[2023-03-18 04:39:40,278] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:39:40,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:39:40,278] [INFO] DQC Reference Directory: /var/lib/cwl/stgec82f51b-794c-41d1-b6e4-37cdec0c80e0/dqc_reference
[2023-03-18 04:39:41,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:39:41,416] [INFO] Task started: Prodigal
[2023-03-18 04:39:41,416] [INFO] Running command: cat /var/lib/cwl/stgafe27d24-eeae-4da8-b219-f389ec0e2256/OceanDNA-b37440.fa | prodigal -d OceanDNA-b37440/cds.fna -a OceanDNA-b37440/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:39:51,394] [INFO] Task succeeded: Prodigal
[2023-03-18 04:39:51,395] [INFO] Task started: HMMsearch
[2023-03-18 04:39:51,395] [INFO] Running command: hmmsearch --tblout OceanDNA-b37440/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec82f51b-794c-41d1-b6e4-37cdec0c80e0/dqc_reference/reference_markers.hmm OceanDNA-b37440/protein.faa > /dev/null
[2023-03-18 04:39:51,562] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:39:51,562] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgafe27d24-eeae-4da8-b219-f389ec0e2256/OceanDNA-b37440.fa]
[2023-03-18 04:39:51,578] [INFO] Query marker FASTA was written to OceanDNA-b37440/markers.fasta
[2023-03-18 04:39:51,578] [INFO] Task started: Blastn
[2023-03-18 04:39:51,578] [INFO] Running command: blastn -query OceanDNA-b37440/markers.fasta -db /var/lib/cwl/stgec82f51b-794c-41d1-b6e4-37cdec0c80e0/dqc_reference/reference_markers.fasta -out OceanDNA-b37440/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:52,134] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:52,135] [INFO] Selected 27 target genomes.
[2023-03-18 04:39:52,135] [INFO] Target genome list was writen to OceanDNA-b37440/target_genomes.txt
[2023-03-18 04:39:52,148] [INFO] Task started: fastANI
[2023-03-18 04:39:52,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe27d24-eeae-4da8-b219-f389ec0e2256/OceanDNA-b37440.fa --refList OceanDNA-b37440/target_genomes.txt --output OceanDNA-b37440/fastani_result.tsv --threads 1
[2023-03-18 04:40:08,698] [INFO] Task succeeded: fastANI
[2023-03-18 04:40:08,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec82f51b-794c-41d1-b6e4-37cdec0c80e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:40:08,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec82f51b-794c-41d1-b6e4-37cdec0c80e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:40:08,699] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:40:08,699] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:40:08,699] [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 04:40:08,699] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37440/tc_result.tsv
[2023-03-18 04:40:08,699] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:40:08,699] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:40:08,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec82f51b-794c-41d1-b6e4-37cdec0c80e0/dqc_reference/checkm_data
[2023-03-18 04:40:08,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:40:08,705] [INFO] Task started: CheckM
[2023-03-18 04:40:08,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37440/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37440/checkm_input OceanDNA-b37440/checkm_result
[2023-03-18 04:40:38,165] [INFO] Task succeeded: CheckM
[2023-03-18 04:40:38,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:40:38,167] [INFO] ===== Completeness check finished =====
[2023-03-18 04:40:38,167] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:40:38,167] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37440/markers.fasta)
[2023-03-18 04:40:38,168] [INFO] Task started: Blastn
[2023-03-18 04:40:38,168] [INFO] Running command: blastn -query OceanDNA-b37440/markers.fasta -db /var/lib/cwl/stgec82f51b-794c-41d1-b6e4-37cdec0c80e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37440/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:40:39,022] [INFO] Task succeeded: Blastn
[2023-03-18 04:40:39,023] [INFO] Selected 13 target genomes.
[2023-03-18 04:40:39,023] [INFO] Target genome list was writen to OceanDNA-b37440/target_genomes_gtdb.txt
[2023-03-18 04:40:39,041] [INFO] Task started: fastANI
[2023-03-18 04:40:39,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe27d24-eeae-4da8-b219-f389ec0e2256/OceanDNA-b37440.fa --refList OceanDNA-b37440/target_genomes_gtdb.txt --output OceanDNA-b37440/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:40:45,740] [INFO] Task succeeded: fastANI
[2023-03-18 04:40:45,744] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:40:45,744] [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_018645765.1	s__UBA9926 sp018645765	98.541	364	531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017854255.1	s__UBA9926 sp003451575	89.9129	475	531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.03	98.40	0.91	0.88	11	-
GCA_018647445.1	s__UBA9926 sp018647445	86.3939	413	531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.28	99.28	0.84	0.84	2	-
GCA_905182155.1	s__UBA9926 sp905182155	80.6942	278	531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:40:45,744] [INFO] GTDB search result was written to OceanDNA-b37440/result_gtdb.tsv
[2023-03-18 04:40:45,744] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:40:45,745] [INFO] DFAST_QC result json was written to OceanDNA-b37440/dqc_result.json
[2023-03-18 04:40:45,745] [INFO] DFAST_QC completed!
[2023-03-18 04:40:45,745] [INFO] Total running time: 0h1m5s