[2023-03-15 17:49:50,389] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:49:50,389] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:49:50,389] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc239d22-f936-4842-b87a-4b471db6a49b/dqc_reference
[2023-03-15 17:49:54,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:49:54,239] [INFO] Task started: Prodigal
[2023-03-15 17:49:54,239] [INFO] Running command: cat /var/lib/cwl/stga1e40f71-0610-4cec-89f2-38f0a0c49071/OceanDNA-b30741.fa | prodigal -d OceanDNA-b30741/cds.fna -a OceanDNA-b30741/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:49:59,141] [INFO] Task succeeded: Prodigal
[2023-03-15 17:49:59,142] [INFO] Task started: HMMsearch
[2023-03-15 17:49:59,142] [INFO] Running command: hmmsearch --tblout OceanDNA-b30741/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc239d22-f936-4842-b87a-4b471db6a49b/dqc_reference/reference_markers.hmm OceanDNA-b30741/protein.faa > /dev/null
[2023-03-15 17:49:59,273] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:49:59,273] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga1e40f71-0610-4cec-89f2-38f0a0c49071/OceanDNA-b30741.fa]
[2023-03-15 17:49:59,287] [INFO] Query marker FASTA was written to OceanDNA-b30741/markers.fasta
[2023-03-15 17:49:59,289] [INFO] Task started: Blastn
[2023-03-15 17:49:59,289] [INFO] Running command: blastn -query OceanDNA-b30741/markers.fasta -db /var/lib/cwl/stgcc239d22-f936-4842-b87a-4b471db6a49b/dqc_reference/reference_markers.fasta -out OceanDNA-b30741/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:49:59,856] [INFO] Task succeeded: Blastn
[2023-03-15 17:49:59,857] [INFO] Selected 15 target genomes.
[2023-03-15 17:49:59,857] [INFO] Target genome list was writen to OceanDNA-b30741/target_genomes.txt
[2023-03-15 17:49:59,866] [INFO] Task started: fastANI
[2023-03-15 17:49:59,866] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e40f71-0610-4cec-89f2-38f0a0c49071/OceanDNA-b30741.fa --refList OceanDNA-b30741/target_genomes.txt --output OceanDNA-b30741/fastani_result.tsv --threads 1
[2023-03-15 17:50:12,503] [INFO] Task succeeded: fastANI
[2023-03-15 17:50:12,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc239d22-f936-4842-b87a-4b471db6a49b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:50:12,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc239d22-f936-4842-b87a-4b471db6a49b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:50:12,504] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:50:12,504] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:50:12,504] [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 17:50:12,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30741/tc_result.tsv
[2023-03-15 17:50:12,504] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:50:12,505] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:50:12,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc239d22-f936-4842-b87a-4b471db6a49b/dqc_reference/checkm_data
[2023-03-15 17:50:12,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:50:12,520] [INFO] Task started: CheckM
[2023-03-15 17:50:12,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30741/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30741/checkm_input OceanDNA-b30741/checkm_result
[2023-03-15 17:50:33,021] [INFO] Task succeeded: CheckM
[2023-03-15 17:50:33,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.01%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:50:33,024] [INFO] ===== Completeness check finished =====
[2023-03-15 17:50:33,024] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:50:33,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30741/markers.fasta)
[2023-03-15 17:50:33,026] [INFO] Task started: Blastn
[2023-03-15 17:50:33,026] [INFO] Running command: blastn -query OceanDNA-b30741/markers.fasta -db /var/lib/cwl/stgcc239d22-f936-4842-b87a-4b471db6a49b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30741/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:50:33,892] [INFO] Task succeeded: Blastn
[2023-03-15 17:50:33,893] [INFO] Selected 11 target genomes.
[2023-03-15 17:50:33,893] [INFO] Target genome list was writen to OceanDNA-b30741/target_genomes_gtdb.txt
[2023-03-15 17:50:33,918] [INFO] Task started: fastANI
[2023-03-15 17:50:33,918] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e40f71-0610-4cec-89f2-38f0a0c49071/OceanDNA-b30741.fa --refList OceanDNA-b30741/target_genomes_gtdb.txt --output OceanDNA-b30741/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:50:39,277] [INFO] Task succeeded: fastANI
[2023-03-15 17:50:39,279] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:50:39,279] [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_018671895.1	s__JABHGV01 sp018671895	99.8361	119	120	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABHGV01	95.0	99.83	99.79	0.94	0.93	6	conclusive
--------------------------------------------------------------------------------
[2023-03-15 17:50:39,279] [INFO] GTDB search result was written to OceanDNA-b30741/result_gtdb.tsv
[2023-03-15 17:50:39,279] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:50:39,280] [INFO] DFAST_QC result json was written to OceanDNA-b30741/dqc_result.json
[2023-03-15 17:50:39,280] [INFO] DFAST_QC completed!
[2023-03-15 17:50:39,280] [INFO] Total running time: 0h0m49s