[2023-03-14 11:33:34,910] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,910] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fc324dd-c70b-4a3b-b6df-590dcd102b44/dqc_reference
[2023-03-14 11:33:36,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,302] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,302] [INFO] Running command: cat /var/lib/cwl/stga714ba1a-8c7c-4ee0-9694-d6e763994a0a/OceanDNA-b15291.fa | prodigal -d OceanDNA-b15291/cds.fna -a OceanDNA-b15291/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:42,295] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:42,296] [INFO] Task started: HMMsearch
[2023-03-14 11:33:42,296] [INFO] Running command: hmmsearch --tblout OceanDNA-b15291/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fc324dd-c70b-4a3b-b6df-590dcd102b44/dqc_reference/reference_markers.hmm OceanDNA-b15291/protein.faa > /dev/null
[2023-03-14 11:33:42,497] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:42,498] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga714ba1a-8c7c-4ee0-9694-d6e763994a0a/OceanDNA-b15291.fa]
[2023-03-14 11:33:42,506] [INFO] Query marker FASTA was written to OceanDNA-b15291/markers.fasta
[2023-03-14 11:33:42,506] [INFO] Task started: Blastn
[2023-03-14 11:33:42,506] [INFO] Running command: blastn -query OceanDNA-b15291/markers.fasta -db /var/lib/cwl/stg1fc324dd-c70b-4a3b-b6df-590dcd102b44/dqc_reference/reference_markers.fasta -out OceanDNA-b15291/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:43,055] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:43,056] [INFO] Selected 3 target genomes.
[2023-03-14 11:33:43,056] [INFO] Target genome list was writen to OceanDNA-b15291/target_genomes.txt
[2023-03-14 11:33:43,058] [INFO] Task started: fastANI
[2023-03-14 11:33:43,058] [INFO] Running command: fastANI --query /var/lib/cwl/stga714ba1a-8c7c-4ee0-9694-d6e763994a0a/OceanDNA-b15291.fa --refList OceanDNA-b15291/target_genomes.txt --output OceanDNA-b15291/fastani_result.tsv --threads 1
[2023-03-14 11:33:45,271] [INFO] Task succeeded: fastANI
[2023-03-14 11:33:45,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fc324dd-c70b-4a3b-b6df-590dcd102b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:33:45,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fc324dd-c70b-4a3b-b6df-590dcd102b44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:33:45,271] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:33:45,271] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:33:45,271] [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
--------------------------------------------------------------------------------
[2023-03-14 11:33:45,272] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15291/tc_result.tsv
[2023-03-14 11:33:45,272] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:33:45,272] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:33:45,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fc324dd-c70b-4a3b-b6df-590dcd102b44/dqc_reference/checkm_data
[2023-03-14 11:33:45,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:33:45,277] [INFO] Task started: CheckM
[2023-03-14 11:33:45,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15291/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15291/checkm_input OceanDNA-b15291/checkm_result
[2023-03-14 11:34:06,025] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:06,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:06,027] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:06,027] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:06,027] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15291/markers.fasta)
[2023-03-14 11:34:06,028] [INFO] Task started: Blastn
[2023-03-14 11:34:06,028] [INFO] Running command: blastn -query OceanDNA-b15291/markers.fasta -db /var/lib/cwl/stg1fc324dd-c70b-4a3b-b6df-590dcd102b44/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15291/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:06,680] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:06,681] [INFO] Selected 16 target genomes.
[2023-03-14 11:34:06,681] [INFO] Target genome list was writen to OceanDNA-b15291/target_genomes_gtdb.txt
[2023-03-14 11:34:06,721] [INFO] Task started: fastANI
[2023-03-14 11:34:06,721] [INFO] Running command: fastANI --query /var/lib/cwl/stga714ba1a-8c7c-4ee0-9694-d6e763994a0a/OceanDNA-b15291.fa --refList OceanDNA-b15291/target_genomes_gtdb.txt --output OceanDNA-b15291/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:34:13,504] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:13,506] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:34:13,506] [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_002717805.1	s__UBA2985 sp002717805	99.2817	334	370	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2985;f__UBA2985;g__UBA2985	95.0	99.39	99.38	0.91	0.86	3	conclusive
--------------------------------------------------------------------------------
[2023-03-14 11:34:13,506] [INFO] GTDB search result was written to OceanDNA-b15291/result_gtdb.tsv
[2023-03-14 11:34:13,507] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:34:13,507] [INFO] DFAST_QC result json was written to OceanDNA-b15291/dqc_result.json
[2023-03-14 11:34:13,507] [INFO] DFAST_QC completed!
[2023-03-14 11:34:13,507] [INFO] Total running time: 0h0m39s