[2024-01-24 14:14:45,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:45,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:45,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgf627fd7a-69c5-4971-802e-53bb67c73ea9/dqc_reference
[2024-01-24 14:14:46,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:46,965] [INFO] Task started: Prodigal
[2024-01-24 14:14:46,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg964b7103-df2a-45b6-9662-e8ac3f455d79/GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/cds.fna -a GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:57,935] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:57,936] [INFO] Task started: HMMsearch
[2024-01-24 14:14:57,936] [INFO] Running command: hmmsearch --tblout GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf627fd7a-69c5-4971-802e-53bb67c73ea9/dqc_reference/reference_markers.hmm GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:58,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:58,193] [INFO] Found 6/6 markers.
[2024-01-24 14:14:58,225] [INFO] Query marker FASTA was written to GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:58,225] [INFO] Task started: Blastn
[2024-01-24 14:14:58,225] [INFO] Running command: blastn -query GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf627fd7a-69c5-4971-802e-53bb67c73ea9/dqc_reference/reference_markers.fasta -out GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:59,031] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:59,034] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:59,034] [INFO] Target genome list was writen to GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:59,042] [INFO] Task started: fastANI
[2024-01-24 14:14:59,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg964b7103-df2a-45b6-9662-e8ac3f455d79/GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna.gz --refList GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:09,277] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:09,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf627fd7a-69c5-4971-802e-53bb67c73ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:09,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf627fd7a-69c5-4971-802e-53bb67c73ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:09,288] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:15:09,288] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:15:09,289] [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
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	100.0	1286	1287	95	inconclusive
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	99.8692	1111	1287	95	inconclusive
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	97.9456	972	1287	95	inconclusive
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	94.5484	853	1287	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	87.6109	867	1287	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	87.5955	908	1287	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	87.2672	871	1287	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.7913	483	1287	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.7524	472	1287	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.539	450	1287	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.7323	285	1287	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.3086	303	1287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:09,299] [INFO] DFAST Taxonomy check result was written to GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:09,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:09,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:09,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf627fd7a-69c5-4971-802e-53bb67c73ea9/dqc_reference/checkm_data
[2024-01-24 14:15:09,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:09,342] [INFO] Task started: CheckM
[2024-01-24 14:15:09,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/checkm_input GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:15:45,418] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:45,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:45,565] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:45,566] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:45,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:15:45,567] [INFO] Task started: Blastn
[2024-01-24 14:15:45,567] [INFO] Running command: blastn -query GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf627fd7a-69c5-4971-802e-53bb67c73ea9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:47,020] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:47,024] [INFO] Selected 7 target genomes.
[2024-01-24 14:15:47,024] [INFO] Target genome list was writen to GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:47,036] [INFO] Task started: fastANI
[2024-01-24 14:15:47,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg964b7103-df2a-45b6-9662-e8ac3f455d79/GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna.gz --refList GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:53,660] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:53,667] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:53,667] [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_900110265.1	s__Halomonas aquamarina	97.9311	973	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	conclusive
GCF_002087295.1	s__Halomonas lionensis	94.5484	853	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846525.1	s__Halomonas sp002696125	88.8653	901	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_012427705.1	s__Halomonas piezotolerans	87.5765	906	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_014640815.1	s__Halomonas lutescens	87.2554	872	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	84.0103	721	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_016107625.1	s__Halomonas alkaliphila	80.3472	584	1287	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	96.32	95.46	0.84	0.80	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:53,668] [INFO] GTDB search result was written to GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:53,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:53,671] [INFO] DFAST_QC result json was written to GCF_900129255.1_IMG-taxon_2698536813_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:15:53,671] [INFO] DFAST_QC completed!
[2024-01-24 14:15:53,672] [INFO] Total running time: 0h1m8s