[2023-03-18 03:59:29,350] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:59:29,350] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:59:29,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b38155d-f249-4f83-bb46-e0c928027074/dqc_reference
[2023-03-18 03:59:30,453] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:59:30,453] [INFO] Task started: Prodigal
[2023-03-18 03:59:30,453] [INFO] Running command: cat /var/lib/cwl/stg7a847715-2868-47a7-8a6c-fb91399db69b/OceanDNA-b15225.fa | prodigal -d OceanDNA-b15225/cds.fna -a OceanDNA-b15225/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:59:37,163] [INFO] Task succeeded: Prodigal
[2023-03-18 03:59:37,164] [INFO] Task started: HMMsearch
[2023-03-18 03:59:37,164] [INFO] Running command: hmmsearch --tblout OceanDNA-b15225/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b38155d-f249-4f83-bb46-e0c928027074/dqc_reference/reference_markers.hmm OceanDNA-b15225/protein.faa > /dev/null
[2023-03-18 03:59:37,314] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:59:37,315] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7a847715-2868-47a7-8a6c-fb91399db69b/OceanDNA-b15225.fa]
[2023-03-18 03:59:37,327] [INFO] Query marker FASTA was written to OceanDNA-b15225/markers.fasta
[2023-03-18 03:59:37,327] [INFO] Task started: Blastn
[2023-03-18 03:59:37,327] [INFO] Running command: blastn -query OceanDNA-b15225/markers.fasta -db /var/lib/cwl/stg6b38155d-f249-4f83-bb46-e0c928027074/dqc_reference/reference_markers.fasta -out OceanDNA-b15225/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:37,810] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:37,811] [INFO] Selected 10 target genomes.
[2023-03-18 03:59:37,811] [INFO] Target genome list was writen to OceanDNA-b15225/target_genomes.txt
[2023-03-18 03:59:37,817] [INFO] Task started: fastANI
[2023-03-18 03:59:37,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a847715-2868-47a7-8a6c-fb91399db69b/OceanDNA-b15225.fa --refList OceanDNA-b15225/target_genomes.txt --output OceanDNA-b15225/fastani_result.tsv --threads 1
[2023-03-18 03:59:42,647] [INFO] Task succeeded: fastANI
[2023-03-18 03:59:42,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b38155d-f249-4f83-bb46-e0c928027074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:59:42,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b38155d-f249-4f83-bb46-e0c928027074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:59:42,647] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:59:42,648] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:59:42,648] [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 03:59:42,648] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15225/tc_result.tsv
[2023-03-18 03:59:42,648] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:59:42,648] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:59:42,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b38155d-f249-4f83-bb46-e0c928027074/dqc_reference/checkm_data
[2023-03-18 03:59:42,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:59:42,653] [INFO] Task started: CheckM
[2023-03-18 03:59:42,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15225/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15225/checkm_input OceanDNA-b15225/checkm_result
[2023-03-18 04:00:05,238] [INFO] Task succeeded: CheckM
[2023-03-18 04:00:05,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 7.23%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-18 04:00:05,240] [INFO] ===== Completeness check finished =====
[2023-03-18 04:00:05,240] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:00:05,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15225/markers.fasta)
[2023-03-18 04:00:05,241] [INFO] Task started: Blastn
[2023-03-18 04:00:05,241] [INFO] Running command: blastn -query OceanDNA-b15225/markers.fasta -db /var/lib/cwl/stg6b38155d-f249-4f83-bb46-e0c928027074/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15225/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:00:05,877] [INFO] Task succeeded: Blastn
[2023-03-18 04:00:05,878] [INFO] Selected 15 target genomes.
[2023-03-18 04:00:05,878] [INFO] Target genome list was writen to OceanDNA-b15225/target_genomes_gtdb.txt
[2023-03-18 04:00:05,951] [INFO] Task started: fastANI
[2023-03-18 04:00:05,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a847715-2868-47a7-8a6c-fb91399db69b/OceanDNA-b15225.fa --refList OceanDNA-b15225/target_genomes_gtdb.txt --output OceanDNA-b15225/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:00:12,143] [INFO] Task succeeded: fastANI
[2023-03-18 04:00:12,145] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:00:12,164] [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_002701625.1	s__UBA2979 sp002701625	97.3895	305	366	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__UBA2979	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-18 04:00:12,164] [INFO] GTDB search result was written to OceanDNA-b15225/result_gtdb.tsv
[2023-03-18 04:00:12,164] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:00:12,165] [INFO] DFAST_QC result json was written to OceanDNA-b15225/dqc_result.json
[2023-03-18 04:00:12,165] [INFO] DFAST_QC completed!
[2023-03-18 04:00:12,165] [INFO] Total running time: 0h0m43s