[2023-03-17 02:31:12,846] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,846] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f302acf-78a1-4bce-ba7f-dac5ba4f9c5e/dqc_reference
[2023-03-17 02:31:14,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stgb49c6a42-93e4-4159-946c-5e807fa922a3/OceanDNA-b209.fa | prodigal -d OceanDNA-b209/cds.fna -a OceanDNA-b209/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:31,312] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:31,313] [INFO] Task started: HMMsearch
[2023-03-17 02:31:31,313] [INFO] Running command: hmmsearch --tblout OceanDNA-b209/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f302acf-78a1-4bce-ba7f-dac5ba4f9c5e/dqc_reference/reference_markers.hmm OceanDNA-b209/protein.faa > /dev/null
[2023-03-17 02:31:31,493] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:31,494] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb49c6a42-93e4-4159-946c-5e807fa922a3/OceanDNA-b209.fa]
[2023-03-17 02:31:31,512] [INFO] Query marker FASTA was written to OceanDNA-b209/markers.fasta
[2023-03-17 02:31:31,512] [INFO] Task started: Blastn
[2023-03-17 02:31:31,512] [INFO] Running command: blastn -query OceanDNA-b209/markers.fasta -db /var/lib/cwl/stg5f302acf-78a1-4bce-ba7f-dac5ba4f9c5e/dqc_reference/reference_markers.fasta -out OceanDNA-b209/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:32,079] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:32,080] [INFO] Selected 30 target genomes.
[2023-03-17 02:31:32,080] [INFO] Target genome list was writen to OceanDNA-b209/target_genomes.txt
[2023-03-17 02:31:32,099] [INFO] Task started: fastANI
[2023-03-17 02:31:32,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgb49c6a42-93e4-4159-946c-5e807fa922a3/OceanDNA-b209.fa --refList OceanDNA-b209/target_genomes.txt --output OceanDNA-b209/fastani_result.tsv --threads 1
[2023-03-17 02:31:54,792] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:54,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f302acf-78a1-4bce-ba7f-dac5ba4f9c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:54,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f302acf-78a1-4bce-ba7f-dac5ba4f9c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:54,793] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:54,793] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:54,793] [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 02:31:54,793] [INFO] DFAST Taxonomy check result was written to OceanDNA-b209/tc_result.tsv
[2023-03-17 02:31:54,793] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:54,793] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:54,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f302acf-78a1-4bce-ba7f-dac5ba4f9c5e/dqc_reference/checkm_data
[2023-03-17 02:31:54,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:54,840] [INFO] Task started: CheckM
[2023-03-17 02:31:54,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b209/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b209/checkm_input OceanDNA-b209/checkm_result
[2023-03-17 02:32:38,683] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:38,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:38,686] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:38,686] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:38,686] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b209/markers.fasta)
[2023-03-17 02:32:38,687] [INFO] Task started: Blastn
[2023-03-17 02:32:38,687] [INFO] Running command: blastn -query OceanDNA-b209/markers.fasta -db /var/lib/cwl/stg5f302acf-78a1-4bce-ba7f-dac5ba4f9c5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b209/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:39,595] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:39,596] [INFO] Selected 23 target genomes.
[2023-03-17 02:32:39,596] [INFO] Target genome list was writen to OceanDNA-b209/target_genomes_gtdb.txt
[2023-03-17 02:32:40,304] [INFO] Task started: fastANI
[2023-03-17 02:32:40,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgb49c6a42-93e4-4159-946c-5e807fa922a3/OceanDNA-b209.fa --refList OceanDNA-b209/target_genomes_gtdb.txt --output OceanDNA-b209/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:55,240] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:55,245] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:32:55,245] [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_011523845.1	s__WTFV01 sp011523845	76.1955	183	914	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838525.1	s__VXRJ01 sp009838525	76.1562	136	914	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__VXRJ01	95.0	98.98	98.07	0.95	0.93	4	-
GCA_009861545.1	s__WTFV01 sp009861545	76.1498	177	914	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_002726085.1	s__NP936 sp002726085	76.0282	85	914	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__NP936	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012271165.1	s__JAAXGX01 sp012271165	76.0207	84	914	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523485.1	s__WTFV01 sp011523485	75.9581	86	914	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:55,245] [INFO] GTDB search result was written to OceanDNA-b209/result_gtdb.tsv
[2023-03-17 02:32:55,245] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:55,246] [INFO] DFAST_QC result json was written to OceanDNA-b209/dqc_result.json
[2023-03-17 02:32:55,246] [INFO] DFAST_QC completed!
[2023-03-17 02:32:55,246] [INFO] Total running time: 0h1m42s