[2023-03-17 23:54:10,799] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:54:10,800] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:54:10,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgb05ae01f-3d5b-4dfa-b3b4-769cd4706abd/dqc_reference
[2023-03-17 23:54:11,981] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:54:11,982] [INFO] Task started: Prodigal
[2023-03-17 23:54:11,982] [INFO] Running command: cat /var/lib/cwl/stgb3667ad0-9e4b-450b-aa3b-7a8b1721a903/OceanDNA-a1026.fa | prodigal -d OceanDNA-a1026/cds.fna -a OceanDNA-a1026/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:54:15,594] [INFO] Task succeeded: Prodigal
[2023-03-17 23:54:15,594] [INFO] Task started: HMMsearch
[2023-03-17 23:54:15,595] [INFO] Running command: hmmsearch --tblout OceanDNA-a1026/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb05ae01f-3d5b-4dfa-b3b4-769cd4706abd/dqc_reference/reference_markers.hmm OceanDNA-a1026/protein.faa > /dev/null
[2023-03-17 23:54:15,732] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:54:15,733] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb3667ad0-9e4b-450b-aa3b-7a8b1721a903/OceanDNA-a1026.fa]
[2023-03-17 23:54:15,748] [INFO] Query marker FASTA was written to OceanDNA-a1026/markers.fasta
[2023-03-17 23:54:15,749] [INFO] Task started: Blastn
[2023-03-17 23:54:15,749] [INFO] Running command: blastn -query OceanDNA-a1026/markers.fasta -db /var/lib/cwl/stgb05ae01f-3d5b-4dfa-b3b4-769cd4706abd/dqc_reference/reference_markers.fasta -out OceanDNA-a1026/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:54:16,276] [INFO] Task succeeded: Blastn
[2023-03-17 23:54:16,283] [INFO] Selected 5 target genomes.
[2023-03-17 23:54:16,283] [INFO] Target genome list was writen to OceanDNA-a1026/target_genomes.txt
[2023-03-17 23:54:16,286] [INFO] Task started: fastANI
[2023-03-17 23:54:16,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3667ad0-9e4b-450b-aa3b-7a8b1721a903/OceanDNA-a1026.fa --refList OceanDNA-a1026/target_genomes.txt --output OceanDNA-a1026/fastani_result.tsv --threads 1
[2023-03-17 23:54:17,525] [INFO] Task succeeded: fastANI
[2023-03-17 23:54:17,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb05ae01f-3d5b-4dfa-b3b4-769cd4706abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:54:17,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb05ae01f-3d5b-4dfa-b3b4-769cd4706abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:54:17,526] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:54:17,526] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:54:17,526] [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
--------------------------------------------------------------------------------
[2023-03-17 23:54:17,528] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1026/tc_result.tsv
[2023-03-17 23:54:17,531] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:54:17,531] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:54:17,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb05ae01f-3d5b-4dfa-b3b4-769cd4706abd/dqc_reference/checkm_data
[2023-03-17 23:54:17,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:54:17,595] [INFO] Task started: CheckM
[2023-03-17 23:54:17,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1026/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1026/checkm_input OceanDNA-a1026/checkm_result
[2023-03-17 23:54:35,178] [INFO] Task succeeded: CheckM
[2023-03-17 23:54:35,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:54:35,202] [INFO] ===== Completeness check finished =====
[2023-03-17 23:54:35,202] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:54:35,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1026/markers.fasta)
[2023-03-17 23:54:35,204] [INFO] Task started: Blastn
[2023-03-17 23:54:35,204] [INFO] Running command: blastn -query OceanDNA-a1026/markers.fasta -db /var/lib/cwl/stgb05ae01f-3d5b-4dfa-b3b4-769cd4706abd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1026/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:54:35,940] [INFO] Task succeeded: Blastn
[2023-03-17 23:54:35,944] [INFO] Selected 10 target genomes.
[2023-03-17 23:54:35,944] [INFO] Target genome list was writen to OceanDNA-a1026/target_genomes_gtdb.txt
[2023-03-17 23:54:35,953] [INFO] Task started: fastANI
[2023-03-17 23:54:35,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3667ad0-9e4b-450b-aa3b-7a8b1721a903/OceanDNA-a1026.fa --refList OceanDNA-a1026/target_genomes_gtdb.txt --output OceanDNA-a1026/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:54:37,893] [INFO] Task succeeded: fastANI
[2023-03-17 23:54:37,895] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:54:37,895] [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_018651605.1	s__JABIDS01 sp018651605	99.1131	109	129	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JABIDS01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 23:54:37,897] [INFO] GTDB search result was written to OceanDNA-a1026/result_gtdb.tsv
[2023-03-17 23:54:37,898] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:54:37,900] [INFO] DFAST_QC result json was written to OceanDNA-a1026/dqc_result.json
[2023-03-17 23:54:37,900] [INFO] DFAST_QC completed!
[2023-03-17 23:54:37,900] [INFO] Total running time: 0h0m27s