[2023-03-16 07:28:30,027] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,027] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg56dee76d-a717-4287-9d70-199b66d28afd/dqc_reference
[2023-03-16 07:28:31,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,204] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,204] [INFO] Running command: cat /var/lib/cwl/stg1ca883f9-4a83-4067-ac7e-3a87fc49b77c/OceanDNA-b35880.fa | prodigal -d OceanDNA-b35880/cds.fna -a OceanDNA-b35880/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:35,866] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:35,866] [INFO] Task started: HMMsearch
[2023-03-16 07:28:35,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b35880/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56dee76d-a717-4287-9d70-199b66d28afd/dqc_reference/reference_markers.hmm OceanDNA-b35880/protein.faa > /dev/null
[2023-03-16 07:28:36,044] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:36,044] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1ca883f9-4a83-4067-ac7e-3a87fc49b77c/OceanDNA-b35880.fa]
[2023-03-16 07:28:36,057] [INFO] Query marker FASTA was written to OceanDNA-b35880/markers.fasta
[2023-03-16 07:28:36,059] [INFO] Task started: Blastn
[2023-03-16 07:28:36,059] [INFO] Running command: blastn -query OceanDNA-b35880/markers.fasta -db /var/lib/cwl/stg56dee76d-a717-4287-9d70-199b66d28afd/dqc_reference/reference_markers.fasta -out OceanDNA-b35880/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:36,569] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:36,571] [INFO] Selected 12 target genomes.
[2023-03-16 07:28:36,571] [INFO] Target genome list was writen to OceanDNA-b35880/target_genomes.txt
[2023-03-16 07:28:36,578] [INFO] Task started: fastANI
[2023-03-16 07:28:36,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca883f9-4a83-4067-ac7e-3a87fc49b77c/OceanDNA-b35880.fa --refList OceanDNA-b35880/target_genomes.txt --output OceanDNA-b35880/fastani_result.tsv --threads 1
[2023-03-16 07:28:42,420] [INFO] Task succeeded: fastANI
[2023-03-16 07:28:42,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56dee76d-a717-4287-9d70-199b66d28afd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:28:42,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56dee76d-a717-4287-9d70-199b66d28afd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:28:42,420] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:28:42,421] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:28:42,421] [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
--------------------------------------------------------------------------------
[2023-03-16 07:28:42,421] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35880/tc_result.tsv
[2023-03-16 07:28:42,422] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:28:42,422] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:28:42,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56dee76d-a717-4287-9d70-199b66d28afd/dqc_reference/checkm_data
[2023-03-16 07:28:42,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:28:42,430] [INFO] Task started: CheckM
[2023-03-16 07:28:42,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35880/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35880/checkm_input OceanDNA-b35880/checkm_result
[2023-03-16 07:29:00,575] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:00,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:00,578] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:00,578] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:00,579] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35880/markers.fasta)
[2023-03-16 07:29:00,580] [INFO] Task started: Blastn
[2023-03-16 07:29:00,580] [INFO] Running command: blastn -query OceanDNA-b35880/markers.fasta -db /var/lib/cwl/stg56dee76d-a717-4287-9d70-199b66d28afd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35880/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:01,328] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:01,330] [INFO] Selected 19 target genomes.
[2023-03-16 07:29:01,330] [INFO] Target genome list was writen to OceanDNA-b35880/target_genomes_gtdb.txt
[2023-03-16 07:29:01,609] [INFO] Task started: fastANI
[2023-03-16 07:29:01,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ca883f9-4a83-4067-ac7e-3a87fc49b77c/OceanDNA-b35880.fa --refList OceanDNA-b35880/target_genomes_gtdb.txt --output OceanDNA-b35880/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:08,557] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:08,558] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:29:08,559] [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_002170535.1	s__TMED69 sp002170535	80.5878	182	255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536_A;f__Ga0077536_A;g__TMED69	95.0	96.40	96.40	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:08,560] [INFO] GTDB search result was written to OceanDNA-b35880/result_gtdb.tsv
[2023-03-16 07:29:08,561] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:08,562] [INFO] DFAST_QC result json was written to OceanDNA-b35880/dqc_result.json
[2023-03-16 07:29:08,562] [INFO] DFAST_QC completed!
[2023-03-16 07:29:08,562] [INFO] Total running time: 0h0m39s