[2024-01-24 13:56:27,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b6c5b1d-5815-4542-b146-d5dc8c56deb0/dqc_reference
[2024-01-24 13:56:28,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,728] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,728] [INFO] Running command: gunzip -c /var/lib/cwl/stga7eca686-e52c-464c-ae17-0b06705efc00/GCF_000230735.2_ASM23073v3_genomic.fna.gz | prodigal -d GCF_000230735.2_ASM23073v3_genomic.fna/cds.fna -a GCF_000230735.2_ASM23073v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:48,748] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:48,749] [INFO] Task started: HMMsearch
[2024-01-24 13:56:48,749] [INFO] Running command: hmmsearch --tblout GCF_000230735.2_ASM23073v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b6c5b1d-5815-4542-b146-d5dc8c56deb0/dqc_reference/reference_markers.hmm GCF_000230735.2_ASM23073v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:49,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:49,009] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga7eca686-e52c-464c-ae17-0b06705efc00/GCF_000230735.2_ASM23073v3_genomic.fna.gz]
[2024-01-24 13:56:49,049] [INFO] Query marker FASTA was written to GCF_000230735.2_ASM23073v3_genomic.fna/markers.fasta
[2024-01-24 13:56:49,050] [INFO] Task started: Blastn
[2024-01-24 13:56:49,050] [INFO] Running command: blastn -query GCF_000230735.2_ASM23073v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b6c5b1d-5815-4542-b146-d5dc8c56deb0/dqc_reference/reference_markers.fasta -out GCF_000230735.2_ASM23073v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:49,584] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:49,589] [INFO] Selected 10 target genomes.
[2024-01-24 13:56:49,590] [INFO] Target genome list was writen to GCF_000230735.2_ASM23073v3_genomic.fna/target_genomes.txt
[2024-01-24 13:56:49,602] [INFO] Task started: fastANI
[2024-01-24 13:56:49,603] [INFO] Running command: fastANI --query /var/lib/cwl/stga7eca686-e52c-464c-ae17-0b06705efc00/GCF_000230735.2_ASM23073v3_genomic.fna.gz --refList GCF_000230735.2_ASM23073v3_genomic.fna/target_genomes.txt --output GCF_000230735.2_ASM23073v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:01,966] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:01,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b6c5b1d-5815-4542-b146-d5dc8c56deb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:01,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b6c5b1d-5815-4542-b146-d5dc8c56deb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:01,982] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:01,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:01,983] [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 pellirubrum	strain=DSM 15624	GCA_000230735.3	69525	69525	type	True	100.0	1448	1449	95	conclusive
Natrinema pellirubrum	strain=DSM 15624	GCA_000337635.1	69525	69525	type	True	99.907	1358	1449	95	conclusive
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	84.7996	915	1449	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	84.7687	883	1449	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	84.7067	952	1449	95	below_threshold
Natrinema gari	strain=JCM 14663	GCA_000337175.1	419186	419186	type	True	84.3962	897	1449	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	83.2875	839	1449	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	83.1073	766	1449	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	82.738	842	1449	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	82.4613	826	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:01,985] [INFO] DFAST Taxonomy check result was written to GCF_000230735.2_ASM23073v3_genomic.fna/tc_result.tsv
[2024-01-24 13:57:01,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:01,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:01,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b6c5b1d-5815-4542-b146-d5dc8c56deb0/dqc_reference/checkm_data
[2024-01-24 13:57:01,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:02,030] [INFO] Task started: CheckM
[2024-01-24 13:57:02,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000230735.2_ASM23073v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000230735.2_ASM23073v3_genomic.fna/checkm_input GCF_000230735.2_ASM23073v3_genomic.fna/checkm_result
[2024-01-24 13:57:58,832] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:58,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:58,855] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:58,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:58,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000230735.2_ASM23073v3_genomic.fna/markers.fasta)
[2024-01-24 13:57:58,857] [INFO] Task started: Blastn
[2024-01-24 13:57:58,857] [INFO] Running command: blastn -query GCF_000230735.2_ASM23073v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b6c5b1d-5815-4542-b146-d5dc8c56deb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000230735.2_ASM23073v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:59,484] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:59,488] [INFO] Selected 8 target genomes.
[2024-01-24 13:57:59,489] [INFO] Target genome list was writen to GCF_000230735.2_ASM23073v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:59,504] [INFO] Task started: fastANI
[2024-01-24 13:57:59,504] [INFO] Running command: fastANI --query /var/lib/cwl/stga7eca686-e52c-464c-ae17-0b06705efc00/GCF_000230735.2_ASM23073v3_genomic.fna.gz --refList GCF_000230735.2_ASM23073v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000230735.2_ASM23073v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:09,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:09,689] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:09,689] [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_000230735.2	s__Natrinema pellirubrum	100.0	1449	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.7501	99.98	99.98	1.00	1.00	2	conclusive
GCF_000337115.1	s__Natrinema thermotolerans	95.5885	1095	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.7501	97.75	97.75	0.90	0.90	2	-
GCA_000690595.2	s__Natrinema mahii	92.4923	1041	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953745.1	s__Natrinema saccharevitans	91.2974	1015	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002572525.1	s__Natrinema sp002572525	83.7153	980	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337475.1	s__Natrinema limicola	83.0953	768	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111485.1	s__Natrinema hispanicum_A	82.8619	802	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	99.65	99.65	0.93	0.93	2	-
GCF_000337495.1	s__Haloterrigena salina	82.7217	844	1449	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:09,691] [INFO] GTDB search result was written to GCF_000230735.2_ASM23073v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:09,692] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:09,695] [INFO] DFAST_QC result json was written to GCF_000230735.2_ASM23073v3_genomic.fna/dqc_result.json
[2024-01-24 13:58:09,695] [INFO] DFAST_QC completed!
[2024-01-24 13:58:09,695] [INFO] Total running time: 0h1m42s