[2023-03-18 09:41:07,241] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,241] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg8de66b4d-df6e-4dae-8f6f-44a9eb038ff7/dqc_reference
[2023-03-18 09:41:08,338] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,338] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,338] [INFO] Running command: cat /var/lib/cwl/stg7e4c9c57-72a6-4eb3-867c-cd54421c338f/OceanDNA-b37268.fa | prodigal -d OceanDNA-b37268/cds.fna -a OceanDNA-b37268/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:26,156] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:26,156] [INFO] Task started: HMMsearch
[2023-03-18 09:41:26,157] [INFO] Running command: hmmsearch --tblout OceanDNA-b37268/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8de66b4d-df6e-4dae-8f6f-44a9eb038ff7/dqc_reference/reference_markers.hmm OceanDNA-b37268/protein.faa > /dev/null
[2023-03-18 09:41:26,395] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:26,396] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7e4c9c57-72a6-4eb3-867c-cd54421c338f/OceanDNA-b37268.fa]
[2023-03-18 09:41:26,419] [INFO] Query marker FASTA was written to OceanDNA-b37268/markers.fasta
[2023-03-18 09:41:26,420] [INFO] Task started: Blastn
[2023-03-18 09:41:26,420] [INFO] Running command: blastn -query OceanDNA-b37268/markers.fasta -db /var/lib/cwl/stg8de66b4d-df6e-4dae-8f6f-44a9eb038ff7/dqc_reference/reference_markers.fasta -out OceanDNA-b37268/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:26,955] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:26,956] [INFO] Selected 27 target genomes.
[2023-03-18 09:41:26,956] [INFO] Target genome list was writen to OceanDNA-b37268/target_genomes.txt
[2023-03-18 09:41:26,973] [INFO] Task started: fastANI
[2023-03-18 09:41:26,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4c9c57-72a6-4eb3-867c-cd54421c338f/OceanDNA-b37268.fa --refList OceanDNA-b37268/target_genomes.txt --output OceanDNA-b37268/fastani_result.tsv --threads 1
[2023-03-18 09:41:43,379] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:43,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8de66b4d-df6e-4dae-8f6f-44a9eb038ff7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:43,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8de66b4d-df6e-4dae-8f6f-44a9eb038ff7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:43,379] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:43,379] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:43,379] [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 09:41:43,379] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37268/tc_result.tsv
[2023-03-18 09:41:43,380] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:43,380] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:43,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8de66b4d-df6e-4dae-8f6f-44a9eb038ff7/dqc_reference/checkm_data
[2023-03-18 09:41:43,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:43,387] [INFO] Task started: CheckM
[2023-03-18 09:41:43,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37268/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37268/checkm_input OceanDNA-b37268/checkm_result
[2023-03-18 09:42:31,163] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:31,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:31,166] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:31,166] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:31,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37268/markers.fasta)
[2023-03-18 09:42:31,167] [INFO] Task started: Blastn
[2023-03-18 09:42:31,167] [INFO] Running command: blastn -query OceanDNA-b37268/markers.fasta -db /var/lib/cwl/stg8de66b4d-df6e-4dae-8f6f-44a9eb038ff7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37268/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:31,946] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:31,947] [INFO] Selected 30 target genomes.
[2023-03-18 09:42:31,948] [INFO] Target genome list was writen to OceanDNA-b37268/target_genomes_gtdb.txt
[2023-03-18 09:42:31,977] [INFO] Task started: fastANI
[2023-03-18 09:42:31,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4c9c57-72a6-4eb3-867c-cd54421c338f/OceanDNA-b37268.fa --refList OceanDNA-b37268/target_genomes_gtdb.txt --output OceanDNA-b37268/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:48,648] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:48,651] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:48,651] [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_002694945.1	s__UBA9659 sp002694945	78.2763	122	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	97.23	97.07	0.74	0.72	3	-
GCA_017642855.1	s__UBA9659 sp017642855	76.6645	51	1021	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.28	99.09	0.95	0.93	7	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:48,651] [INFO] GTDB search result was written to OceanDNA-b37268/result_gtdb.tsv
[2023-03-18 09:42:48,652] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:48,652] [INFO] DFAST_QC result json was written to OceanDNA-b37268/dqc_result.json
[2023-03-18 09:42:48,652] [INFO] DFAST_QC completed!
[2023-03-18 09:42:48,652] [INFO] Total running time: 0h1m41s