[2024-01-25 19:56:50,467] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:50,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:50,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg97779462-9ab6-41d3-aa3a-93f289ea0f44/dqc_reference
[2024-01-25 19:56:51,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:51,595] [INFO] Task started: Prodigal
[2024-01-25 19:56:51,596] [INFO] Running command: gunzip -c /var/lib/cwl/stga315a4c2-a00e-40dc-a853-1699976a6e86/GCF_000172995.2_ASM17299v2_genomic.fna.gz | prodigal -d GCF_000172995.2_ASM17299v2_genomic.fna/cds.fna -a GCF_000172995.2_ASM17299v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:09,221] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:09,221] [INFO] Task started: HMMsearch
[2024-01-25 19:57:09,221] [INFO] Running command: hmmsearch --tblout GCF_000172995.2_ASM17299v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97779462-9ab6-41d3-aa3a-93f289ea0f44/dqc_reference/reference_markers.hmm GCF_000172995.2_ASM17299v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:09,447] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:09,448] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga315a4c2-a00e-40dc-a853-1699976a6e86/GCF_000172995.2_ASM17299v2_genomic.fna.gz]
[2024-01-25 19:57:09,479] [INFO] Query marker FASTA was written to GCF_000172995.2_ASM17299v2_genomic.fna/markers.fasta
[2024-01-25 19:57:09,480] [INFO] Task started: Blastn
[2024-01-25 19:57:09,480] [INFO] Running command: blastn -query GCF_000172995.2_ASM17299v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg97779462-9ab6-41d3-aa3a-93f289ea0f44/dqc_reference/reference_markers.fasta -out GCF_000172995.2_ASM17299v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:09,958] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:09,961] [INFO] Selected 5 target genomes.
[2024-01-25 19:57:09,961] [INFO] Target genome list was writen to GCF_000172995.2_ASM17299v2_genomic.fna/target_genomes.txt
[2024-01-25 19:57:09,970] [INFO] Task started: fastANI
[2024-01-25 19:57:09,970] [INFO] Running command: fastANI --query /var/lib/cwl/stga315a4c2-a00e-40dc-a853-1699976a6e86/GCF_000172995.2_ASM17299v2_genomic.fna.gz --refList GCF_000172995.2_ASM17299v2_genomic.fna/target_genomes.txt --output GCF_000172995.2_ASM17299v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:15,041] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:15,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97779462-9ab6-41d3-aa3a-93f289ea0f44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:15,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97779462-9ab6-41d3-aa3a-93f289ea0f44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:15,047] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:57:15,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:15,047] [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
Halogeometricum borinquense	strain=PR 3	GCA_000172995.2	60847	60847	type	True	100.0	1311	1312	95	conclusive
Halogeometricum borinquense	strain=DSM 11551	GCA_000337855.1	60847	60847	type	True	99.9626	1276	1312	95	conclusive
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	83.1548	825	1312	95	below_threshold
Halogeometricum limi	strain=CGMCC 1.8711	GCA_900115785.1	555875	555875	type	True	82.417	746	1312	95	below_threshold
Halogeometricum pallidum	strain=JCM 14848	GCA_000337095.1	411361	411361	type	True	81.5217	688	1312	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:15,048] [INFO] DFAST Taxonomy check result was written to GCF_000172995.2_ASM17299v2_genomic.fna/tc_result.tsv
[2024-01-25 19:57:15,049] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:15,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:15,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97779462-9ab6-41d3-aa3a-93f289ea0f44/dqc_reference/checkm_data
[2024-01-25 19:57:15,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:15,092] [INFO] Task started: CheckM
[2024-01-25 19:57:15,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000172995.2_ASM17299v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000172995.2_ASM17299v2_genomic.fna/checkm_input GCF_000172995.2_ASM17299v2_genomic.fna/checkm_result
[2024-01-25 19:58:03,797] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:03,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:03,826] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:03,826] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:03,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000172995.2_ASM17299v2_genomic.fna/markers.fasta)
[2024-01-25 19:58:03,827] [INFO] Task started: Blastn
[2024-01-25 19:58:03,827] [INFO] Running command: blastn -query GCF_000172995.2_ASM17299v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg97779462-9ab6-41d3-aa3a-93f289ea0f44/dqc_reference/reference_markers_gtdb.fasta -out GCF_000172995.2_ASM17299v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:04,331] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:04,333] [INFO] Selected 5 target genomes.
[2024-01-25 19:58:04,334] [INFO] Target genome list was writen to GCF_000172995.2_ASM17299v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:04,338] [INFO] Task started: fastANI
[2024-01-25 19:58:04,338] [INFO] Running command: fastANI --query /var/lib/cwl/stga315a4c2-a00e-40dc-a853-1699976a6e86/GCF_000172995.2_ASM17299v2_genomic.fna.gz --refList GCF_000172995.2_ASM17299v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000172995.2_ASM17299v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:09,236] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:09,241] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:09,241] [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_000172995.2	s__Halogeometricum borinquense	100.0	1311	1312	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.42	96.84	0.96	0.91	5	conclusive
GCF_900112175.1	s__Halogeometricum rufum	83.1265	829	1312	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCF_900115785.1	s__Halogeometricum limi	82.4227	746	1312	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337095.1	s__Halogeometricum pallidum	81.4917	691	1312	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100875.1	s__Halopelagius longus	80.1084	587	1312	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopelagius	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:09,242] [INFO] GTDB search result was written to GCF_000172995.2_ASM17299v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:09,242] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:09,244] [INFO] DFAST_QC result json was written to GCF_000172995.2_ASM17299v2_genomic.fna/dqc_result.json
[2024-01-25 19:58:09,245] [INFO] DFAST_QC completed!
[2024-01-25 19:58:09,245] [INFO] Total running time: 0h1m19s