_markers.fasta -out GCF_004346085.1_ASM434608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:24,749] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:24,753] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:24,754] [INFO] Target genome list was writen to GCF_004346085.1_ASM434608v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:24,783] [INFO] Task started: fastANI
[2024-01-24 13:17:24,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg54baff59-28f9-42c0-a2f0-5da48f9476ec/GCF_004346085.1_ASM434608v1_genomic.fna.gz --refList GCF_004346085.1_ASM434608v1_genomic.fna/target_genomes.txt --output GCF_004346085.1_ASM434608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:38,504] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:38,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71f68f83-178c-45db-a8eb-13aa151ded96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:38,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71f68f83-178c-45db-a8eb-13aa151ded96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:38,530] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:38,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:38,530] [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
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	100.0	873	877	95	conclusive
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	99.9988	876	877	95	conclusive
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	78.9334	300	877	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.2023	249	877	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.1907	263	877	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	77.9584	265	877	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.9274	251	877	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.884	188	877	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	77.8641	190	877	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	77.81	244	877	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	77.8063	187	877	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	77.6435	262	877	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	77.6393	207	877	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	77.6087	262	877	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	77.5137	233	877	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	77.4034	231	877	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.9723	215	877	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	76.9476	214	877	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	76.817	169	877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:38,532] [INFO] DFAST Taxonomy check result was written to GCF_004346085.1_ASM434608v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:38,533] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:38,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:38,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71f68f83-178c-45db-a8eb-13aa151ded96/dqc_reference/checkm_data
[2024-01-24 13:17:38,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:38,565] [INFO] Task started: CheckM
[2024-01-24 13:17:38,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346085.1_ASM434608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346085.1_ASM434608v1_genomic.fna/checkm_input GCF_004346085.1_ASM434608v1_genomic.fna/checkm_result
[2024-01-24 13:18:06,993] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:06,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:07,015] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:07,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:07,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346085.1_ASM434608v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:07,016] [INFO] Task started: Blastn
[2024-01-24 13:18:07,016] [INFO] Running command: blastn -query GCF_004346085.1_ASM434608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71f68f83-178c-45db-a8eb-13aa151ded96/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346085.1_ASM434608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,820] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,824] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:08,824] [INFO] Target genome list was writen to GCF_004346085.1_ASM434608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:08,858] [INFO] Task started: fastANI
[2024-01-24 13:18:08,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg54baff59-28f9-42c0-a2f0-5da48f9476ec/GCF_004346085.1_ASM434608v1_genomic.fna.gz --refList GCF_004346085.1_ASM434608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346085.1_ASM434608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:17,650] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:17,661] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:17,661] [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_003967275.1	s__Sulfuritortus calidifontis	99.9988	876	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002339725.1	s__Sulfuritortus sp002339725	88.5339	637	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389055.1	s__Sulfuritortus sp013389055	87.4725	533	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234655.1	s__Sulfuritortus sp016234655	85.6344	602	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013335435.1	s__Parasulfuritortus sp013335435	81.1007	405	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337445.1	s__Parasulfuritortus cantonensis	80.8763	408	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772925.1	s__PFJX01 sp009772925	80.3818	428	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.99	99.98	1.00	0.99	4	-
GCA_016719465.1	s__PFJX01 sp016719465	80.3409	417	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.31	99.27	0.95	0.94	3	-
GCA_002360535.1	s__UBA3361 sp002360535	80.261	419	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA3361	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002782005.1	s__Parasulfuritortus sp002782005	79.3099	291	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	99.86	99.81	0.92	0.91	9	-
GCA_006212015.1	s__28-57-27 sp006212015	77.8083	164	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__Halothiobacillaceae;g__28-57-27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:17,663] [INFO] GTDB search result was written to GCF_004346085.1_ASM434608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:17,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:17,668] [INFO] DFAST_QC result json was written to GCF_004346085.1_ASM434608v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:17,669] [INFO] DFAST_QC completed!
[2024-01-24 13:18:17,669] [INFO] Total running time: 0h1m4s