[2024-01-24 11:59:51,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,985] [INFO] DQC Reference Directory: /var/lib/cwl/stg95ab0dc9-0f6e-4cd9-85c9-d675516cd68a/dqc_reference
[2024-01-24 11:59:55,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,382] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,383] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e2dc699-4290-4517-9efb-10b8d1fd2a02/GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/cds.fna -a GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:15,243] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:15,243] [INFO] Task started: HMMsearch
[2024-01-24 12:00:15,243] [INFO] Running command: hmmsearch --tblout GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95ab0dc9-0f6e-4cd9-85c9-d675516cd68a/dqc_reference/reference_markers.hmm GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:15,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:15,482] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8e2dc699-4290-4517-9efb-10b8d1fd2a02/GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna.gz]
[2024-01-24 12:00:15,519] [INFO] Query marker FASTA was written to GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:00:15,520] [INFO] Task started: Blastn
[2024-01-24 12:00:15,520] [INFO] Running command: blastn -query GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ab0dc9-0f6e-4cd9-85c9-d675516cd68a/dqc_reference/reference_markers.fasta -out GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:16,066] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:16,071] [INFO] Selected 5 target genomes.
[2024-01-24 12:00:16,072] [INFO] Target genome list was writen to GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:00:16,075] [INFO] Task started: fastANI
[2024-01-24 12:00:16,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e2dc699-4290-4517-9efb-10b8d1fd2a02/GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna.gz --refList GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:21,863] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:21,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95ab0dc9-0f6e-4cd9-85c9-d675516cd68a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:21,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95ab0dc9-0f6e-4cd9-85c9-d675516cd68a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:21,876] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:21,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:21,877] [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 rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	100.0	1391	1394	95	conclusive
Halogeometricum limi	strain=CGMCC 1.8711	GCA_900115785.1	555875	555875	type	True	85.2618	930	1394	95	below_threshold
Halogeometricum pallidum	strain=JCM 14848	GCA_000337095.1	411361	411361	type	True	85.0978	892	1394	95	below_threshold
Halogeometricum borinquense	strain=PR 3	GCA_000172995.2	60847	60847	type	True	83.044	819	1394	95	below_threshold
Halogeometricum borinquense	strain=DSM 11551	GCA_000337855.1	60847	60847	type	True	83.0392	809	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:21,879] [INFO] DFAST Taxonomy check result was written to GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:00:21,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:21,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:21,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95ab0dc9-0f6e-4cd9-85c9-d675516cd68a/dqc_reference/checkm_data
[2024-01-24 12:00:21,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:21,923] [INFO] Task started: CheckM
[2024-01-24 12:00:21,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/checkm_input GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:01:15,089] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:15,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:15,115] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:15,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:15,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:01:15,117] [INFO] Task started: Blastn
[2024-01-24 12:01:15,117] [INFO] Running command: blastn -query GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ab0dc9-0f6e-4cd9-85c9-d675516cd68a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:15,643] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:15,647] [INFO] Selected 7 target genomes.
[2024-01-24 12:01:15,647] [INFO] Target genome list was writen to GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:15,653] [INFO] Task started: fastANI
[2024-01-24 12:01:15,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e2dc699-4290-4517-9efb-10b8d1fd2a02/GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna.gz --refList GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:23,087] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:23,099] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:23,099] [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_900112175.1	s__Halogeometricum rufum	100.0	1391	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	conclusive
GCF_900115785.1	s__Halogeometricum limi	85.2394	932	1394	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	85.0507	896	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172995.2	s__Halogeometricum borinquense	83.0298	820	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.42	96.84	0.96	0.91	5	-
GCF_900100875.1	s__Halopelagius longus	82.4137	773	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopelagius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000739575.1	s__Halobellus rufus	80.0317	533	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469865.1	s__Haloferax profundi	79.5039	509	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:23,101] [INFO] GTDB search result was written to GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:23,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:23,104] [INFO] DFAST_QC result json was written to GCF_900112175.1_IMG-taxon_2617270920_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:01:23,105] [INFO] DFAST_QC completed!
[2024-01-24 12:01:23,105] [INFO] Total running time: 0h1m31s