[2024-01-24 13:13:51,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg13c7beaa-368e-405c-a962-c911f3be6dc6/dqc_reference
[2024-01-24 13:13:52,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,677] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg11baedbc-dea5-4973-9475-79be57817790/GCF_004087915.1_ASM408791v1_genomic.fna.gz | prodigal -d GCF_004087915.1_ASM408791v1_genomic.fna/cds.fna -a GCF_004087915.1_ASM408791v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:00,139] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:00,139] [INFO] Task started: HMMsearch
[2024-01-24 13:14:00,140] [INFO] Running command: hmmsearch --tblout GCF_004087915.1_ASM408791v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13c7beaa-368e-405c-a962-c911f3be6dc6/dqc_reference/reference_markers.hmm GCF_004087915.1_ASM408791v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:00,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:00,411] [INFO] Found 6/6 markers.
[2024-01-24 13:14:00,443] [INFO] Query marker FASTA was written to GCF_004087915.1_ASM408791v1_genomic.fna/markers.fasta
[2024-01-24 13:14:00,444] [INFO] Task started: Blastn
[2024-01-24 13:14:00,444] [INFO] Running command: blastn -query GCF_004087915.1_ASM408791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c7beaa-368e-405c-a962-c911f3be6dc6/dqc_reference/reference_markers.fasta -out GCF_004087915.1_ASM408791v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:01,082] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:01,087] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:01,088] [INFO] Target genome list was writen to GCF_004087915.1_ASM408791v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:01,096] [INFO] Task started: fastANI
[2024-01-24 13:14:01,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg11baedbc-dea5-4973-9475-79be57817790/GCF_004087915.1_ASM408791v1_genomic.fna.gz --refList GCF_004087915.1_ASM408791v1_genomic.fna/target_genomes.txt --output GCF_004087915.1_ASM408791v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:09,684] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13c7beaa-368e-405c-a962-c911f3be6dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:09,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13c7beaa-368e-405c-a962-c911f3be6dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:09,689] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:09,689] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:09,689] [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
Geovibrio thiophilus	strain=DSM 11263	GCA_004087915.1	139438	139438	type	True	100.0	999	999	95	conclusive
Denitrovibrio acetiphilus	strain=DSM 12809	GCA_000025725.1	118000	118000	type	True	77.5776	50	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,693] [INFO] DFAST Taxonomy check result was written to GCF_004087915.1_ASM408791v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:09,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:09,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:09,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13c7beaa-368e-405c-a962-c911f3be6dc6/dqc_reference/checkm_data
[2024-01-24 13:14:09,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:09,738] [INFO] Task started: CheckM
[2024-01-24 13:14:09,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004087915.1_ASM408791v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004087915.1_ASM408791v1_genomic.fna/checkm_input GCF_004087915.1_ASM408791v1_genomic.fna/checkm_result
[2024-01-24 13:14:38,519] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:38,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:38,543] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:38,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:38,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004087915.1_ASM408791v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:38,544] [INFO] Task started: Blastn
[2024-01-24 13:14:38,544] [INFO] Running command: blastn -query GCF_004087915.1_ASM408791v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c7beaa-368e-405c-a962-c911f3be6dc6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004087915.1_ASM408791v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:39,444] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:39,456] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:39,456] [INFO] Target genome list was writen to GCF_004087915.1_ASM408791v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:39,477] [INFO] Task started: fastANI
[2024-01-24 13:14:39,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg11baedbc-dea5-4973-9475-79be57817790/GCF_004087915.1_ASM408791v1_genomic.fna.gz --refList GCF_004087915.1_ASM408791v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004087915.1_ASM408791v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:48,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:48,766] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:48,766] [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_004087915.1	s__Geovibrio thiophilus	100.0	998	999	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Geovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001603805.1	s__Geovibrio sp001603805	81.701	689	999	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Geovibrio	95.0	98.03	98.03	0.90	0.90	2	-
GCA_002452405.1	s__Seleniivibrio sp002452405	76.1181	62	999	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Seleniivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:48,768] [INFO] GTDB search result was written to GCF_004087915.1_ASM408791v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:48,770] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:48,774] [INFO] DFAST_QC result json was written to GCF_004087915.1_ASM408791v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:48,774] [INFO] DFAST_QC completed!
[2024-01-24 13:14:48,774] [INFO] Total running time: 0h0m57s