[2023-03-16 09:15:41,447] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:15:41,447] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:15:41,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b1bb6c9-bd22-4a29-b211-581fa406a078/dqc_reference
[2023-03-16 09:15:42,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:15:42,579] [INFO] Task started: Prodigal
[2023-03-16 09:15:42,579] [INFO] Running command: cat /var/lib/cwl/stg795df865-bbca-4fc9-8bea-396b1a44888b/OceanDNA-b9819.fa | prodigal -d OceanDNA-b9819/cds.fna -a OceanDNA-b9819/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:15:47,882] [INFO] Task succeeded: Prodigal
[2023-03-16 09:15:47,883] [INFO] Task started: HMMsearch
[2023-03-16 09:15:47,883] [INFO] Running command: hmmsearch --tblout OceanDNA-b9819/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b1bb6c9-bd22-4a29-b211-581fa406a078/dqc_reference/reference_markers.hmm OceanDNA-b9819/protein.faa > /dev/null
[2023-03-16 09:15:48,022] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:15:48,023] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg795df865-bbca-4fc9-8bea-396b1a44888b/OceanDNA-b9819.fa]
[2023-03-16 09:15:48,033] [INFO] Query marker FASTA was written to OceanDNA-b9819/markers.fasta
[2023-03-16 09:15:48,034] [INFO] Task started: Blastn
[2023-03-16 09:15:48,034] [INFO] Running command: blastn -query OceanDNA-b9819/markers.fasta -db /var/lib/cwl/stg1b1bb6c9-bd22-4a29-b211-581fa406a078/dqc_reference/reference_markers.fasta -out OceanDNA-b9819/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:15:48,484] [INFO] Task succeeded: Blastn
[2023-03-16 09:15:48,485] [INFO] Selected 17 target genomes.
[2023-03-16 09:15:48,485] [INFO] Target genome list was writen to OceanDNA-b9819/target_genomes.txt
[2023-03-16 09:15:48,498] [INFO] Task started: fastANI
[2023-03-16 09:15:48,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg795df865-bbca-4fc9-8bea-396b1a44888b/OceanDNA-b9819.fa --refList OceanDNA-b9819/target_genomes.txt --output OceanDNA-b9819/fastani_result.tsv --threads 1
[2023-03-16 09:15:56,590] [INFO] Task succeeded: fastANI
[2023-03-16 09:15:56,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b1bb6c9-bd22-4a29-b211-581fa406a078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:15:56,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b1bb6c9-bd22-4a29-b211-581fa406a078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:15:56,591] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:15:56,591] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:15:56,591] [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 09:15:56,591] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9819/tc_result.tsv
[2023-03-16 09:15:56,591] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:15:56,591] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:15:56,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b1bb6c9-bd22-4a29-b211-581fa406a078/dqc_reference/checkm_data
[2023-03-16 09:15:56,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:15:56,597] [INFO] Task started: CheckM
[2023-03-16 09:15:56,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9819/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9819/checkm_input OceanDNA-b9819/checkm_result
[2023-03-16 09:16:16,643] [INFO] Task succeeded: CheckM
[2023-03-16 09:16:16,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:16:16,646] [INFO] ===== Completeness check finished =====
[2023-03-16 09:16:16,646] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:16:16,646] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9819/markers.fasta)
[2023-03-16 09:16:16,647] [INFO] Task started: Blastn
[2023-03-16 09:16:16,647] [INFO] Running command: blastn -query OceanDNA-b9819/markers.fasta -db /var/lib/cwl/stg1b1bb6c9-bd22-4a29-b211-581fa406a078/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9819/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:16:17,107] [INFO] Task succeeded: Blastn
[2023-03-16 09:16:17,109] [INFO] Selected 17 target genomes.
[2023-03-16 09:16:17,109] [INFO] Target genome list was writen to OceanDNA-b9819/target_genomes_gtdb.txt
[2023-03-16 09:16:17,149] [INFO] Task started: fastANI
[2023-03-16 09:16:17,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg795df865-bbca-4fc9-8bea-396b1a44888b/OceanDNA-b9819.fa --refList OceanDNA-b9819/target_genomes_gtdb.txt --output OceanDNA-b9819/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:16:25,696] [INFO] Task succeeded: fastANI
[2023-03-16 09:16:25,698] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:16:25,698] [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_002471825.1	s__Polaribacter sp002471825	78.9203	98	165	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:16:25,699] [INFO] GTDB search result was written to OceanDNA-b9819/result_gtdb.tsv
[2023-03-16 09:16:25,699] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:16:25,700] [INFO] DFAST_QC result json was written to OceanDNA-b9819/dqc_result.json
[2023-03-16 09:16:25,700] [INFO] DFAST_QC completed!
[2023-03-16 09:16:25,700] [INFO] Total running time: 0h0m44s