[2023-03-16 16:43:21,350] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:43:21,350] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:43:21,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg4aa3aa87-8bf5-4805-8ef5-c1a47cd289d8/dqc_reference
[2023-03-16 16:43:22,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:43:22,503] [INFO] Task started: Prodigal
[2023-03-16 16:43:22,504] [INFO] Running command: cat /var/lib/cwl/stg8f5b50b1-aa6c-41be-8945-d3e08790c96b/OceanDNA-b42706.fa | prodigal -d OceanDNA-b42706/cds.fna -a OceanDNA-b42706/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:43:28,640] [INFO] Task succeeded: Prodigal
[2023-03-16 16:43:28,640] [INFO] Task started: HMMsearch
[2023-03-16 16:43:28,640] [INFO] Running command: hmmsearch --tblout OceanDNA-b42706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4aa3aa87-8bf5-4805-8ef5-c1a47cd289d8/dqc_reference/reference_markers.hmm OceanDNA-b42706/protein.faa > /dev/null
[2023-03-16 16:43:28,897] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:43:28,898] [INFO] Found 6/6 markers.
[2023-03-16 16:43:28,907] [INFO] Query marker FASTA was written to OceanDNA-b42706/markers.fasta
[2023-03-16 16:43:28,908] [INFO] Task started: Blastn
[2023-03-16 16:43:28,909] [INFO] Running command: blastn -query OceanDNA-b42706/markers.fasta -db /var/lib/cwl/stg4aa3aa87-8bf5-4805-8ef5-c1a47cd289d8/dqc_reference/reference_markers.fasta -out OceanDNA-b42706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:43:29,666] [INFO] Task succeeded: Blastn
[2023-03-16 16:43:29,667] [INFO] Selected 16 target genomes.
[2023-03-16 16:43:29,667] [INFO] Target genome list was writen to OceanDNA-b42706/target_genomes.txt
[2023-03-16 16:43:29,677] [INFO] Task started: fastANI
[2023-03-16 16:43:29,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f5b50b1-aa6c-41be-8945-d3e08790c96b/OceanDNA-b42706.fa --refList OceanDNA-b42706/target_genomes.txt --output OceanDNA-b42706/fastani_result.tsv --threads 1
[2023-03-16 16:43:39,433] [INFO] Task succeeded: fastANI
[2023-03-16 16:43:39,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4aa3aa87-8bf5-4805-8ef5-c1a47cd289d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:43:39,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4aa3aa87-8bf5-4805-8ef5-c1a47cd289d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:43:39,434] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:43:39,434] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:43:39,435] [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
--------------------------------------------------------------------------------
[2023-03-16 16:43:39,435] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42706/tc_result.tsv
[2023-03-16 16:43:39,435] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:43:39,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:43:39,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4aa3aa87-8bf5-4805-8ef5-c1a47cd289d8/dqc_reference/checkm_data
[2023-03-16 16:43:39,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:43:39,451] [INFO] Task started: CheckM
[2023-03-16 16:43:39,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42706/checkm_input OceanDNA-b42706/checkm_result
[2023-03-16 16:44:08,948] [INFO] Task succeeded: CheckM
[2023-03-16 16:44:08,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 16:44:08,952] [INFO] ===== Completeness check finished =====
[2023-03-16 16:44:08,952] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:44:08,952] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42706/markers.fasta)
[2023-03-16 16:44:08,953] [INFO] Task started: Blastn
[2023-03-16 16:44:08,954] [INFO] Running command: blastn -query OceanDNA-b42706/markers.fasta -db /var/lib/cwl/stg4aa3aa87-8bf5-4805-8ef5-c1a47cd289d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:44:09,795] [INFO] Task succeeded: Blastn
[2023-03-16 16:44:09,797] [INFO] Selected 21 target genomes.
[2023-03-16 16:44:09,797] [INFO] Target genome list was writen to OceanDNA-b42706/target_genomes_gtdb.txt
[2023-03-16 16:44:09,876] [INFO] Task started: fastANI
[2023-03-16 16:44:09,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f5b50b1-aa6c-41be-8945-d3e08790c96b/OceanDNA-b42706.fa --refList OceanDNA-b42706/target_genomes_gtdb.txt --output OceanDNA-b42706/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:44:13,629] [INFO] Task succeeded: fastANI
[2023-03-16 16:44:13,633] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:44:13,633] [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_902610995.1	s__TMED112 sp902610995	95.7788	252	355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	98.48	96.99	0.80	0.72	6	conclusive
GCA_002716745.1	s__TMED112 sp002716745	79.045	186	355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.67	96.57	0.91	0.90	3	-
GCA_016779525.1	s__TMED112 sp016779525	76.8295	50	355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	98.73	98.73	0.85	0.85	2	-
GCA_003331605.1	s__TMED112 sp003331605	76.6011	61	355	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:44:13,635] [INFO] GTDB search result was written to OceanDNA-b42706/result_gtdb.tsv
[2023-03-16 16:44:13,635] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:44:13,637] [INFO] DFAST_QC result json was written to OceanDNA-b42706/dqc_result.json
[2023-03-16 16:44:13,637] [INFO] DFAST_QC completed!
[2023-03-16 16:44:13,637] [INFO] Total running time: 0h0m52s