[2023-03-18 21:15:29,379] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,381] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg611ae98b-29e0-4b46-a168-bd8182ada100/dqc_reference
[2023-03-18 21:15:31,041] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,043] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,043] [INFO] Running command: cat /var/lib/cwl/stg1483da90-3f18-43d6-8f8f-b153312d1fc3/OceanDNA-b36862.fa | prodigal -d OceanDNA-b36862/cds.fna -a OceanDNA-b36862/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:43,563] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:43,563] [INFO] Task started: HMMsearch
[2023-03-18 21:15:43,564] [INFO] Running command: hmmsearch --tblout OceanDNA-b36862/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg611ae98b-29e0-4b46-a168-bd8182ada100/dqc_reference/reference_markers.hmm OceanDNA-b36862/protein.faa > /dev/null
[2023-03-18 21:15:43,763] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:43,764] [INFO] Found 6/6 markers.
[2023-03-18 21:15:43,787] [INFO] Query marker FASTA was written to OceanDNA-b36862/markers.fasta
[2023-03-18 21:15:43,787] [INFO] Task started: Blastn
[2023-03-18 21:15:43,788] [INFO] Running command: blastn -query OceanDNA-b36862/markers.fasta -db /var/lib/cwl/stg611ae98b-29e0-4b46-a168-bd8182ada100/dqc_reference/reference_markers.fasta -out OceanDNA-b36862/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:44,369] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:44,372] [INFO] Selected 23 target genomes.
[2023-03-18 21:15:44,373] [INFO] Target genome list was writen to OceanDNA-b36862/target_genomes.txt
[2023-03-18 21:15:44,387] [INFO] Task started: fastANI
[2023-03-18 21:15:44,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg1483da90-3f18-43d6-8f8f-b153312d1fc3/OceanDNA-b36862.fa --refList OceanDNA-b36862/target_genomes.txt --output OceanDNA-b36862/fastani_result.tsv --threads 1
[2023-03-18 21:15:57,446] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:57,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg611ae98b-29e0-4b46-a168-bd8182ada100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:57,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg611ae98b-29e0-4b46-a168-bd8182ada100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:57,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:57,447] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:57,447] [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 21:15:57,449] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36862/tc_result.tsv
[2023-03-18 21:15:57,449] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:57,449] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:57,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg611ae98b-29e0-4b46-a168-bd8182ada100/dqc_reference/checkm_data
[2023-03-18 21:15:57,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:57,456] [INFO] Task started: CheckM
[2023-03-18 21:15:57,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36862/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36862/checkm_input OceanDNA-b36862/checkm_result
[2023-03-18 21:16:32,338] [INFO] Task succeeded: CheckM
[2023-03-18 21:16:32,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:16:33,250] [INFO] ===== Completeness check finished =====
[2023-03-18 21:16:33,250] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:16:33,251] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36862/markers.fasta)
[2023-03-18 21:16:33,251] [INFO] Task started: Blastn
[2023-03-18 21:16:33,251] [INFO] Running command: blastn -query OceanDNA-b36862/markers.fasta -db /var/lib/cwl/stg611ae98b-29e0-4b46-a168-bd8182ada100/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36862/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:16:34,212] [INFO] Task succeeded: Blastn
[2023-03-18 21:16:34,217] [INFO] Selected 20 target genomes.
[2023-03-18 21:16:34,217] [INFO] Target genome list was writen to OceanDNA-b36862/target_genomes_gtdb.txt
[2023-03-18 21:16:34,241] [INFO] Task started: fastANI
[2023-03-18 21:16:34,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg1483da90-3f18-43d6-8f8f-b153312d1fc3/OceanDNA-b36862.fa --refList OceanDNA-b36862/target_genomes_gtdb.txt --output OceanDNA-b36862/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:44,604] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:44,607] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:16:44,607] [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_002719135.1	s__UBA11889 sp002719135	98.4116	490	652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.11	97.65	0.74	0.72	3	conclusive
GCA_002313255.1	s__UBA11889 sp002313255	93.311	587	652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.77	98.77	0.86	0.86	2	-
GCA_002715785.1	s__UBA11889 sp002715785	85.0807	463	652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	99.18	99.12	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:44,609] [INFO] GTDB search result was written to OceanDNA-b36862/result_gtdb.tsv
[2023-03-18 21:16:44,613] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:44,618] [INFO] DFAST_QC result json was written to OceanDNA-b36862/dqc_result.json
[2023-03-18 21:16:44,619] [INFO] DFAST_QC completed!
[2023-03-18 21:16:44,619] [INFO] Total running time: 0h1m15s