[2024-01-24 15:11:04,515] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:11:04,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:11:04,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg39a4c423-a0f9-401f-a441-a9cac330b786/dqc_reference
[2024-01-24 15:11:05,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:11:05,776] [INFO] Task started: Prodigal
[2024-01-24 15:11:05,776] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf3315c5-9b4a-469d-9e5a-50f9c2861649/GCF_014230055.1_ASM1423005v1_genomic.fna.gz | prodigal -d GCF_014230055.1_ASM1423005v1_genomic.fna/cds.fna -a GCF_014230055.1_ASM1423005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:35,258] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:35,258] [INFO] Task started: HMMsearch
[2024-01-24 15:11:35,258] [INFO] Running command: hmmsearch --tblout GCF_014230055.1_ASM1423005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39a4c423-a0f9-401f-a441-a9cac330b786/dqc_reference/reference_markers.hmm GCF_014230055.1_ASM1423005v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:35,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:35,559] [INFO] Found 6/6 markers.
[2024-01-24 15:11:35,605] [INFO] Query marker FASTA was written to GCF_014230055.1_ASM1423005v1_genomic.fna/markers.fasta
[2024-01-24 15:11:35,605] [INFO] Task started: Blastn
[2024-01-24 15:11:35,605] [INFO] Running command: blastn -query GCF_014230055.1_ASM1423005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a4c423-a0f9-401f-a441-a9cac330b786/dqc_reference/reference_markers.fasta -out GCF_014230055.1_ASM1423005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:36,298] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:36,303] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:36,304] [INFO] Target genome list was writen to GCF_014230055.1_ASM1423005v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:36,313] [INFO] Task started: fastANI
[2024-01-24 15:11:36,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf3315c5-9b4a-469d-9e5a-50f9c2861649/GCF_014230055.1_ASM1423005v1_genomic.fna.gz --refList GCF_014230055.1_ASM1423005v1_genomic.fna/target_genomes.txt --output GCF_014230055.1_ASM1423005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:51,353] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:51,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39a4c423-a0f9-401f-a441-a9cac330b786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:51,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39a4c423-a0f9-401f-a441-a9cac330b786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:51,357] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:51,357] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:51,357] [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
Puniceicoccus vermicola	strain=JCM14086	GCA_014230055.1	388746	388746	type	True	100.0	1665	1673	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 15:11:51,359] [INFO] DFAST Taxonomy check result was written to GCF_014230055.1_ASM1423005v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:51,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:51,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:51,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39a4c423-a0f9-401f-a441-a9cac330b786/dqc_reference/checkm_data
[2024-01-24 15:11:51,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:51,414] [INFO] Task started: CheckM
[2024-01-24 15:11:51,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014230055.1_ASM1423005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014230055.1_ASM1423005v1_genomic.fna/checkm_input GCF_014230055.1_ASM1423005v1_genomic.fna/checkm_result
[2024-01-24 15:13:07,678] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:07,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:07,702] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:07,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:07,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014230055.1_ASM1423005v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:07,703] [INFO] Task started: Blastn
[2024-01-24 15:13:07,703] [INFO] Running command: blastn -query GCF_014230055.1_ASM1423005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a4c423-a0f9-401f-a441-a9cac330b786/dqc_reference/reference_markers_gtdb.fasta -out GCF_014230055.1_ASM1423005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:08,563] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:08,567] [INFO] Selected 20 target genomes.
[2024-01-24 15:13:08,567] [INFO] Target genome list was writen to GCF_014230055.1_ASM1423005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:08,633] [INFO] Task started: fastANI
[2024-01-24 15:13:08,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf3315c5-9b4a-469d-9e5a-50f9c2861649/GCF_014230055.1_ASM1423005v1_genomic.fna.gz --refList GCF_014230055.1_ASM1423005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014230055.1_ASM1423005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:23,440] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:23,446] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:23,447] [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_014230055.1	s__Puniceicoccus vermicola	100.0	1666	1673	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Puniceicoccaceae;g__Puniceicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002388665.1	s__Puniceicoccus sp002388665	77.8571	247	1673	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Puniceicoccaceae;g__Puniceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:23,448] [INFO] GTDB search result was written to GCF_014230055.1_ASM1423005v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:23,449] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:23,451] [INFO] DFAST_QC result json was written to GCF_014230055.1_ASM1423005v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:23,451] [INFO] DFAST_QC completed!
[2024-01-24 15:13:23,451] [INFO] Total running time: 0h2m19s