[2023-06-30 09:06:25,048] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:06:25,050] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:06:25,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg12c34ca4-9ed7-47c8-b827-b4d3245ce617/dqc_reference
[2023-06-30 09:06:26,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:06:26,253] [INFO] Task started: Prodigal
[2023-06-30 09:06:26,253] [INFO] Running command: gunzip -c /var/lib/cwl/stga55b815e-4b5b-4959-bcd0-d7b2414fa20f/GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna.gz | prodigal -d GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/cds.fna -a GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:06:33,539] [INFO] Task succeeded: Prodigal
[2023-06-30 09:06:33,539] [INFO] Task started: HMMsearch
[2023-06-30 09:06:33,540] [INFO] Running command: hmmsearch --tblout GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12c34ca4-9ed7-47c8-b827-b4d3245ce617/dqc_reference/reference_markers.hmm GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:06:33,745] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:06:33,746] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga55b815e-4b5b-4959-bcd0-d7b2414fa20f/GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna.gz]
[2023-06-30 09:06:33,771] [INFO] Query marker FASTA was written to GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/markers.fasta
[2023-06-30 09:06:33,771] [INFO] Task started: Blastn
[2023-06-30 09:06:33,772] [INFO] Running command: blastn -query GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c34ca4-9ed7-47c8-b827-b4d3245ce617/dqc_reference/reference_markers.fasta -out GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:06:34,264] [INFO] Task succeeded: Blastn
[2023-06-30 09:06:34,269] [INFO] Selected 15 target genomes.
[2023-06-30 09:06:34,270] [INFO] Target genome list was writen to GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/target_genomes.txt
[2023-06-30 09:06:34,273] [INFO] Task started: fastANI
[2023-06-30 09:06:34,274] [INFO] Running command: fastANI --query /var/lib/cwl/stga55b815e-4b5b-4959-bcd0-d7b2414fa20f/GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna.gz --refList GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/target_genomes.txt --output GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:06:42,758] [INFO] Task succeeded: fastANI
[2023-06-30 09:06:42,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12c34ca4-9ed7-47c8-b827-b4d3245ce617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:06:42,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12c34ca4-9ed7-47c8-b827-b4d3245ce617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:06:42,762] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:06:42,762] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 09:06:42,762] [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 09:06:42,764] [INFO] DFAST Taxonomy check result was written to GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/tc_result.tsv
[2023-06-30 09:06:42,765] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:06:42,766] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:06:42,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12c34ca4-9ed7-47c8-b827-b4d3245ce617/dqc_reference/checkm_data
[2023-06-30 09:06:42,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:06:42,797] [INFO] Task started: CheckM
[2023-06-30 09:06:42,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/checkm_input GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/checkm_result
[2023-06-30 09:07:09,554] [INFO] Task succeeded: CheckM
[2023-06-30 09:07:09,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.37%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:07:09,579] [INFO] ===== Completeness check finished =====
[2023-06-30 09:07:09,579] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:07:09,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/markers.fasta)
[2023-06-30 09:07:09,580] [INFO] Task started: Blastn
[2023-06-30 09:07:09,580] [INFO] Running command: blastn -query GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c34ca4-9ed7-47c8-b827-b4d3245ce617/dqc_reference/reference_markers_gtdb.fasta -out GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:07:10,005] [INFO] Task succeeded: Blastn
[2023-06-30 09:07:10,010] [INFO] Selected 12 target genomes.
[2023-06-30 09:07:10,010] [INFO] Target genome list was writen to GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:07:10,016] [INFO] Task started: fastANI
[2023-06-30 09:07:10,016] [INFO] Running command: fastANI --query /var/lib/cwl/stga55b815e-4b5b-4959-bcd0-d7b2414fa20f/GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna.gz --refList GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/target_genomes_gtdb.txt --output GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:07:16,608] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:16,614] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 09:07:16,615] [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_014190515.1	s__BJGN01 sp014190515	93.9858	163	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__BJGN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858735.1	s__BJGN01 sp017858735	92.8851	180	194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__BJGN01	95.0	99.65	99.65	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-30 09:07:16,617] [INFO] GTDB search result was written to GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/result_gtdb.tsv
[2023-06-30 09:07:16,618] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:07:16,621] [INFO] DFAST_QC result json was written to GCA_903953115.1_freshwater_MAG_---_Loc090402-8-9m_bin-0910_genomic.fna/dqc_result.json
[2023-06-30 09:07:16,621] [INFO] DFAST_QC completed!
[2023-06-30 09:07:16,621] [INFO] Total running time: 0h0m52s