[2024-01-24 14:22:01,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg974092c9-edd2-4e44-bb2e-ba8f81c6ff98/dqc_reference
[2024-01-24 14:22:02,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,463] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg02b77813-0e50-46e0-a719-a5a7fe8cbc7f/GCF_014467015.1_ASM1446701v1_genomic.fna.gz | prodigal -d GCF_014467015.1_ASM1446701v1_genomic.fna/cds.fna -a GCF_014467015.1_ASM1446701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:09,672] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:09,673] [INFO] Task started: HMMsearch
[2024-01-24 14:22:09,673] [INFO] Running command: hmmsearch --tblout GCF_014467015.1_ASM1446701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg974092c9-edd2-4e44-bb2e-ba8f81c6ff98/dqc_reference/reference_markers.hmm GCF_014467015.1_ASM1446701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:09,898] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:09,899] [INFO] Found 6/6 markers.
[2024-01-24 14:22:09,932] [INFO] Query marker FASTA was written to GCF_014467015.1_ASM1446701v1_genomic.fna/markers.fasta
[2024-01-24 14:22:09,932] [INFO] Task started: Blastn
[2024-01-24 14:22:09,932] [INFO] Running command: blastn -query GCF_014467015.1_ASM1446701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg974092c9-edd2-4e44-bb2e-ba8f81c6ff98/dqc_reference/reference_markers.fasta -out GCF_014467015.1_ASM1446701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:10,480] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:10,483] [INFO] Selected 17 target genomes.
[2024-01-24 14:22:10,484] [INFO] Target genome list was writen to GCF_014467015.1_ASM1446701v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:10,494] [INFO] Task started: fastANI
[2024-01-24 14:22:10,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg02b77813-0e50-46e0-a719-a5a7fe8cbc7f/GCF_014467015.1_ASM1446701v1_genomic.fna.gz --refList GCF_014467015.1_ASM1446701v1_genomic.fna/target_genomes.txt --output GCF_014467015.1_ASM1446701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:20,710] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:20,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg974092c9-edd2-4e44-bb2e-ba8f81c6ff98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:20,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg974092c9-edd2-4e44-bb2e-ba8f81c6ff98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:20,715] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:20,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:20,715] [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
Alkalicella caledoniensis	strain=LB2	GCA_014467015.1	2731377	2731377	type	True	100.0	1229	1231	95	conclusive
Anaerobranca californiensis	strain=DSM 14826	GCA_900142275.1	182411	182411	type	True	77.0418	92	1231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:20,717] [INFO] DFAST Taxonomy check result was written to GCF_014467015.1_ASM1446701v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:20,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:20,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:20,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg974092c9-edd2-4e44-bb2e-ba8f81c6ff98/dqc_reference/checkm_data
[2024-01-24 14:22:20,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:20,756] [INFO] Task started: CheckM
[2024-01-24 14:22:20,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014467015.1_ASM1446701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014467015.1_ASM1446701v1_genomic.fna/checkm_input GCF_014467015.1_ASM1446701v1_genomic.fna/checkm_result
[2024-01-24 14:22:49,036] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:49,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:49,063] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:49,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:49,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014467015.1_ASM1446701v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:49,063] [INFO] Task started: Blastn
[2024-01-24 14:22:49,064] [INFO] Running command: blastn -query GCF_014467015.1_ASM1446701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg974092c9-edd2-4e44-bb2e-ba8f81c6ff98/dqc_reference/reference_markers_gtdb.fasta -out GCF_014467015.1_ASM1446701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:49,775] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:49,778] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:49,778] [INFO] Target genome list was writen to GCF_014467015.1_ASM1446701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:49,795] [INFO] Task started: fastANI
[2024-01-24 14:22:49,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg02b77813-0e50-46e0-a719-a5a7fe8cbc7f/GCF_014467015.1_ASM1446701v1_genomic.fna.gz --refList GCF_014467015.1_ASM1446701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014467015.1_ASM1446701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:02,761] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:02,764] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:02,764] [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_014467015.1	s__Alkalicella caledoniensis	100.0	1228	1231	d__Bacteria;p__Firmicutes_D;c__Proteinivoracia;o__Proteinivoracales;f__Proteinivoraceae;g__Alkalicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142275.1	s__Anaerobranca californiensis	77.0654	92	1231	d__Bacteria;p__Firmicutes_D;c__Proteinivoracia;o__Proteinivoracales;f__Proteinivoraceae;g__Anaerobranca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:02,766] [INFO] GTDB search result was written to GCF_014467015.1_ASM1446701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:02,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:02,769] [INFO] DFAST_QC result json was written to GCF_014467015.1_ASM1446701v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:02,769] [INFO] DFAST_QC completed!
[2024-01-24 14:23:02,769] [INFO] Total running time: 0h1m2s