[2023-06-28 11:37:42,111] [INFO] DFAST_QC pipeline started.
[2023-06-28 11:37:42,114] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 11:37:42,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg67379fa0-8843-4244-9f83-2bf763477fa2/dqc_reference
[2023-06-28 11:37:43,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 11:37:43,378] [INFO] Task started: Prodigal
[2023-06-28 11:37:43,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg078dc8df-284e-42b8-b4c9-8406b8ede247/GCA_002708785.1_ASM270878v1_genomic.fna.gz | prodigal -d GCA_002708785.1_ASM270878v1_genomic.fna/cds.fna -a GCA_002708785.1_ASM270878v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 11:37:46,558] [INFO] Task succeeded: Prodigal
[2023-06-28 11:37:46,559] [INFO] Task started: HMMsearch
[2023-06-28 11:37:46,560] [INFO] Running command: hmmsearch --tblout GCA_002708785.1_ASM270878v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67379fa0-8843-4244-9f83-2bf763477fa2/dqc_reference/reference_markers.hmm GCA_002708785.1_ASM270878v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 11:37:46,780] [INFO] Task succeeded: HMMsearch
[2023-06-28 11:37:46,782] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg078dc8df-284e-42b8-b4c9-8406b8ede247/GCA_002708785.1_ASM270878v1_genomic.fna.gz]
[2023-06-28 11:37:46,802] [INFO] Query marker FASTA was written to GCA_002708785.1_ASM270878v1_genomic.fna/markers.fasta
[2023-06-28 11:37:46,802] [INFO] Task started: Blastn
[2023-06-28 11:37:46,802] [INFO] Running command: blastn -query GCA_002708785.1_ASM270878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67379fa0-8843-4244-9f83-2bf763477fa2/dqc_reference/reference_markers.fasta -out GCA_002708785.1_ASM270878v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:37:47,353] [INFO] Task succeeded: Blastn
[2023-06-28 11:37:47,358] [INFO] Selected 8 target genomes.
[2023-06-28 11:37:47,359] [INFO] Target genome list was writen to GCA_002708785.1_ASM270878v1_genomic.fna/target_genomes.txt
[2023-06-28 11:37:47,362] [INFO] Task started: fastANI
[2023-06-28 11:37:47,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg078dc8df-284e-42b8-b4c9-8406b8ede247/GCA_002708785.1_ASM270878v1_genomic.fna.gz --refList GCA_002708785.1_ASM270878v1_genomic.fna/target_genomes.txt --output GCA_002708785.1_ASM270878v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 11:37:51,496] [INFO] Task succeeded: fastANI
[2023-06-28 11:37:51,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67379fa0-8843-4244-9f83-2bf763477fa2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 11:37:51,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67379fa0-8843-4244-9f83-2bf763477fa2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 11:37:51,501] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 11:37:51,501] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 11:37:51,501] [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
--------------------------------------------------------------------------------
[2023-06-28 11:37:51,503] [INFO] DFAST Taxonomy check result was written to GCA_002708785.1_ASM270878v1_genomic.fna/tc_result.tsv
[2023-06-28 11:37:51,503] [INFO] ===== Taxonomy check completed =====
[2023-06-28 11:37:51,504] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 11:37:51,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67379fa0-8843-4244-9f83-2bf763477fa2/dqc_reference/checkm_data
[2023-06-28 11:37:51,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 11:37:51,533] [INFO] Task started: CheckM
[2023-06-28 11:37:51,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708785.1_ASM270878v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708785.1_ASM270878v1_genomic.fna/checkm_input GCA_002708785.1_ASM270878v1_genomic.fna/checkm_result
[2023-06-28 11:38:09,491] [INFO] Task succeeded: CheckM
[2023-06-28 11:38:09,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 11:38:09,513] [INFO] ===== Completeness check finished =====
[2023-06-28 11:38:09,514] [INFO] ===== Start GTDB Search =====
[2023-06-28 11:38:09,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708785.1_ASM270878v1_genomic.fna/markers.fasta)
[2023-06-28 11:38:09,514] [INFO] Task started: Blastn
[2023-06-28 11:38:09,514] [INFO] Running command: blastn -query GCA_002708785.1_ASM270878v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67379fa0-8843-4244-9f83-2bf763477fa2/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708785.1_ASM270878v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 11:38:10,238] [INFO] Task succeeded: Blastn
[2023-06-28 11:38:10,243] [INFO] Selected 12 target genomes.
[2023-06-28 11:38:10,243] [INFO] Target genome list was writen to GCA_002708785.1_ASM270878v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 11:38:10,266] [INFO] Task started: fastANI
[2023-06-28 11:38:10,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg078dc8df-284e-42b8-b4c9-8406b8ede247/GCA_002708785.1_ASM270878v1_genomic.fna.gz --refList GCA_002708785.1_ASM270878v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708785.1_ASM270878v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 11:38:13,549] [INFO] Task succeeded: fastANI
[2023-06-28 11:38:13,556] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 11:38:13,556] [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
GCA_013329865.1	s__MGIIa-L1 sp8725u	98.3999	254	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCA_013329355.1	s__MGIIa-L1 sp9354u	90.743	235	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.57	99.13	0.80	0.62	3	-
--------------------------------------------------------------------------------
[2023-06-28 11:38:13,558] [INFO] GTDB search result was written to GCA_002708785.1_ASM270878v1_genomic.fna/result_gtdb.tsv
[2023-06-28 11:38:13,559] [INFO] ===== GTDB Search completed =====
[2023-06-28 11:38:13,561] [INFO] DFAST_QC result json was written to GCA_002708785.1_ASM270878v1_genomic.fna/dqc_result.json
[2023-06-28 11:38:13,562] [INFO] DFAST_QC completed!
[2023-06-28 11:38:13,562] [INFO] Total running time: 0h0m31s