[2023-03-18 09:41:07,186] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,186] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,186] [INFO] DQC Reference Directory: /var/lib/cwl/stg89744027-f6b2-470c-8e0d-8b602a40780b/dqc_reference
[2023-03-18 09:41:08,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,271] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,271] [INFO] Running command: cat /var/lib/cwl/stgeaa3c6b6-260d-4cda-b77a-69734a98cceb/OceanDNA-b35572.fa | prodigal -d OceanDNA-b35572/cds.fna -a OceanDNA-b35572/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:13,164] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:13,164] [INFO] Task started: HMMsearch
[2023-03-18 09:41:13,164] [INFO] Running command: hmmsearch --tblout OceanDNA-b35572/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89744027-f6b2-470c-8e0d-8b602a40780b/dqc_reference/reference_markers.hmm OceanDNA-b35572/protein.faa > /dev/null
[2023-03-18 09:41:13,349] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:13,350] [INFO] Found 6/6 markers.
[2023-03-18 09:41:13,357] [INFO] Query marker FASTA was written to OceanDNA-b35572/markers.fasta
[2023-03-18 09:41:13,357] [INFO] Task started: Blastn
[2023-03-18 09:41:13,358] [INFO] Running command: blastn -query OceanDNA-b35572/markers.fasta -db /var/lib/cwl/stg89744027-f6b2-470c-8e0d-8b602a40780b/dqc_reference/reference_markers.fasta -out OceanDNA-b35572/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:13,908] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:13,909] [INFO] Selected 19 target genomes.
[2023-03-18 09:41:13,909] [INFO] Target genome list was writen to OceanDNA-b35572/target_genomes.txt
[2023-03-18 09:41:13,921] [INFO] Task started: fastANI
[2023-03-18 09:41:13,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa3c6b6-260d-4cda-b77a-69734a98cceb/OceanDNA-b35572.fa --refList OceanDNA-b35572/target_genomes.txt --output OceanDNA-b35572/fastani_result.tsv --threads 1
[2023-03-18 09:41:22,627] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:22,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89744027-f6b2-470c-8e0d-8b602a40780b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:22,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89744027-f6b2-470c-8e0d-8b602a40780b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:22,628] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:22,628] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:22,628] [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
--------------------------------------------------------------------------------
[2023-03-18 09:41:22,628] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35572/tc_result.tsv
[2023-03-18 09:41:22,629] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:22,629] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:22,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89744027-f6b2-470c-8e0d-8b602a40780b/dqc_reference/checkm_data
[2023-03-18 09:41:22,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:22,634] [INFO] Task started: CheckM
[2023-03-18 09:41:22,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35572/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35572/checkm_input OceanDNA-b35572/checkm_result
[2023-03-18 09:41:40,550] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:40,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:41:40,552] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:40,552] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:40,552] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35572/markers.fasta)
[2023-03-18 09:41:40,552] [INFO] Task started: Blastn
[2023-03-18 09:41:40,552] [INFO] Running command: blastn -query OceanDNA-b35572/markers.fasta -db /var/lib/cwl/stg89744027-f6b2-470c-8e0d-8b602a40780b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35572/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:41,451] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:41,452] [INFO] Selected 27 target genomes.
[2023-03-18 09:41:41,452] [INFO] Target genome list was writen to OceanDNA-b35572/target_genomes_gtdb.txt
[2023-03-18 09:41:41,479] [INFO] Task started: fastANI
[2023-03-18 09:41:41,479] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaa3c6b6-260d-4cda-b77a-69734a98cceb/OceanDNA-b35572.fa --refList OceanDNA-b35572/target_genomes_gtdb.txt --output OceanDNA-b35572/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:41:47,240] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:47,244] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:41:47,244] [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_018667355.1	s__GCA-2698665 sp018667355	77.6227	105	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	99.95	99.92	0.96	0.95	8	-
GCA_905479195.1	s__GCA-2698665 sp905479195	77.6042	116	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718845.1	s__GCA-2718845 sp002718845	77.0341	62	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2718845	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698665.1	s__GCA-2698665 sp002698665	76.7586	88	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2698665	95.0	98.38	98.38	0.83	0.83	2	-
GCA_002716945.1	s__GCA-2716945 sp002716945	76.5326	56	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002716945;g__GCA-2716945	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:41:47,245] [INFO] GTDB search result was written to OceanDNA-b35572/result_gtdb.tsv
[2023-03-18 09:41:47,245] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:41:47,245] [INFO] DFAST_QC result json was written to OceanDNA-b35572/dqc_result.json
[2023-03-18 09:41:47,246] [INFO] DFAST_QC completed!
[2023-03-18 09:41:47,246] [INFO] Total running time: 0h0m40s