[2024-01-24 14:53:50,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg25be33ea-5e6b-4df6-bfd1-25b7e68fcf7d/dqc_reference
[2024-01-24 14:53:51,653] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,654] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,654] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a61d624-8a77-4411-8720-8a8958bacae3/GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/cds.fna -a GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:07,478] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:07,479] [INFO] Task started: HMMsearch
[2024-01-24 14:54:07,479] [INFO] Running command: hmmsearch --tblout GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25be33ea-5e6b-4df6-bfd1-25b7e68fcf7d/dqc_reference/reference_markers.hmm GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:07,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:07,729] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5a61d624-8a77-4411-8720-8a8958bacae3/GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna.gz]
[2024-01-24 14:54:07,757] [INFO] Query marker FASTA was written to GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:54:07,757] [INFO] Task started: Blastn
[2024-01-24 14:54:07,757] [INFO] Running command: blastn -query GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg25be33ea-5e6b-4df6-bfd1-25b7e68fcf7d/dqc_reference/reference_markers.fasta -out GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:08,330] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:08,332] [INFO] Selected 6 target genomes.
[2024-01-24 14:54:08,333] [INFO] Target genome list was writen to GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:54:08,337] [INFO] Task started: fastANI
[2024-01-24 14:54:08,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a61d624-8a77-4411-8720-8a8958bacae3/GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna.gz --refList GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:14,324] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:14,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25be33ea-5e6b-4df6-bfd1-25b7e68fcf7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:14,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25be33ea-5e6b-4df6-bfd1-25b7e68fcf7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:14,331] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:14,331] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:14,331] [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
Halobaculum gomorrense	strain=DSM 9297	GCA_900129775.1	43928	43928	type	True	100.0	1057	1060	95	conclusive
Halobaculum roseum	strain=CGMCC 1.15501	GCA_019880245.1	2175149	2175149	type	True	87.8807	818	1060	95	below_threshold
Halobaculum magnesiiphilum	strain=NBRC 109044	GCA_019823105.1	1017351	1017351	type	True	87.8738	822	1060	95	below_threshold
Halobaculum rubrum	strain=C46	GCA_019880225.1	2872158	2872158	type	True	87.3428	776	1060	95	below_threshold
Halobaculum saliterrae	strain=WSA2	GCA_009831625.1	2073113	2073113	type	True	86.973	811	1060	95	below_threshold
Halobaculum salinum	strain=NJ-3-1	GCA_013402875.1	2743089	2743089	type	True	80.5346	616	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:14,333] [INFO] DFAST Taxonomy check result was written to GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:54:14,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:14,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:14,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25be33ea-5e6b-4df6-bfd1-25b7e68fcf7d/dqc_reference/checkm_data
[2024-01-24 14:54:14,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:14,366] [INFO] Task started: CheckM
[2024-01-24 14:54:14,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/checkm_input GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:54:59,043] [INFO] Task succeeded: CheckM
[2024-01-24 14:54:59,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:54:59,064] [INFO] ===== Completeness check finished =====
[2024-01-24 14:54:59,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:54:59,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:54:59,066] [INFO] Task started: Blastn
[2024-01-24 14:54:59,066] [INFO] Running command: blastn -query GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg25be33ea-5e6b-4df6-bfd1-25b7e68fcf7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:59,573] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:59,575] [INFO] Selected 7 target genomes.
[2024-01-24 14:54:59,575] [INFO] Target genome list was writen to GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:54:59,586] [INFO] Task started: fastANI
[2024-01-24 14:54:59,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a61d624-8a77-4411-8720-8a8958bacae3/GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna.gz --refList GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:06,327] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:06,337] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:06,337] [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_900129775.1	s__Halobaculum gomorrense	100.0	1057	1060	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009831625.1	s__Halobaculum sp009831625	87.0297	807	1060	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020945.1	s__Halobaculum sp003020945	84.0526	652	1060	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013401515.1	s__Halobaculum sp013401515	80.6825	613	1060	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013402875.1	s__Halobaculum sp013402875	80.5497	614	1060	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495475.1	s__Halobaculum tyrrellense	80.4802	572	1060	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176545.1	s__Salinigranum salinum	77.858	468	1060	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:06,340] [INFO] GTDB search result was written to GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:06,340] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:06,343] [INFO] DFAST_QC result json was written to GCF_900129775.1_IMG-taxon_2695420988_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:55:06,343] [INFO] DFAST_QC completed!
[2024-01-24 14:55:06,343] [INFO] Total running time: 0h1m16s