[2024-01-24 15:18:47,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:47,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:47,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg15d71e49-2b99-4d5f-9472-f2279412b2e3/dqc_reference
[2024-01-24 15:18:51,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:51,765] [INFO] Task started: Prodigal
[2024-01-24 15:18:51,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg8933acde-6d85-42a4-b6d2-972ac341bfc3/GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/cds.fna -a GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:06,086] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:06,087] [INFO] Task started: HMMsearch
[2024-01-24 15:19:06,087] [INFO] Running command: hmmsearch --tblout GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15d71e49-2b99-4d5f-9472-f2279412b2e3/dqc_reference/reference_markers.hmm GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:06,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:06,334] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8933acde-6d85-42a4-b6d2-972ac341bfc3/GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna.gz]
[2024-01-24 15:19:06,365] [INFO] Query marker FASTA was written to GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:19:06,365] [INFO] Task started: Blastn
[2024-01-24 15:19:06,366] [INFO] Running command: blastn -query GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d71e49-2b99-4d5f-9472-f2279412b2e3/dqc_reference/reference_markers.fasta -out GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:06,888] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:06,892] [INFO] Selected 6 target genomes.
[2024-01-24 15:19:06,893] [INFO] Target genome list was writen to GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:19:06,935] [INFO] Task started: fastANI
[2024-01-24 15:19:06,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg8933acde-6d85-42a4-b6d2-972ac341bfc3/GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna.gz --refList GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:13,615] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:13,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15d71e49-2b99-4d5f-9472-f2279412b2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:13,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15d71e49-2b99-4d5f-9472-f2279412b2e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:13,624] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:13,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:13,624] [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
Halorubrum aquaticum	strain=CGMCC 1.6377	GCA_900113615.1	387340	387340	type	True	100.0	1043	1045	95	conclusive
Halorubrum cibi	strain=DSM 19504	GCA_900182635.1	413815	413815	type	True	92.0526	818	1045	95	below_threshold
Halorubrum aethiopicum	strain=SAH-A6	GCA_001542905.1	1758255	1758255	type	True	90.6596	809	1045	95	below_threshold
Halorubrum rubrum	strain=YC87	GCA_024494685.1	1126240	1126240	type	True	90.2656	804	1045	95	below_threshold
Halorubrum halodurans	strain=Cb34	GCA_002252985.1	1383851	1383851	type	True	90.0093	739	1045	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	83.7254	650	1045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:13,626] [INFO] DFAST Taxonomy check result was written to GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:19:13,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:13,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:13,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15d71e49-2b99-4d5f-9472-f2279412b2e3/dqc_reference/checkm_data
[2024-01-24 15:19:13,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:13,658] [INFO] Task started: CheckM
[2024-01-24 15:19:13,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/checkm_input GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:19:55,008] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:55,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:55,032] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:55,033] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:55,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:19:55,034] [INFO] Task started: Blastn
[2024-01-24 15:19:55,034] [INFO] Running command: blastn -query GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d71e49-2b99-4d5f-9472-f2279412b2e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:55,523] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:55,527] [INFO] Selected 6 target genomes.
[2024-01-24 15:19:55,528] [INFO] Target genome list was writen to GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:55,535] [INFO] Task started: fastANI
[2024-01-24 15:19:55,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg8933acde-6d85-42a4-b6d2-972ac341bfc3/GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna.gz --refList GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:01,899] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:01,906] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:01,906] [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_900113615.1	s__Halorubrum aquaticum	100.0	1043	1045	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900182635.1	s__Halorubrum cibi	92.0526	818	1045	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542905.1	s__Halorubrum aethiopicum	90.6596	809	1045	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252985.1	s__Halorubrum halodurans	90.0383	737	1045	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697845.1	s__Halorubrum sp003697845	89.6701	816	1045	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287355.1	s__Halorubrum sp003287355	88.8163	787	1045	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:01,908] [INFO] GTDB search result was written to GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:01,909] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:01,911] [INFO] DFAST_QC result json was written to GCF_900113615.1_IMG-taxon_2617270873_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:20:01,911] [INFO] DFAST_QC completed!
[2024-01-24 15:20:01,911] [INFO] Total running time: 0h1m14s