[2024-01-24 11:19:54,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:54,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:54,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cb7929d-c667-476b-84ee-46994742d87b/dqc_reference
[2024-01-24 11:19:55,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,898] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg67566e1b-f27d-4392-b7d0-83a6db369e02/GCF_030160855.1_ASM3016085v1_genomic.fna.gz | prodigal -d GCF_030160855.1_ASM3016085v1_genomic.fna/cds.fna -a GCF_030160855.1_ASM3016085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:09,037] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:09,037] [INFO] Task started: HMMsearch
[2024-01-24 11:20:09,038] [INFO] Running command: hmmsearch --tblout GCF_030160855.1_ASM3016085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cb7929d-c667-476b-84ee-46994742d87b/dqc_reference/reference_markers.hmm GCF_030160855.1_ASM3016085v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:09,353] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:09,355] [INFO] Found 6/6 markers.
[2024-01-24 11:20:09,401] [INFO] Query marker FASTA was written to GCF_030160855.1_ASM3016085v1_genomic.fna/markers.fasta
[2024-01-24 11:20:09,403] [INFO] Task started: Blastn
[2024-01-24 11:20:09,403] [INFO] Running command: blastn -query GCF_030160855.1_ASM3016085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cb7929d-c667-476b-84ee-46994742d87b/dqc_reference/reference_markers.fasta -out GCF_030160855.1_ASM3016085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:10,230] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:10,234] [INFO] Selected 25 target genomes.
[2024-01-24 11:20:10,235] [INFO] Target genome list was writen to GCF_030160855.1_ASM3016085v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:10,275] [INFO] Task started: fastANI
[2024-01-24 11:20:10,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg67566e1b-f27d-4392-b7d0-83a6db369e02/GCF_030160855.1_ASM3016085v1_genomic.fna.gz --refList GCF_030160855.1_ASM3016085v1_genomic.fna/target_genomes.txt --output GCF_030160855.1_ASM3016085v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:25,879] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:25,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cb7929d-c667-476b-84ee-46994742d87b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:25,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cb7929d-c667-476b-84ee-46994742d87b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:25,886] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:25,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:25,886] [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
Marinibactrum halimedae	strain=NBRC 110095	GCA_021234875.1	1444977	1444977	type	True	99.9892	1631	1644	95	conclusive
Sessilibacter corallicola	strain=C21	GCA_021290925.1	2904075	2904075	type	True	77.0814	60	1644	95	below_threshold
Saccharophagus degradans	strain=2-40	GCA_000013665.1	86304	86304	type	True	76.3921	50	1644	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:25,888] [INFO] DFAST Taxonomy check result was written to GCF_030160855.1_ASM3016085v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:25,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:25,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:25,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cb7929d-c667-476b-84ee-46994742d87b/dqc_reference/checkm_data
[2024-01-24 11:20:25,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:25,942] [INFO] Task started: CheckM
[2024-01-24 11:20:25,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160855.1_ASM3016085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160855.1_ASM3016085v1_genomic.fna/checkm_input GCF_030160855.1_ASM3016085v1_genomic.fna/checkm_result
[2024-01-24 11:21:10,010] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:10,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:10,034] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:10,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:10,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160855.1_ASM3016085v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:10,035] [INFO] Task started: Blastn
[2024-01-24 11:21:10,035] [INFO] Running command: blastn -query GCF_030160855.1_ASM3016085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cb7929d-c667-476b-84ee-46994742d87b/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160855.1_ASM3016085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:11,109] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:11,113] [INFO] Selected 34 target genomes.
[2024-01-24 11:21:11,113] [INFO] Target genome list was writen to GCF_030160855.1_ASM3016085v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:11,162] [INFO] Task started: fastANI
[2024-01-24 11:21:11,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg67566e1b-f27d-4392-b7d0-83a6db369e02/GCF_030160855.1_ASM3016085v1_genomic.fna.gz --refList GCF_030160855.1_ASM3016085v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160855.1_ASM3016085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:32,553] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:32,560] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:21:32,560] [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_000013665.1	s__Saccharophagus degradans	76.4762	52	1644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Saccharophagus	95.0	96.22	96.22	0.89	0.89	2	-
GCF_018863235.1	s__Pseudomaricurvus sp018863235	75.5295	50	1644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:32,562] [INFO] GTDB search result was written to GCF_030160855.1_ASM3016085v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:32,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:32,565] [INFO] DFAST_QC result json was written to GCF_030160855.1_ASM3016085v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:32,565] [INFO] DFAST_QC completed!
[2024-01-24 11:21:32,565] [INFO] Total running time: 0h1m38s