[2024-01-24 11:06:04,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg66a697b5-d41f-49bc-891a-ed6edd6e7b64/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,012] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fefb3a2-3fa2-4776-b9dc-f938aabcea75/GCF_000744435.1_ASM74443v1_genomic.fna.gz | prodigal -d GCF_000744435.1_ASM74443v1_genomic.fna/cds.fna -a GCF_000744435.1_ASM74443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:10,578] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:10,579] [INFO] Task started: HMMsearch
[2024-01-24 11:06:10,579] [INFO] Running command: hmmsearch --tblout GCF_000744435.1_ASM74443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66a697b5-d41f-49bc-891a-ed6edd6e7b64/dqc_reference/reference_markers.hmm GCF_000744435.1_ASM74443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:10,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:10,792] [INFO] Found 6/6 markers.
[2024-01-24 11:06:10,815] [INFO] Query marker FASTA was written to GCF_000744435.1_ASM74443v1_genomic.fna/markers.fasta
[2024-01-24 11:06:10,815] [INFO] Task started: Blastn
[2024-01-24 11:06:10,815] [INFO] Running command: blastn -query GCF_000744435.1_ASM74443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66a697b5-d41f-49bc-891a-ed6edd6e7b64/dqc_reference/reference_markers.fasta -out GCF_000744435.1_ASM74443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:13,270] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:13,274] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:13,274] [INFO] Target genome list was writen to GCF_000744435.1_ASM74443v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:13,329] [INFO] Task started: fastANI
[2024-01-24 11:06:13,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fefb3a2-3fa2-4776-b9dc-f938aabcea75/GCF_000744435.1_ASM74443v1_genomic.fna.gz --refList GCF_000744435.1_ASM74443v1_genomic.fna/target_genomes.txt --output GCF_000744435.1_ASM74443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:19,650] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:19,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66a697b5-d41f-49bc-891a-ed6edd6e7b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:19,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66a697b5-d41f-49bc-891a-ed6edd6e7b64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:19,660] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:19,660] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:19,660] [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
Hippea jasoniae	strain=Mar08-272r	GCA_000744435.1	944479	944479	type	True	100.0	561	562	95	conclusive
Hippea alviniae	strain=EP5-r	GCA_000420385.1	1279027	1279027	type	True	77.2403	118	562	95	below_threshold
Hippea maritima	strain=DSM 10411	GCA_000194135.1	84405	84405	type	True	77.1474	105	562	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:19,662] [INFO] DFAST Taxonomy check result was written to GCF_000744435.1_ASM74443v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:19,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:19,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:19,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66a697b5-d41f-49bc-891a-ed6edd6e7b64/dqc_reference/checkm_data
[2024-01-24 11:06:19,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:19,687] [INFO] Task started: CheckM
[2024-01-24 11:06:19,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000744435.1_ASM74443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000744435.1_ASM74443v1_genomic.fna/checkm_input GCF_000744435.1_ASM74443v1_genomic.fna/checkm_result
[2024-01-24 11:06:38,115] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:38,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:38,135] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:38,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:38,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000744435.1_ASM74443v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:38,136] [INFO] Task started: Blastn
[2024-01-24 11:06:38,137] [INFO] Running command: blastn -query GCF_000744435.1_ASM74443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66a697b5-d41f-49bc-891a-ed6edd6e7b64/dqc_reference/reference_markers_gtdb.fasta -out GCF_000744435.1_ASM74443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:38,995] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:38,998] [INFO] Selected 20 target genomes.
[2024-01-24 11:06:38,998] [INFO] Target genome list was writen to GCF_000744435.1_ASM74443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:39,013] [INFO] Task started: fastANI
[2024-01-24 11:06:39,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fefb3a2-3fa2-4776-b9dc-f938aabcea75/GCF_000744435.1_ASM74443v1_genomic.fna.gz --refList GCF_000744435.1_ASM74443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000744435.1_ASM74443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:46,648] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:46,657] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:46,658] [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_000744435.1	s__Hippea_A jasoniae	100.0	561	562	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000420385.1	s__Hippea alviniae	77.2403	118	562	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526195.1	s__Hippea sp000526195	77.2194	105	562	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194135.1	s__Hippea maritima	77.0518	104	562	d__Bacteria;p__Campylobacterota;c__Desulfurellia;o__Desulfurellales;f__Hippeaceae;g__Hippea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:46,668] [INFO] GTDB search result was written to GCF_000744435.1_ASM74443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:46,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:46,671] [INFO] DFAST_QC result json was written to GCF_000744435.1_ASM74443v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:46,672] [INFO] DFAST_QC completed!
[2024-01-24 11:06:46,672] [INFO] Total running time: 0h0m42s