[2023-03-15 15:06:33,802] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:06:33,802] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:06:33,802] [INFO] DQC Reference Directory: /var/lib/cwl/stgb83093b0-49bd-4404-a9bd-160657d81656/dqc_reference
[2023-03-15 15:06:34,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:06:34,972] [INFO] Task started: Prodigal
[2023-03-15 15:06:34,972] [INFO] Running command: cat /var/lib/cwl/stg4365da10-be7b-439c-9ea6-4d81564854ed/OceanDNA-b24356.fa | prodigal -d OceanDNA-b24356/cds.fna -a OceanDNA-b24356/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:06:39,646] [INFO] Task succeeded: Prodigal
[2023-03-15 15:06:39,646] [INFO] Task started: HMMsearch
[2023-03-15 15:06:39,646] [INFO] Running command: hmmsearch --tblout OceanDNA-b24356/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb83093b0-49bd-4404-a9bd-160657d81656/dqc_reference/reference_markers.hmm OceanDNA-b24356/protein.faa > /dev/null
[2023-03-15 15:06:39,797] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:06:39,797] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4365da10-be7b-439c-9ea6-4d81564854ed/OceanDNA-b24356.fa]
[2023-03-15 15:06:39,819] [INFO] Query marker FASTA was written to OceanDNA-b24356/markers.fasta
[2023-03-15 15:06:39,821] [INFO] Task started: Blastn
[2023-03-15 15:06:39,821] [INFO] Running command: blastn -query OceanDNA-b24356/markers.fasta -db /var/lib/cwl/stgb83093b0-49bd-4404-a9bd-160657d81656/dqc_reference/reference_markers.fasta -out OceanDNA-b24356/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:06:40,255] [INFO] Task succeeded: Blastn
[2023-03-15 15:06:40,262] [INFO] Selected 10 target genomes.
[2023-03-15 15:06:40,263] [INFO] Target genome list was writen to OceanDNA-b24356/target_genomes.txt
[2023-03-15 15:06:40,268] [INFO] Task started: fastANI
[2023-03-15 15:06:40,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg4365da10-be7b-439c-9ea6-4d81564854ed/OceanDNA-b24356.fa --refList OceanDNA-b24356/target_genomes.txt --output OceanDNA-b24356/fastani_result.tsv --threads 1
[2023-03-15 15:06:43,310] [INFO] Task succeeded: fastANI
[2023-03-15 15:06:43,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb83093b0-49bd-4404-a9bd-160657d81656/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:06:43,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb83093b0-49bd-4404-a9bd-160657d81656/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:06:43,311] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:06:43,311] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:06:43,311] [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
--------------------------------------------------------------------------------
[2023-03-15 15:06:43,315] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24356/tc_result.tsv
[2023-03-15 15:06:43,324] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:06:43,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:06:43,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb83093b0-49bd-4404-a9bd-160657d81656/dqc_reference/checkm_data
[2023-03-15 15:06:43,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:06:43,624] [INFO] Task started: CheckM
[2023-03-15 15:06:43,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24356/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24356/checkm_input OceanDNA-b24356/checkm_result
[2023-03-15 15:07:04,418] [INFO] Task succeeded: CheckM
[2023-03-15 15:07:04,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:07:04,595] [INFO] ===== Completeness check finished =====
[2023-03-15 15:07:04,595] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:07:04,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24356/markers.fasta)
[2023-03-15 15:07:04,598] [INFO] Task started: Blastn
[2023-03-15 15:07:04,598] [INFO] Running command: blastn -query OceanDNA-b24356/markers.fasta -db /var/lib/cwl/stgb83093b0-49bd-4404-a9bd-160657d81656/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24356/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:07:05,606] [INFO] Task succeeded: Blastn
[2023-03-15 15:07:05,618] [INFO] Selected 17 target genomes.
[2023-03-15 15:07:05,618] [INFO] Target genome list was writen to OceanDNA-b24356/target_genomes_gtdb.txt
[2023-03-15 15:07:05,643] [INFO] Task started: fastANI
[2023-03-15 15:07:05,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg4365da10-be7b-439c-9ea6-4d81564854ed/OceanDNA-b24356.fa --refList OceanDNA-b24356/target_genomes_gtdb.txt --output OceanDNA-b24356/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:07:08,967] [INFO] Task succeeded: fastANI
[2023-03-15 15:07:08,970] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:07:08,971] [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_002937855.1	s__MarineAlpha5-Bin12 sp002937855	99.7721	280	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin12	95.0	99.77	99.77	0.93	0.93	2	conclusive
GCA_002937895.1	s__PTKV01 sp002937895	76.8727	64	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__PTKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577425.1	s__MarineAlpha5-Bin3 sp902577425	76.1486	66	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	75.8565	54	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-15 15:07:08,973] [INFO] GTDB search result was written to OceanDNA-b24356/result_gtdb.tsv
[2023-03-15 15:07:08,978] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:07:08,982] [INFO] DFAST_QC result json was written to OceanDNA-b24356/dqc_result.json
[2023-03-15 15:07:08,982] [INFO] DFAST_QC completed!
[2023-03-15 15:07:08,982] [INFO] Total running time: 0h0m35s