[2023-03-18 02:27:59,066] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:59,066] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:59,066] [INFO] DQC Reference Directory: /var/lib/cwl/stgc306f23d-5363-4888-9750-494c32b196d5/dqc_reference
[2023-03-18 02:28:00,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:28:00,157] [INFO] Task started: Prodigal
[2023-03-18 02:28:00,157] [INFO] Running command: cat /var/lib/cwl/stgee0a3efb-b9e1-44fc-a5ff-b8935a328d25/OceanDNA-b37297.fa | prodigal -d OceanDNA-b37297/cds.fna -a OceanDNA-b37297/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:08,229] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:08,230] [INFO] Task started: HMMsearch
[2023-03-18 02:28:08,230] [INFO] Running command: hmmsearch --tblout OceanDNA-b37297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc306f23d-5363-4888-9750-494c32b196d5/dqc_reference/reference_markers.hmm OceanDNA-b37297/protein.faa > /dev/null
[2023-03-18 02:28:08,407] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:08,407] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgee0a3efb-b9e1-44fc-a5ff-b8935a328d25/OceanDNA-b37297.fa]
[2023-03-18 02:28:08,421] [INFO] Query marker FASTA was written to OceanDNA-b37297/markers.fasta
[2023-03-18 02:28:08,422] [INFO] Task started: Blastn
[2023-03-18 02:28:08,422] [INFO] Running command: blastn -query OceanDNA-b37297/markers.fasta -db /var/lib/cwl/stgc306f23d-5363-4888-9750-494c32b196d5/dqc_reference/reference_markers.fasta -out OceanDNA-b37297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:08,932] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:08,932] [INFO] Selected 18 target genomes.
[2023-03-18 02:28:08,933] [INFO] Target genome list was writen to OceanDNA-b37297/target_genomes.txt
[2023-03-18 02:28:08,942] [INFO] Task started: fastANI
[2023-03-18 02:28:08,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgee0a3efb-b9e1-44fc-a5ff-b8935a328d25/OceanDNA-b37297.fa --refList OceanDNA-b37297/target_genomes.txt --output OceanDNA-b37297/fastani_result.tsv --threads 1
[2023-03-18 02:28:20,428] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:20,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc306f23d-5363-4888-9750-494c32b196d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:20,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc306f23d-5363-4888-9750-494c32b196d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:20,429] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:20,429] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:28:20,429] [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 02:28:20,429] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37297/tc_result.tsv
[2023-03-18 02:28:20,429] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:20,430] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:20,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc306f23d-5363-4888-9750-494c32b196d5/dqc_reference/checkm_data
[2023-03-18 02:28:20,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:20,436] [INFO] Task started: CheckM
[2023-03-18 02:28:20,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37297/checkm_input OceanDNA-b37297/checkm_result
[2023-03-18 02:28:46,098] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:46,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.85%
Contamintation: 6.02%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 02:28:46,101] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:46,101] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:46,101] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37297/markers.fasta)
[2023-03-18 02:28:46,101] [INFO] Task started: Blastn
[2023-03-18 02:28:46,101] [INFO] Running command: blastn -query OceanDNA-b37297/markers.fasta -db /var/lib/cwl/stgc306f23d-5363-4888-9750-494c32b196d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:46,846] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:46,846] [INFO] Selected 12 target genomes.
[2023-03-18 02:28:46,847] [INFO] Target genome list was writen to OceanDNA-b37297/target_genomes_gtdb.txt
[2023-03-18 02:28:46,860] [INFO] Task started: fastANI
[2023-03-18 02:28:46,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgee0a3efb-b9e1-44fc-a5ff-b8935a328d25/OceanDNA-b37297.fa --refList OceanDNA-b37297/target_genomes_gtdb.txt --output OceanDNA-b37297/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:55,094] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:55,098] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:28:55,098] [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_012961165.1	s__UBA9659 sp012961165	88.138	322	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.55	99.55	0.89	0.89	2	-
GCA_018665025.1	s__UBA9659 sp018665025	87.0812	309	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	-
GCA_018645845.1	s__UBA9659 sp018645845	86.4013	287	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	98.73	98.60	0.77	0.73	4	-
GCA_018667205.1	s__UBA9659 sp018667205	79.8575	186	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607685.1	s__UBA9659 sp018607685	79.3726	184	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:55,098] [INFO] GTDB search result was written to OceanDNA-b37297/result_gtdb.tsv
[2023-03-18 02:28:55,098] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:55,099] [INFO] DFAST_QC result json was written to OceanDNA-b37297/dqc_result.json
[2023-03-18 02:28:55,099] [INFO] DFAST_QC completed!
[2023-03-18 02:28:55,099] [INFO] Total running time: 0h0m56s