[2023-03-17 04:15:14,764] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c79f267-e717-4d8b-8f30-d3594c9fa69f/dqc_reference
[2023-03-17 04:15:16,097] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,097] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,097] [INFO] Running command: cat /var/lib/cwl/stgbf23bcbe-8bb1-48a5-bb0d-a0f0c33607df/OceanDNA-b16747.fa | prodigal -d OceanDNA-b16747/cds.fna -a OceanDNA-b16747/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:28,523] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:28,524] [INFO] Task started: HMMsearch
[2023-03-17 04:15:28,524] [INFO] Running command: hmmsearch --tblout OceanDNA-b16747/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c79f267-e717-4d8b-8f30-d3594c9fa69f/dqc_reference/reference_markers.hmm OceanDNA-b16747/protein.faa > /dev/null
[2023-03-17 04:15:28,746] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:28,746] [INFO] Found 6/6 markers.
[2023-03-17 04:15:28,764] [INFO] Query marker FASTA was written to OceanDNA-b16747/markers.fasta
[2023-03-17 04:15:28,764] [INFO] Task started: Blastn
[2023-03-17 04:15:28,764] [INFO] Running command: blastn -query OceanDNA-b16747/markers.fasta -db /var/lib/cwl/stg5c79f267-e717-4d8b-8f30-d3594c9fa69f/dqc_reference/reference_markers.fasta -out OceanDNA-b16747/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:29,302] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:29,303] [INFO] Selected 14 target genomes.
[2023-03-17 04:15:29,303] [INFO] Target genome list was writen to OceanDNA-b16747/target_genomes.txt
[2023-03-17 04:15:29,311] [INFO] Task started: fastANI
[2023-03-17 04:15:29,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf23bcbe-8bb1-48a5-bb0d-a0f0c33607df/OceanDNA-b16747.fa --refList OceanDNA-b16747/target_genomes.txt --output OceanDNA-b16747/fastani_result.tsv --threads 1
[2023-03-17 04:15:35,248] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:35,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c79f267-e717-4d8b-8f30-d3594c9fa69f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:35,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c79f267-e717-4d8b-8f30-d3594c9fa69f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:35,248] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:35,249] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:15:35,249] [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
--------------------------------------------------------------------------------
[2023-03-17 04:15:35,249] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16747/tc_result.tsv
[2023-03-17 04:15:35,249] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:35,249] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:35,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c79f267-e717-4d8b-8f30-d3594c9fa69f/dqc_reference/checkm_data
[2023-03-17 04:15:35,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:35,256] [INFO] Task started: CheckM
[2023-03-17 04:15:35,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16747/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16747/checkm_input OceanDNA-b16747/checkm_result
[2023-03-17 04:16:09,715] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:09,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:09,718] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:09,718] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:09,718] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16747/markers.fasta)
[2023-03-17 04:16:09,719] [INFO] Task started: Blastn
[2023-03-17 04:16:09,719] [INFO] Running command: blastn -query OceanDNA-b16747/markers.fasta -db /var/lib/cwl/stg5c79f267-e717-4d8b-8f30-d3594c9fa69f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16747/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:10,445] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:10,446] [INFO] Selected 17 target genomes.
[2023-03-17 04:16:10,446] [INFO] Target genome list was writen to OceanDNA-b16747/target_genomes_gtdb.txt
[2023-03-17 04:16:10,734] [INFO] Task started: fastANI
[2023-03-17 04:16:10,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf23bcbe-8bb1-48a5-bb0d-a0f0c33607df/OceanDNA-b16747.fa --refList OceanDNA-b16747/target_genomes_gtdb.txt --output OceanDNA-b16747/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:17,040] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:17,044] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:17,044] [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_013216135.1	s__DT-14 sp013216135	80.8957	374	810	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Caenarcaniphilales;f__LMEP-6097;g__DT-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970325.1	s__LMEP-6097 sp018970325	76.8142	57	810	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Caenarcaniphilales;f__LMEP-6097;g__LMEP-6097	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924885.1	s__LMEP-6097 sp009924885	76.4123	58	810	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Caenarcaniphilales;f__LMEP-6097;g__LMEP-6097	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005110385.1	s__LMEP-6097 sp005110385	76.4077	59	810	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Caenarcaniphilales;f__LMEP-6097;g__LMEP-6097	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:17,044] [INFO] GTDB search result was written to OceanDNA-b16747/result_gtdb.tsv
[2023-03-17 04:16:17,044] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:17,045] [INFO] DFAST_QC result json was written to OceanDNA-b16747/dqc_result.json
[2023-03-17 04:16:17,045] [INFO] DFAST_QC completed!
[2023-03-17 04:16:17,045] [INFO] Total running time: 0h1m2s