[2024-01-24 13:48:59,882] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,883] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg22de927a-c138-4711-8cfc-5cab96afe07e/dqc_reference
[2024-01-24 13:49:01,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,208] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,208] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e73f194-0ce6-4427-9681-661469ff2f73/GCF_000337855.1_ASM33785v1_genomic.fna.gz | prodigal -d GCF_000337855.1_ASM33785v1_genomic.fna/cds.fna -a GCF_000337855.1_ASM33785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:21,824] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:21,825] [INFO] Task started: HMMsearch
[2024-01-24 13:49:21,825] [INFO] Running command: hmmsearch --tblout GCF_000337855.1_ASM33785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22de927a-c138-4711-8cfc-5cab96afe07e/dqc_reference/reference_markers.hmm GCF_000337855.1_ASM33785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:22,061] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:22,062] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8e73f194-0ce6-4427-9681-661469ff2f73/GCF_000337855.1_ASM33785v1_genomic.fna.gz]
[2024-01-24 13:49:22,096] [INFO] Query marker FASTA was written to GCF_000337855.1_ASM33785v1_genomic.fna/markers.fasta
[2024-01-24 13:49:22,097] [INFO] Task started: Blastn
[2024-01-24 13:49:22,097] [INFO] Running command: blastn -query GCF_000337855.1_ASM33785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22de927a-c138-4711-8cfc-5cab96afe07e/dqc_reference/reference_markers.fasta -out GCF_000337855.1_ASM33785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:22,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:22,629] [INFO] Selected 5 target genomes.
[2024-01-24 13:49:22,630] [INFO] Target genome list was writen to GCF_000337855.1_ASM33785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:22,647] [INFO] Task started: fastANI
[2024-01-24 13:49:22,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e73f194-0ce6-4427-9681-661469ff2f73/GCF_000337855.1_ASM33785v1_genomic.fna.gz --refList GCF_000337855.1_ASM33785v1_genomic.fna/target_genomes.txt --output GCF_000337855.1_ASM33785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:27,642] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:27,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22de927a-c138-4711-8cfc-5cab96afe07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:27,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22de927a-c138-4711-8cfc-5cab96afe07e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:27,652] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:27,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:27,652] [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=DSM 11551	GCA_000337855.1	60847	60847	type	True	100.0	1283	1285	95	conclusive
Halogeometricum borinquense	strain=PR 3	GCA_000172995.2	60847	60847	type	True	99.9892	1281	1285	95	conclusive
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	83.1887	812	1285	95	below_threshold
Halogeometricum limi	strain=CGMCC 1.8711	GCA_900115785.1	555875	555875	type	True	82.3845	730	1285	95	below_threshold
Halogeometricum pallidum	strain=JCM 14848	GCA_000337095.1	411361	411361	type	True	81.4957	688	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:27,654] [INFO] DFAST Taxonomy check result was written to GCF_000337855.1_ASM33785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:27,654] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:27,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:27,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22de927a-c138-4711-8cfc-5cab96afe07e/dqc_reference/checkm_data
[2024-01-24 13:49:27,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:27,701] [INFO] Task started: CheckM
[2024-01-24 13:49:27,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337855.1_ASM33785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337855.1_ASM33785v1_genomic.fna/checkm_input GCF_000337855.1_ASM33785v1_genomic.fna/checkm_result
[2024-01-24 13:50:24,927] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:24,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:24,949] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:24,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:24,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337855.1_ASM33785v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:24,951] [INFO] Task started: Blastn
[2024-01-24 13:50:24,951] [INFO] Running command: blastn -query GCF_000337855.1_ASM33785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22de927a-c138-4711-8cfc-5cab96afe07e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337855.1_ASM33785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:25,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:25,425] [INFO] Selected 5 target genomes.
[2024-01-24 13:50:25,426] [INFO] Target genome list was writen to GCF_000337855.1_ASM33785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:25,452] [INFO] Task started: fastANI
[2024-01-24 13:50:25,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e73f194-0ce6-4427-9681-661469ff2f73/GCF_000337855.1_ASM33785v1_genomic.fna.gz --refList GCF_000337855.1_ASM33785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337855.1_ASM33785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:30,316] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:30,322] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:30,323] [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	99.9892	1281	1285	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	83.1692	815	1285	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	82.3845	730	1285	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	81.4755	690	1285	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	80.0808	589	1285	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopelagius	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,324] [INFO] GTDB search result was written to GCF_000337855.1_ASM33785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:30,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:30,328] [INFO] DFAST_QC result json was written to GCF_000337855.1_ASM33785v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:30,328] [INFO] DFAST_QC completed!
[2024-01-24 13:50:30,328] [INFO] Total running time: 0h1m30s