[2023-06-28 20:40:49,623] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:40:49,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:40:49,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg46d6cde1-a5cf-430c-bd4d-548f8fbf0d91/dqc_reference
[2023-06-28 20:40:50,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:40:50,870] [INFO] Task started: Prodigal
[2023-06-28 20:40:50,870] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fb49bcd-4ad7-4d81-b0d6-3a01437e7a18/GCA_020404065.1_ASM2040406v1_genomic.fna.gz | prodigal -d GCA_020404065.1_ASM2040406v1_genomic.fna/cds.fna -a GCA_020404065.1_ASM2040406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:41:00,633] [INFO] Task succeeded: Prodigal
[2023-06-28 20:41:00,633] [INFO] Task started: HMMsearch
[2023-06-28 20:41:00,633] [INFO] Running command: hmmsearch --tblout GCA_020404065.1_ASM2040406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46d6cde1-a5cf-430c-bd4d-548f8fbf0d91/dqc_reference/reference_markers.hmm GCA_020404065.1_ASM2040406v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:41:00,943] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:41:00,945] [INFO] Found 6/6 markers.
[2023-06-28 20:41:00,988] [INFO] Query marker FASTA was written to GCA_020404065.1_ASM2040406v1_genomic.fna/markers.fasta
[2023-06-28 20:41:00,988] [INFO] Task started: Blastn
[2023-06-28 20:41:00,989] [INFO] Running command: blastn -query GCA_020404065.1_ASM2040406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d6cde1-a5cf-430c-bd4d-548f8fbf0d91/dqc_reference/reference_markers.fasta -out GCA_020404065.1_ASM2040406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:01,556] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:01,560] [INFO] Selected 27 target genomes.
[2023-06-28 20:41:01,560] [INFO] Target genome list was writen to GCA_020404065.1_ASM2040406v1_genomic.fna/target_genomes.txt
[2023-06-28 20:41:01,561] [INFO] Task started: fastANI
[2023-06-28 20:41:01,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb49bcd-4ad7-4d81-b0d6-3a01437e7a18/GCA_020404065.1_ASM2040406v1_genomic.fna.gz --refList GCA_020404065.1_ASM2040406v1_genomic.fna/target_genomes.txt --output GCA_020404065.1_ASM2040406v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:41:18,334] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:18,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46d6cde1-a5cf-430c-bd4d-548f8fbf0d91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:41:18,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46d6cde1-a5cf-430c-bd4d-548f8fbf0d91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:41:18,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:41:18,340] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 20:41:18,340] [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 20:41:18,342] [INFO] DFAST Taxonomy check result was written to GCA_020404065.1_ASM2040406v1_genomic.fna/tc_result.tsv
[2023-06-28 20:41:18,343] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:41:18,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:41:18,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46d6cde1-a5cf-430c-bd4d-548f8fbf0d91/dqc_reference/checkm_data
[2023-06-28 20:41:18,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:41:18,394] [INFO] Task started: CheckM
[2023-06-28 20:41:18,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020404065.1_ASM2040406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020404065.1_ASM2040406v1_genomic.fna/checkm_input GCA_020404065.1_ASM2040406v1_genomic.fna/checkm_result
[2023-06-28 20:41:52,854] [INFO] Task succeeded: CheckM
[2023-06-28 20:41:52,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:41:52,880] [INFO] ===== Completeness check finished =====
[2023-06-28 20:41:52,880] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:41:52,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020404065.1_ASM2040406v1_genomic.fna/markers.fasta)
[2023-06-28 20:41:52,881] [INFO] Task started: Blastn
[2023-06-28 20:41:52,881] [INFO] Running command: blastn -query GCA_020404065.1_ASM2040406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d6cde1-a5cf-430c-bd4d-548f8fbf0d91/dqc_reference/reference_markers_gtdb.fasta -out GCA_020404065.1_ASM2040406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:53,613] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:53,618] [INFO] Selected 8 target genomes.
[2023-06-28 20:41:53,618] [INFO] Target genome list was writen to GCA_020404065.1_ASM2040406v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:41:53,620] [INFO] Task started: fastANI
[2023-06-28 20:41:53,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fb49bcd-4ad7-4d81-b0d6-3a01437e7a18/GCA_020404065.1_ASM2040406v1_genomic.fna.gz --refList GCA_020404065.1_ASM2040406v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020404065.1_ASM2040406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:42:05,775] [INFO] Task succeeded: fastANI
[2023-06-28 20:42:05,788] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:42:05,789] [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_006937785.1	s__Pseudanabaena sp006937785	91.8793	1162	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002914585.1	s__Pseudanabaena sp002914585	89.5555	1144	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584665.1	s__Pseudanabaena sp016584665	88.3286	1125	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249035.1	s__Pseudanabaena sp003249035	85.6266	961	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696925.1	s__Pseudanabaena sp014696925	84.4072	1089	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251945.1	s__Pseudanabaena sp002251945	84.1229	1042	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242085.1	s__Pseudanabaena frigida	80.8821	883	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696355.1	s__Pseudanabaena sp014696355	80.3454	756	1514	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:42:05,791] [INFO] GTDB search result was written to GCA_020404065.1_ASM2040406v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:42:05,792] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:42:05,795] [INFO] DFAST_QC result json was written to GCA_020404065.1_ASM2040406v1_genomic.fna/dqc_result.json
[2023-06-28 20:42:05,795] [INFO] DFAST_QC completed!
[2023-06-28 20:42:05,796] [INFO] Total running time: 0h1m16s