[2024-01-24 10:47:24,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,215] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg4639241e-2ffe-4ffc-a887-cc671bbeac20/dqc_reference
[2024-01-24 10:47:26,337] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,337] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,338] [INFO] Running command: gunzip -c /var/lib/cwl/stg58082d18-c41c-40d2-a973-2df716c8e88b/GCF_000731985.1_ASM73198v1_genomic.fna.gz | prodigal -d GCF_000731985.1_ASM73198v1_genomic.fna/cds.fna -a GCF_000731985.1_ASM73198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:43,760] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:43,760] [INFO] Task started: HMMsearch
[2024-01-24 10:47:43,760] [INFO] Running command: hmmsearch --tblout GCF_000731985.1_ASM73198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4639241e-2ffe-4ffc-a887-cc671bbeac20/dqc_reference/reference_markers.hmm GCF_000731985.1_ASM73198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:44,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:44,018] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg58082d18-c41c-40d2-a973-2df716c8e88b/GCF_000731985.1_ASM73198v1_genomic.fna.gz]
[2024-01-24 10:47:44,052] [INFO] Query marker FASTA was written to GCF_000731985.1_ASM73198v1_genomic.fna/markers.fasta
[2024-01-24 10:47:44,053] [INFO] Task started: Blastn
[2024-01-24 10:47:44,053] [INFO] Running command: blastn -query GCF_000731985.1_ASM73198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4639241e-2ffe-4ffc-a887-cc671bbeac20/dqc_reference/reference_markers.fasta -out GCF_000731985.1_ASM73198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:44,562] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:44,566] [INFO] Selected 6 target genomes.
[2024-01-24 10:47:44,566] [INFO] Target genome list was writen to GCF_000731985.1_ASM73198v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:44,584] [INFO] Task started: fastANI
[2024-01-24 10:47:44,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg58082d18-c41c-40d2-a973-2df716c8e88b/GCF_000731985.1_ASM73198v1_genomic.fna.gz --refList GCF_000731985.1_ASM73198v1_genomic.fna/target_genomes.txt --output GCF_000731985.1_ASM73198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:51,032] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:51,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4639241e-2ffe-4ffc-a887-cc671bbeac20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:51,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4639241e-2ffe-4ffc-a887-cc671bbeac20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:51,044] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:51,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:51,044] [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
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	100.0	1248	1248	95	conclusive
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	99.966	1222	1248	95	conclusive
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	93.5239	1021	1248	95	below_threshold
Natrinema gari	strain=JCM 14663	GCA_000337175.1	419186	419186	type	True	93.2217	1036	1248	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	87.5704	964	1248	95	below_threshold
Natronorubrum sulfidifaciens	strain=JCM 14089	GCA_000337735.1	388259	388259	type	True	80.6064	615	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:51,046] [INFO] DFAST Taxonomy check result was written to GCF_000731985.1_ASM73198v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:51,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:51,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:51,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4639241e-2ffe-4ffc-a887-cc671bbeac20/dqc_reference/checkm_data
[2024-01-24 10:47:51,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:51,086] [INFO] Task started: CheckM
[2024-01-24 10:47:51,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000731985.1_ASM73198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000731985.1_ASM73198v1_genomic.fna/checkm_input GCF_000731985.1_ASM73198v1_genomic.fna/checkm_result
[2024-01-24 10:48:40,138] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:40,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:40,162] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:40,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:40,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000731985.1_ASM73198v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:40,163] [INFO] Task started: Blastn
[2024-01-24 10:48:40,163] [INFO] Running command: blastn -query GCF_000731985.1_ASM73198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4639241e-2ffe-4ffc-a887-cc671bbeac20/dqc_reference/reference_markers_gtdb.fasta -out GCF_000731985.1_ASM73198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:40,650] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:40,654] [INFO] Selected 9 target genomes.
[2024-01-24 10:48:40,654] [INFO] Target genome list was writen to GCF_000731985.1_ASM73198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:40,661] [INFO] Task started: fastANI
[2024-01-24 10:48:40,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg58082d18-c41c-40d2-a973-2df716c8e88b/GCF_000731985.1_ASM73198v1_genomic.fna.gz --refList GCF_000731985.1_ASM73198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000731985.1_ASM73198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:50,409] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:50,433] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:50,434] [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_000731985.1	s__Natrinema altunense	100.0	1248	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	conclusive
GCF_000337615.1	s__Natrinema pallidum	93.5404	1020	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
GCF_000337175.1	s__Natrinema gari	93.2483	1034	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.50	98.45	0.93	0.92	3	-
GCF_005576615.1	s__Natrinema versiforme_A	85.3876	920	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	85.3807	959	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_001953745.1	s__Natrinema saccharevitans	84.668	850	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	84.6411	960	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	82.4505	808	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000337735.1	s__Natronorubrum sulfidifaciens	80.6127	614	1248	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 10:48:50,435] [INFO] GTDB search result was written to GCF_000731985.1_ASM73198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:50,437] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:50,440] [INFO] DFAST_QC result json was written to GCF_000731985.1_ASM73198v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:50,440] [INFO] DFAST_QC completed!
[2024-01-24 10:48:50,440] [INFO] Total running time: 0h1m26s