[2024-01-25 20:00:05,639] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:05,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:05,640] [INFO] DQC Reference Directory: /var/lib/cwl/stge77b458e-37ef-4d76-ad94-303154789084/dqc_reference
[2024-01-25 20:00:06,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:06,858] [INFO] Task started: Prodigal
[2024-01-25 20:00:06,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7435639-4079-4627-a215-71909939765d/GCF_030159955.1_ASM3015995v1_genomic.fna.gz | prodigal -d GCF_030159955.1_ASM3015995v1_genomic.fna/cds.fna -a GCF_030159955.1_ASM3015995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:15,186] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:15,186] [INFO] Task started: HMMsearch
[2024-01-25 20:00:15,186] [INFO] Running command: hmmsearch --tblout GCF_030159955.1_ASM3015995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge77b458e-37ef-4d76-ad94-303154789084/dqc_reference/reference_markers.hmm GCF_030159955.1_ASM3015995v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:15,393] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:15,394] [INFO] Found 6/6 markers.
[2024-01-25 20:00:15,422] [INFO] Query marker FASTA was written to GCF_030159955.1_ASM3015995v1_genomic.fna/markers.fasta
[2024-01-25 20:00:15,422] [INFO] Task started: Blastn
[2024-01-25 20:00:15,422] [INFO] Running command: blastn -query GCF_030159955.1_ASM3015995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77b458e-37ef-4d76-ad94-303154789084/dqc_reference/reference_markers.fasta -out GCF_030159955.1_ASM3015995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:16,072] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:16,075] [INFO] Selected 30 target genomes.
[2024-01-25 20:00:16,075] [INFO] Target genome list was writen to GCF_030159955.1_ASM3015995v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:16,106] [INFO] Task started: fastANI
[2024-01-25 20:00:16,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7435639-4079-4627-a215-71909939765d/GCF_030159955.1_ASM3015995v1_genomic.fna.gz --refList GCF_030159955.1_ASM3015995v1_genomic.fna/target_genomes.txt --output GCF_030159955.1_ASM3015995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:35,393] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:35,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge77b458e-37ef-4d76-ad94-303154789084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:35,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge77b458e-37ef-4d76-ad94-303154789084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:35,398] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:00:35,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:00:35,398] [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
Algimonas arctica	strain=KCTC 32513	GCA_014652695.1	1479486	1479486	type	True	77.7138	284	1083	95	below_threshold
Hellea balneolensis	strain=DSM 19091	GCA_000428525.1	287478	287478	type	True	77.0526	55	1083	95	below_threshold
Litorimonas cladophorae	strain=KCTC 23968	GCA_014652455.1	1220491	1220491	type	True	76.7539	76	1083	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:35,400] [INFO] DFAST Taxonomy check result was written to GCF_030159955.1_ASM3015995v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:35,400] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:35,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:35,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge77b458e-37ef-4d76-ad94-303154789084/dqc_reference/checkm_data
[2024-01-25 20:00:35,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:35,435] [INFO] Task started: CheckM
[2024-01-25 20:00:35,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159955.1_ASM3015995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159955.1_ASM3015995v1_genomic.fna/checkm_input GCF_030159955.1_ASM3015995v1_genomic.fna/checkm_result
[2024-01-25 20:01:03,240] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:03,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:03,272] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:03,272] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:03,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159955.1_ASM3015995v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:03,273] [INFO] Task started: Blastn
[2024-01-25 20:01:03,273] [INFO] Running command: blastn -query GCF_030159955.1_ASM3015995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77b458e-37ef-4d76-ad94-303154789084/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159955.1_ASM3015995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:04,398] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:04,405] [INFO] Selected 31 target genomes.
[2024-01-25 20:01:04,405] [INFO] Target genome list was writen to GCF_030159955.1_ASM3015995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:04,445] [INFO] Task started: fastANI
[2024-01-25 20:01:04,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7435639-4079-4627-a215-71909939765d/GCF_030159955.1_ASM3015995v1_genomic.fna.gz --refList GCF_030159955.1_ASM3015995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159955.1_ASM3015995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:26,642] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:26,646] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:01:26,646] [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_014652695.1	s__Litorimonas arctica	77.7138	284	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428525.1	s__Hellea balneolensis	77.0602	54	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hellea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652455.1	s__Litorimonas cladophorae	76.7539	76	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Litorimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002305.1	s__JACOMS01 sp013002305	76.1965	51	1083	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__JACOMS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:26,677] [INFO] GTDB search result was written to GCF_030159955.1_ASM3015995v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:26,677] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:26,679] [INFO] DFAST_QC result json was written to GCF_030159955.1_ASM3015995v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:26,679] [INFO] DFAST_QC completed!
[2024-01-25 20:01:26,679] [INFO] Total running time: 0h1m21s