[2024-01-24 12:31:03,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg4710d166-e61d-4327-ad45-5108cf37ea15/dqc_reference
[2024-01-24 12:31:04,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,932] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg13b48add-0e59-4813-a49f-d5967898c4e7/GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/cds.fna -a GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:12,047] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:12,047] [INFO] Task started: HMMsearch
[2024-01-24 12:31:12,047] [INFO] Running command: hmmsearch --tblout GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4710d166-e61d-4327-ad45-5108cf37ea15/dqc_reference/reference_markers.hmm GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:12,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:12,317] [INFO] Found 6/6 markers.
[2024-01-24 12:31:12,344] [INFO] Query marker FASTA was written to GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:12,344] [INFO] Task started: Blastn
[2024-01-24 12:31:12,344] [INFO] Running command: blastn -query GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4710d166-e61d-4327-ad45-5108cf37ea15/dqc_reference/reference_markers.fasta -out GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:12,997] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:13,001] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:13,001] [INFO] Target genome list was writen to GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:13,007] [INFO] Task started: fastANI
[2024-01-24 12:31:13,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b48add-0e59-4813-a49f-d5967898c4e7/GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna.gz --refList GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:23,381] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:23,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4710d166-e61d-4327-ad45-5108cf37ea15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:23,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4710d166-e61d-4327-ad45-5108cf37ea15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:23,390] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:31:23,390] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:31:23,391] [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
Salisediminibacterium haloalkalitolerans	strain=10nlg	GCA_900111285.1	1464123	1464123	type	True	100.0	939	943	95	inconclusive
Salisediminibacterium halotolerans	strain=DSM 26530	GCA_003814815.1	517425	517425	type	True	97.6013	856	943	95	inconclusive
Salisediminibacterium halotolerans	strain=NBRC 104935	GCA_007988985.1	517425	517425	type	True	97.5475	772	943	95	inconclusive
Salisediminibacterium halotolerans	strain=CGMCC 1.7654	GCA_007993825.1	517425	517425	type	True	97.5217	858	943	95	inconclusive
Salisediminibacterium selenitireducens	strain=MLS10	GCA_000093085.1	85683	85683	type	True	77.025	67	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:23,392] [INFO] DFAST Taxonomy check result was written to GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:23,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:23,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:23,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4710d166-e61d-4327-ad45-5108cf37ea15/dqc_reference/checkm_data
[2024-01-24 12:31:23,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:23,425] [INFO] Task started: CheckM
[2024-01-24 12:31:23,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/checkm_input GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:31:51,130] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:51,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:51,154] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:51,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:51,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:31:51,155] [INFO] Task started: Blastn
[2024-01-24 12:31:51,155] [INFO] Running command: blastn -query GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4710d166-e61d-4327-ad45-5108cf37ea15/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:52,218] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:52,222] [INFO] Selected 26 target genomes.
[2024-01-24 12:31:52,223] [INFO] Target genome list was writen to GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:52,253] [INFO] Task started: fastANI
[2024-01-24 12:31:52,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b48add-0e59-4813-a49f-d5967898c4e7/GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna.gz --refList GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:08,684] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:08,690] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:08,691] [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_003814815.1	s__Salisediminibacterium halotolerans	97.6013	856	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	99.40	97.60	0.97	0.91	5	conclusive
GCA_000093085.1	s__Salisediminibacterium selenitireducens	77.0654	66	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:08,694] [INFO] GTDB search result was written to GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:08,695] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:08,697] [INFO] DFAST_QC result json was written to GCF_900111285.1_IMG-taxon_2675903025_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:08,697] [INFO] DFAST_QC completed!
[2024-01-24 12:32:08,697] [INFO] Total running time: 0h1m5s