[2023-06-05 18:29:42,958] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:29:42,960] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:29:42,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg4284a022-99d0-4ad3-8cf0-d2907baeb36d/dqc_reference
[2023-06-05 18:29:44,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:29:44,147] [INFO] Task started: Prodigal
[2023-06-05 18:29:44,147] [INFO] Running command: gunzip -c /var/lib/cwl/stg666167dd-c9ee-43f4-a3b1-d1fa0acd38a5/GCA_001784565.1_ASM178456v1_genomic.fna.gz | prodigal -d GCA_001784565.1_ASM178456v1_genomic.fna/cds.fna -a GCA_001784565.1_ASM178456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:29:48,151] [INFO] Task succeeded: Prodigal
[2023-06-05 18:29:48,152] [INFO] Task started: HMMsearch
[2023-06-05 18:29:48,152] [INFO] Running command: hmmsearch --tblout GCA_001784565.1_ASM178456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4284a022-99d0-4ad3-8cf0-d2907baeb36d/dqc_reference/reference_markers.hmm GCA_001784565.1_ASM178456v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:29:48,415] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:29:48,416] [INFO] Found 6/6 markers.
[2023-06-05 18:29:48,445] [INFO] Query marker FASTA was written to GCA_001784565.1_ASM178456v1_genomic.fna/markers.fasta
[2023-06-05 18:29:48,445] [INFO] Task started: Blastn
[2023-06-05 18:29:48,445] [INFO] Running command: blastn -query GCA_001784565.1_ASM178456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4284a022-99d0-4ad3-8cf0-d2907baeb36d/dqc_reference/reference_markers.fasta -out GCA_001784565.1_ASM178456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:29:49,212] [INFO] Task succeeded: Blastn
[2023-06-05 18:29:49,215] [INFO] Selected 13 target genomes.
[2023-06-05 18:29:49,215] [INFO] Target genome list was writen to GCA_001784565.1_ASM178456v1_genomic.fna/target_genomes.txt
[2023-06-05 18:29:49,220] [INFO] Task started: fastANI
[2023-06-05 18:29:49,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg666167dd-c9ee-43f4-a3b1-d1fa0acd38a5/GCA_001784565.1_ASM178456v1_genomic.fna.gz --refList GCA_001784565.1_ASM178456v1_genomic.fna/target_genomes.txt --output GCA_001784565.1_ASM178456v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:29:58,058] [INFO] Task succeeded: fastANI
[2023-06-05 18:29:58,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4284a022-99d0-4ad3-8cf0-d2907baeb36d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:29:58,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4284a022-99d0-4ad3-8cf0-d2907baeb36d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:29:58,060] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:29:58,060] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:29:58,061] [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
--------------------------------------------------------------------------------
[2023-06-05 18:29:58,062] [INFO] DFAST Taxonomy check result was written to GCA_001784565.1_ASM178456v1_genomic.fna/tc_result.tsv
[2023-06-05 18:29:58,063] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:29:58,063] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:29:58,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4284a022-99d0-4ad3-8cf0-d2907baeb36d/dqc_reference/checkm_data
[2023-06-05 18:29:58,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:29:58,090] [INFO] Task started: CheckM
[2023-06-05 18:29:58,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001784565.1_ASM178456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001784565.1_ASM178456v1_genomic.fna/checkm_input GCA_001784565.1_ASM178456v1_genomic.fna/checkm_result
[2023-06-05 18:30:15,667] [INFO] Task succeeded: CheckM
[2023-06-05 18:30:15,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:30:15,683] [INFO] ===== Completeness check finished =====
[2023-06-05 18:30:15,684] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:30:15,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001784565.1_ASM178456v1_genomic.fna/markers.fasta)
[2023-06-05 18:30:15,685] [INFO] Task started: Blastn
[2023-06-05 18:30:15,685] [INFO] Running command: blastn -query GCA_001784565.1_ASM178456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4284a022-99d0-4ad3-8cf0-d2907baeb36d/dqc_reference/reference_markers_gtdb.fasta -out GCA_001784565.1_ASM178456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:30:16,538] [INFO] Task succeeded: Blastn
[2023-06-05 18:30:16,542] [INFO] Selected 17 target genomes.
[2023-06-05 18:30:16,542] [INFO] Target genome list was writen to GCA_001784565.1_ASM178456v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:30:16,629] [INFO] Task started: fastANI
[2023-06-05 18:30:16,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg666167dd-c9ee-43f4-a3b1-d1fa0acd38a5/GCA_001784565.1_ASM178456v1_genomic.fna.gz --refList GCA_001784565.1_ASM178456v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001784565.1_ASM178456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:30:24,048] [INFO] Task succeeded: fastANI
[2023-06-05 18:30:24,051] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:30:24,051] [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_001784565.1	s__GWF2-37-15 sp001784565	100.0	695	700	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__UBA9579;g__GWF2-37-15	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003499955.1	s__UBA9971 sp003499955	75.67	55	700	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__UBA9579;g__UBA9971	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:30:24,067] [INFO] GTDB search result was written to GCA_001784565.1_ASM178456v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:30:24,067] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:30:24,069] [INFO] DFAST_QC result json was written to GCA_001784565.1_ASM178456v1_genomic.fna/dqc_result.json
[2023-06-05 18:30:24,070] [INFO] DFAST_QC completed!
[2023-06-05 18:30:24,070] [INFO] Total running time: 0h0m41s