[2023-03-15 07:49:00,016] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:49:00,016] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:49:00,016] [INFO] DQC Reference Directory: /var/lib/cwl/stg04ab0e58-4d68-478d-a900-6fe71e293cde/dqc_reference
[2023-03-15 07:49:01,152] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:49:01,153] [INFO] Task started: Prodigal
[2023-03-15 07:49:01,153] [INFO] Running command: cat /var/lib/cwl/stg528c54b4-bf43-4849-8f68-44d0e31ea8a1/OceanDNA-b6928.fa | prodigal -d OceanDNA-b6928/cds.fna -a OceanDNA-b6928/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:49:07,615] [INFO] Task succeeded: Prodigal
[2023-03-15 07:49:07,615] [INFO] Task started: HMMsearch
[2023-03-15 07:49:07,615] [INFO] Running command: hmmsearch --tblout OceanDNA-b6928/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04ab0e58-4d68-478d-a900-6fe71e293cde/dqc_reference/reference_markers.hmm OceanDNA-b6928/protein.faa > /dev/null
[2023-03-15 07:49:07,787] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:49:07,787] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg528c54b4-bf43-4849-8f68-44d0e31ea8a1/OceanDNA-b6928.fa]
[2023-03-15 07:49:07,864] [INFO] Query marker FASTA was written to OceanDNA-b6928/markers.fasta
[2023-03-15 07:49:07,865] [INFO] Task started: Blastn
[2023-03-15 07:49:07,865] [INFO] Running command: blastn -query OceanDNA-b6928/markers.fasta -db /var/lib/cwl/stg04ab0e58-4d68-478d-a900-6fe71e293cde/dqc_reference/reference_markers.fasta -out OceanDNA-b6928/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:49:08,368] [INFO] Task succeeded: Blastn
[2023-03-15 07:49:08,379] [INFO] Selected 13 target genomes.
[2023-03-15 07:49:08,379] [INFO] Target genome list was writen to OceanDNA-b6928/target_genomes.txt
[2023-03-15 07:49:08,386] [INFO] Task started: fastANI
[2023-03-15 07:49:08,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg528c54b4-bf43-4849-8f68-44d0e31ea8a1/OceanDNA-b6928.fa --refList OceanDNA-b6928/target_genomes.txt --output OceanDNA-b6928/fastani_result.tsv --threads 1
[2023-03-15 07:49:15,139] [INFO] Task succeeded: fastANI
[2023-03-15 07:49:15,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04ab0e58-4d68-478d-a900-6fe71e293cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:49:15,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04ab0e58-4d68-478d-a900-6fe71e293cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:49:15,140] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:49:15,140] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:49:15,140] [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 07:49:15,145] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6928/tc_result.tsv
[2023-03-15 07:49:15,154] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:49:15,154] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:49:15,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04ab0e58-4d68-478d-a900-6fe71e293cde/dqc_reference/checkm_data
[2023-03-15 07:49:15,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:49:15,168] [INFO] Task started: CheckM
[2023-03-15 07:49:15,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6928/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6928/checkm_input OceanDNA-b6928/checkm_result
[2023-03-15 07:49:36,758] [INFO] Task succeeded: CheckM
[2023-03-15 07:49:36,758] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:49:36,820] [INFO] ===== Completeness check finished =====
[2023-03-15 07:49:36,821] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:49:36,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6928/markers.fasta)
[2023-03-15 07:49:36,822] [INFO] Task started: Blastn
[2023-03-15 07:49:36,822] [INFO] Running command: blastn -query OceanDNA-b6928/markers.fasta -db /var/lib/cwl/stg04ab0e58-4d68-478d-a900-6fe71e293cde/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6928/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:49:37,442] [INFO] Task succeeded: Blastn
[2023-03-15 07:49:37,446] [INFO] Selected 15 target genomes.
[2023-03-15 07:49:37,446] [INFO] Target genome list was writen to OceanDNA-b6928/target_genomes_gtdb.txt
[2023-03-15 07:49:37,462] [INFO] Task started: fastANI
[2023-03-15 07:49:37,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg528c54b4-bf43-4849-8f68-44d0e31ea8a1/OceanDNA-b6928.fa --refList OceanDNA-b6928/target_genomes_gtdb.txt --output OceanDNA-b6928/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:49:41,849] [INFO] Task succeeded: fastANI
[2023-03-15 07:49:41,852] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:49:41,852] [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_002702405.1	s__GCA-002728855 sp002702405	98.2494	260	350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002728855	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002728855.1	s__GCA-002728855 sp002728855	84.2445	299	350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002728855	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:49:41,856] [INFO] GTDB search result was written to OceanDNA-b6928/result_gtdb.tsv
[2023-03-15 07:49:41,861] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:49:41,866] [INFO] DFAST_QC result json was written to OceanDNA-b6928/dqc_result.json
[2023-03-15 07:49:41,866] [INFO] DFAST_QC completed!
[2023-03-15 07:49:41,866] [INFO] Total running time: 0h0m42s