[2024-01-24 14:39:34,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:34,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:34,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg109ea729-cd0a-4351-a6bc-06e06cdfba53/dqc_reference
[2024-01-24 14:39:36,892] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:36,896] [INFO] Task started: Prodigal
[2024-01-24 14:39:36,896] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9f5ff90-da7e-4b1c-bb39-8fc39810d716/GCF_004799645.1_ASM479964v1_genomic.fna.gz | prodigal -d GCF_004799645.1_ASM479964v1_genomic.fna/cds.fna -a GCF_004799645.1_ASM479964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:01,439] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:01,440] [INFO] Task started: HMMsearch
[2024-01-24 14:40:01,440] [INFO] Running command: hmmsearch --tblout GCF_004799645.1_ASM479964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg109ea729-cd0a-4351-a6bc-06e06cdfba53/dqc_reference/reference_markers.hmm GCF_004799645.1_ASM479964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:01,732] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:01,733] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf9f5ff90-da7e-4b1c-bb39-8fc39810d716/GCF_004799645.1_ASM479964v1_genomic.fna.gz]
[2024-01-24 14:40:01,772] [INFO] Query marker FASTA was written to GCF_004799645.1_ASM479964v1_genomic.fna/markers.fasta
[2024-01-24 14:40:01,772] [INFO] Task started: Blastn
[2024-01-24 14:40:01,773] [INFO] Running command: blastn -query GCF_004799645.1_ASM479964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg109ea729-cd0a-4351-a6bc-06e06cdfba53/dqc_reference/reference_markers.fasta -out GCF_004799645.1_ASM479964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:02,414] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:02,418] [INFO] Selected 7 target genomes.
[2024-01-24 14:40:02,418] [INFO] Target genome list was writen to GCF_004799645.1_ASM479964v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:02,435] [INFO] Task started: fastANI
[2024-01-24 14:40:02,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f5ff90-da7e-4b1c-bb39-8fc39810d716/GCF_004799645.1_ASM479964v1_genomic.fna.gz --refList GCF_004799645.1_ASM479964v1_genomic.fna/target_genomes.txt --output GCF_004799645.1_ASM479964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:10,929] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:10,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg109ea729-cd0a-4351-a6bc-06e06cdfba53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:10,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg109ea729-cd0a-4351-a6bc-06e06cdfba53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:10,940] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:10,940] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:10,940] [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
Natronorubrum bangense	strain=JCM 10635	GCA_004799645.1	61858	61858	type	True	100.0	1404	1458	95	conclusive
Natronorubrum bangense	strain=JCM 10635	GCA_000337715.1	61858	61858	type	True	99.942	1293	1458	95	conclusive
Natronorubrum sulfidifaciens	strain=JCM 14089	GCA_000337735.1	388259	388259	type	True	88.8303	924	1458	95	below_threshold
Natronorubrum aibiense	strain=7-3	GCA_009392895.1	348826	348826	type	True	85.6839	940	1458	95	below_threshold
Natronorubrum tibetense	strain=GA33	GCA_000383975.1	63128	63128	type	True	81.6632	850	1458	95	below_threshold
Natronorubrum halophilum	strain=SHR37	GCA_003670115.1	1702106	1702106	type	True	81.5073	774	1458	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	81.3587	781	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:10,942] [INFO] DFAST Taxonomy check result was written to GCF_004799645.1_ASM479964v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:10,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:10,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:10,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg109ea729-cd0a-4351-a6bc-06e06cdfba53/dqc_reference/checkm_data
[2024-01-24 14:40:10,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:10,986] [INFO] Task started: CheckM
[2024-01-24 14:40:10,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004799645.1_ASM479964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004799645.1_ASM479964v1_genomic.fna/checkm_input GCF_004799645.1_ASM479964v1_genomic.fna/checkm_result
[2024-01-24 14:41:18,914] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:18,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 28.79%
Strain heterogeneity: 87.50%
--------------------------------------------------------------------------------
[2024-01-24 14:41:18,945] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:18,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:18,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004799645.1_ASM479964v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:18,946] [INFO] Task started: Blastn
[2024-01-24 14:41:18,946] [INFO] Running command: blastn -query GCF_004799645.1_ASM479964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg109ea729-cd0a-4351-a6bc-06e06cdfba53/dqc_reference/reference_markers_gtdb.fasta -out GCF_004799645.1_ASM479964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:19,741] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:19,745] [INFO] Selected 7 target genomes.
[2024-01-24 14:41:19,746] [INFO] Target genome list was writen to GCF_004799645.1_ASM479964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:19,753] [INFO] Task started: fastANI
[2024-01-24 14:41:19,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9f5ff90-da7e-4b1c-bb39-8fc39810d716/GCF_004799645.1_ASM479964v1_genomic.fna.gz --refList GCF_004799645.1_ASM479964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004799645.1_ASM479964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:28,133] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:28,147] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:28,147] [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_004799645.1	s__Natronorubrum bangense	100.0	1404	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.90	95.84	0.96	0.96	3	conclusive
GCF_000337735.1	s__Natronorubrum sulfidifaciens	88.8018	926	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156475.1	s__Natronorubrum thiooxidans	87.3184	972	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009392895.1	s__Natronorubrum aibiense	85.6478	944	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100335.1	s__Natronorubrum texcoconense	81.6127	789	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670115.1	s__Natronorubrum sp003670115	81.4817	776	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.42	97.42	0.91	0.91	2	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	81.3531	781	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:28,150] [INFO] GTDB search result was written to GCF_004799645.1_ASM479964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:28,150] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:28,153] [INFO] DFAST_QC result json was written to GCF_004799645.1_ASM479964v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:28,153] [INFO] DFAST_QC completed!
[2024-01-24 14:41:28,153] [INFO] Total running time: 0h1m54s