[2023-06-30 21:26:16,883] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:26:16,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:26:16,885] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b8a7d8a-8724-4317-9bed-9a2e9644f593/dqc_reference
[2023-06-30 21:26:18,790] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:26:18,791] [INFO] Task started: Prodigal
[2023-06-30 21:26:18,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg3858b782-9373-4a61-89eb-ea7965f6c1c5/GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna.gz | prodigal -d GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/cds.fna -a GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:26:20,371] [INFO] Task succeeded: Prodigal
[2023-06-30 21:26:20,371] [INFO] Task started: HMMsearch
[2023-06-30 21:26:20,371] [INFO] Running command: hmmsearch --tblout GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b8a7d8a-8724-4317-9bed-9a2e9644f593/dqc_reference/reference_markers.hmm GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:26:20,480] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:26:20,481] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3858b782-9373-4a61-89eb-ea7965f6c1c5/GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna.gz]
[2023-06-30 21:26:20,496] [INFO] Query marker FASTA was written to GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/markers.fasta
[2023-06-30 21:26:20,496] [INFO] Task started: Blastn
[2023-06-30 21:26:20,496] [INFO] Running command: blastn -query GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b8a7d8a-8724-4317-9bed-9a2e9644f593/dqc_reference/reference_markers.fasta -out GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:26:22,381] [INFO] Task succeeded: Blastn
[2023-06-30 21:26:22,385] [INFO] Selected 9 target genomes.
[2023-06-30 21:26:22,385] [INFO] Target genome list was writen to GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/target_genomes.txt
[2023-06-30 21:26:22,386] [INFO] Task started: fastANI
[2023-06-30 21:26:22,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg3858b782-9373-4a61-89eb-ea7965f6c1c5/GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna.gz --refList GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/target_genomes.txt --output GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:26:25,378] [INFO] Task succeeded: fastANI
[2023-06-30 21:26:25,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b8a7d8a-8724-4317-9bed-9a2e9644f593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:26:25,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b8a7d8a-8724-4317-9bed-9a2e9644f593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:26:25,380] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:26:25,380] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:26:25,380] [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 21:26:25,382] [INFO] DFAST Taxonomy check result was written to GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/tc_result.tsv
[2023-06-30 21:26:25,383] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:26:25,383] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:26:25,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b8a7d8a-8724-4317-9bed-9a2e9644f593/dqc_reference/checkm_data
[2023-06-30 21:26:25,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:26:25,394] [INFO] Task started: CheckM
[2023-06-30 21:26:25,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/checkm_input GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/checkm_result
[2023-06-30 21:26:38,738] [INFO] Task succeeded: CheckM
[2023-06-30 21:26:38,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:26:38,758] [INFO] ===== Completeness check finished =====
[2023-06-30 21:26:38,758] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:26:38,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/markers.fasta)
[2023-06-30 21:26:38,759] [INFO] Task started: Blastn
[2023-06-30 21:26:38,759] [INFO] Running command: blastn -query GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b8a7d8a-8724-4317-9bed-9a2e9644f593/dqc_reference/reference_markers_gtdb.fasta -out GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:26:39,365] [INFO] Task succeeded: Blastn
[2023-06-30 21:26:39,369] [INFO] Selected 10 target genomes.
[2023-06-30 21:26:39,369] [INFO] Target genome list was writen to GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:26:39,395] [INFO] Task started: fastANI
[2023-06-30 21:26:39,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg3858b782-9373-4a61-89eb-ea7965f6c1c5/GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna.gz --refList GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/target_genomes_gtdb.txt --output GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:26:41,912] [INFO] Task succeeded: fastANI
[2023-06-30 21:26:41,915] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:26:41,916] [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_903933735.1	s__CAIZLB01 sp903933735	99.8763	67	70	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__CAIZLB01;g__CAIZLB01	95.0	99.82	99.72	0.95	0.91	4	conclusive
--------------------------------------------------------------------------------
[2023-06-30 21:26:41,918] [INFO] GTDB search result was written to GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/result_gtdb.tsv
[2023-06-30 21:26:41,918] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:26:41,920] [INFO] DFAST_QC result json was written to GCA_903944065.1_freshwater_MAG_---_Loc090907-8m_bin-822_genomic.fna/dqc_result.json
[2023-06-30 21:26:41,921] [INFO] DFAST_QC completed!
[2023-06-30 21:26:41,921] [INFO] Total running time: 0h0m25s