[2023-06-30 10:58:47,067] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:58:47,071] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:58:47,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cd90364-1ada-4341-8b21-b556cdd0cec8/dqc_reference
[2023-06-30 10:58:48,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:58:48,540] [INFO] Task started: Prodigal
[2023-06-30 10:58:48,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg53c08a20-36ac-4582-bcac-ae94c420958a/GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna.gz | prodigal -d GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/cds.fna -a GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:58:50,779] [INFO] Task succeeded: Prodigal
[2023-06-30 10:58:50,780] [INFO] Task started: HMMsearch
[2023-06-30 10:58:50,780] [INFO] Running command: hmmsearch --tblout GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cd90364-1ada-4341-8b21-b556cdd0cec8/dqc_reference/reference_markers.hmm GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:58:50,938] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:58:50,940] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg53c08a20-36ac-4582-bcac-ae94c420958a/GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna.gz]
[2023-06-30 10:58:50,961] [INFO] Query marker FASTA was written to GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/markers.fasta
[2023-06-30 10:58:50,962] [INFO] Task started: Blastn
[2023-06-30 10:58:50,962] [INFO] Running command: blastn -query GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd90364-1ada-4341-8b21-b556cdd0cec8/dqc_reference/reference_markers.fasta -out GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:58:51,500] [INFO] Task succeeded: Blastn
[2023-06-30 10:58:51,504] [INFO] Selected 5 target genomes.
[2023-06-30 10:58:51,505] [INFO] Target genome list was writen to GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/target_genomes.txt
[2023-06-30 10:58:51,527] [INFO] Task started: fastANI
[2023-06-30 10:58:51,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg53c08a20-36ac-4582-bcac-ae94c420958a/GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna.gz --refList GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/target_genomes.txt --output GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:58:53,718] [INFO] Task succeeded: fastANI
[2023-06-30 10:58:53,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cd90364-1ada-4341-8b21-b556cdd0cec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:58:53,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cd90364-1ada-4341-8b21-b556cdd0cec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:58:53,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:58:53,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:58:53,721] [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
--------------------------------------------------------------------------------
[2023-06-30 10:58:53,724] [INFO] DFAST Taxonomy check result was written to GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/tc_result.tsv
[2023-06-30 10:58:53,724] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:58:53,725] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:58:53,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cd90364-1ada-4341-8b21-b556cdd0cec8/dqc_reference/checkm_data
[2023-06-30 10:58:53,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:58:53,751] [INFO] Task started: CheckM
[2023-06-30 10:58:53,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/checkm_input GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/checkm_result
[2023-06-30 10:59:08,622] [INFO] Task succeeded: CheckM
[2023-06-30 10:59:08,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:59:08,646] [INFO] ===== Completeness check finished =====
[2023-06-30 10:59:08,646] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:59:08,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/markers.fasta)
[2023-06-30 10:59:08,647] [INFO] Task started: Blastn
[2023-06-30 10:59:08,647] [INFO] Running command: blastn -query GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cd90364-1ada-4341-8b21-b556cdd0cec8/dqc_reference/reference_markers_gtdb.fasta -out GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:59:09,269] [INFO] Task succeeded: Blastn
[2023-06-30 10:59:09,274] [INFO] Selected 9 target genomes.
[2023-06-30 10:59:09,274] [INFO] Target genome list was writen to GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:59:09,279] [INFO] Task started: fastANI
[2023-06-30 10:59:09,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg53c08a20-36ac-4582-bcac-ae94c420958a/GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna.gz --refList GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/target_genomes_gtdb.txt --output GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:59:12,288] [INFO] Task succeeded: fastANI
[2023-06-30 10:59:12,291] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:59:12,292] [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_009699875.1	s__CAIUMH01 sp009699875	98.1559	69	73	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__CAIUMH01	95.0	99.42	98.25	0.97	0.96	4	conclusive
--------------------------------------------------------------------------------
[2023-06-30 10:59:12,294] [INFO] GTDB search result was written to GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/result_gtdb.tsv
[2023-06-30 10:59:12,294] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:59:12,297] [INFO] DFAST_QC result json was written to GCA_903877855.1_freshwater_MAG_---_KR3_bin-0622_genomic.fna/dqc_result.json
[2023-06-30 10:59:12,297] [INFO] DFAST_QC completed!
[2023-06-30 10:59:12,297] [INFO] Total running time: 0h0m25s