[2023-03-16 05:09:10,920] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:10,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:10,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg4695561e-765b-4d9d-8801-790c18cace64/dqc_reference
[2023-03-16 05:09:12,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:12,026] [INFO] Task started: Prodigal
[2023-03-16 05:09:12,026] [INFO] Running command: cat /var/lib/cwl/stg6c9a6d78-4227-4b22-887f-df6c0d246eed/OceanDNA-b36934.fa | prodigal -d OceanDNA-b36934/cds.fna -a OceanDNA-b36934/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:24,650] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:24,650] [INFO] Task started: HMMsearch
[2023-03-16 05:09:24,650] [INFO] Running command: hmmsearch --tblout OceanDNA-b36934/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4695561e-765b-4d9d-8801-790c18cace64/dqc_reference/reference_markers.hmm OceanDNA-b36934/protein.faa > /dev/null
[2023-03-16 05:09:24,858] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:24,858] [INFO] Found 6/6 markers.
[2023-03-16 05:09:24,876] [INFO] Query marker FASTA was written to OceanDNA-b36934/markers.fasta
[2023-03-16 05:09:24,877] [INFO] Task started: Blastn
[2023-03-16 05:09:24,877] [INFO] Running command: blastn -query OceanDNA-b36934/markers.fasta -db /var/lib/cwl/stg4695561e-765b-4d9d-8801-790c18cace64/dqc_reference/reference_markers.fasta -out OceanDNA-b36934/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:25,460] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:25,461] [INFO] Selected 38 target genomes.
[2023-03-16 05:09:25,461] [INFO] Target genome list was writen to OceanDNA-b36934/target_genomes.txt
[2023-03-16 05:09:25,484] [INFO] Task started: fastANI
[2023-03-16 05:09:25,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c9a6d78-4227-4b22-887f-df6c0d246eed/OceanDNA-b36934.fa --refList OceanDNA-b36934/target_genomes.txt --output OceanDNA-b36934/fastani_result.tsv --threads 1
[2023-03-16 05:09:47,984] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:47,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4695561e-765b-4d9d-8801-790c18cace64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:47,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4695561e-765b-4d9d-8801-790c18cace64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:47,985] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:09:47,985] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:09:47,985] [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 05:09:47,986] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36934/tc_result.tsv
[2023-03-16 05:09:47,986] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:47,986] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:47,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4695561e-765b-4d9d-8801-790c18cace64/dqc_reference/checkm_data
[2023-03-16 05:09:47,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:47,993] [INFO] Task started: CheckM
[2023-03-16 05:09:47,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36934/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36934/checkm_input OceanDNA-b36934/checkm_result
[2023-03-16 05:10:23,121] [INFO] Task succeeded: CheckM
[2023-03-16 05:10:23,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.01%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 05:10:23,125] [INFO] ===== Completeness check finished =====
[2023-03-16 05:10:23,125] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:10:23,125] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36934/markers.fasta)
[2023-03-16 05:10:23,126] [INFO] Task started: Blastn
[2023-03-16 05:10:23,127] [INFO] Running command: blastn -query OceanDNA-b36934/markers.fasta -db /var/lib/cwl/stg4695561e-765b-4d9d-8801-790c18cace64/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36934/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:10:24,083] [INFO] Task succeeded: Blastn
[2023-03-16 05:10:24,085] [INFO] Selected 17 target genomes.
[2023-03-16 05:10:24,085] [INFO] Target genome list was writen to OceanDNA-b36934/target_genomes_gtdb.txt
[2023-03-16 05:10:24,131] [INFO] Task started: fastANI
[2023-03-16 05:10:24,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c9a6d78-4227-4b22-887f-df6c0d246eed/OceanDNA-b36934.fa --refList OceanDNA-b36934/target_genomes_gtdb.txt --output OceanDNA-b36934/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:10:31,950] [INFO] Task succeeded: fastANI
[2023-03-16 05:10:31,956] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:10:31,956] [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_902528515.1	s__UBA4421 sp902528515	96.8551	417	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902613475.1	s__UBA4421 sp902613475	90.4913	350	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779425.1	s__UBA4421 sp016779425	89.0743	366	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	97.24	97.24	0.58	0.58	2	-
GCA_004213835.1	s__UBA4421 sp004213835	79.4213	237	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	97.72	97.72	0.50	0.50	2	-
GCA_002726925.1	s__UBA4421 sp002726925	79.4026	240	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.34	98.19	0.75	0.72	3	-
GCA_002731575.1	s__UBA4421 sp002731575	77.189	83	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.29	99.29	0.71	0.71	2	-
GCA_009936775.1	s__UBA4421 sp009936775	76.819	86	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704225.1	s__UBA4421 sp002704225	76.7661	109	657	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.56	99.05	0.92	0.86	4	-
--------------------------------------------------------------------------------
[2023-03-16 05:10:31,956] [INFO] GTDB search result was written to OceanDNA-b36934/result_gtdb.tsv
[2023-03-16 05:10:31,957] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:10:31,958] [INFO] DFAST_QC result json was written to OceanDNA-b36934/dqc_result.json
[2023-03-16 05:10:31,958] [INFO] DFAST_QC completed!
[2023-03-16 05:10:31,958] [INFO] Total running time: 0h1m21s