[2024-01-24 13:12:38,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb0f425e-bf21-4734-8f1d-16b580c5d788/dqc_reference
[2024-01-24 13:12:40,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,296] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,297] [INFO] Running command: gunzip -c /var/lib/cwl/stgf81f2ec2-1201-4d3d-8172-4e9de721475b/GCF_014644735.1_ASM1464473v1_genomic.fna.gz | prodigal -d GCF_014644735.1_ASM1464473v1_genomic.fna/cds.fna -a GCF_014644735.1_ASM1464473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:48,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:48,960] [INFO] Task started: HMMsearch
[2024-01-24 13:12:48,960] [INFO] Running command: hmmsearch --tblout GCF_014644735.1_ASM1464473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb0f425e-bf21-4734-8f1d-16b580c5d788/dqc_reference/reference_markers.hmm GCF_014644735.1_ASM1464473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:49,292] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:49,294] [INFO] Found 6/6 markers.
[2024-01-24 13:12:49,328] [INFO] Query marker FASTA was written to GCF_014644735.1_ASM1464473v1_genomic.fna/markers.fasta
[2024-01-24 13:12:49,328] [INFO] Task started: Blastn
[2024-01-24 13:12:49,328] [INFO] Running command: blastn -query GCF_014644735.1_ASM1464473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb0f425e-bf21-4734-8f1d-16b580c5d788/dqc_reference/reference_markers.fasta -out GCF_014644735.1_ASM1464473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:50,076] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:50,080] [INFO] Selected 26 target genomes.
[2024-01-24 13:12:50,081] [INFO] Target genome list was writen to GCF_014644735.1_ASM1464473v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:50,113] [INFO] Task started: fastANI
[2024-01-24 13:12:50,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81f2ec2-1201-4d3d-8172-4e9de721475b/GCF_014644735.1_ASM1464473v1_genomic.fna.gz --refList GCF_014644735.1_ASM1464473v1_genomic.fna/target_genomes.txt --output GCF_014644735.1_ASM1464473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:10,079] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:10,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb0f425e-bf21-4734-8f1d-16b580c5d788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:10,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb0f425e-bf21-4734-8f1d-16b580c5d788/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:10,084] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:10,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:10,084] [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
Caldalkalibacillus thermarum	strain=CGMCC 1.4242	GCA_014644735.1	296745	296745	type	True	100.0	977	994	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:13:10,086] [INFO] DFAST Taxonomy check result was written to GCF_014644735.1_ASM1464473v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:10,086] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:10,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:10,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb0f425e-bf21-4734-8f1d-16b580c5d788/dqc_reference/checkm_data
[2024-01-24 13:13:10,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:10,123] [INFO] Task started: CheckM
[2024-01-24 13:13:10,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644735.1_ASM1464473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644735.1_ASM1464473v1_genomic.fna/checkm_input GCF_014644735.1_ASM1464473v1_genomic.fna/checkm_result
[2024-01-24 13:13:42,353] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:42,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:42,380] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:42,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:42,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644735.1_ASM1464473v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:42,382] [INFO] Task started: Blastn
[2024-01-24 13:13:42,382] [INFO] Running command: blastn -query GCF_014644735.1_ASM1464473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb0f425e-bf21-4734-8f1d-16b580c5d788/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644735.1_ASM1464473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:43,409] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:43,413] [INFO] Selected 26 target genomes.
[2024-01-24 13:13:43,414] [INFO] Target genome list was writen to GCF_014644735.1_ASM1464473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:43,448] [INFO] Task started: fastANI
[2024-01-24 13:13:43,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81f2ec2-1201-4d3d-8172-4e9de721475b/GCF_014644735.1_ASM1464473v1_genomic.fna.gz --refList GCF_014644735.1_ASM1464473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644735.1_ASM1464473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:03,953] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,957] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:03,957] [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_014644735.1	s__Caldalkalibacillus thermarum	100.0	976	994	d__Bacteria;p__Firmicutes;c__Bacilli;o__Caldalkalibacillales;f__Caldalkalibacillaceae;g__Caldalkalibacillus	95.0	97.90	97.90	0.83	0.83	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,959] [INFO] GTDB search result was written to GCF_014644735.1_ASM1464473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:03,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:03,962] [INFO] DFAST_QC result json was written to GCF_014644735.1_ASM1464473v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:03,962] [INFO] DFAST_QC completed!
[2024-01-24 13:14:03,962] [INFO] Total running time: 0h1m25s