[2023-03-19 02:05:13,409] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:13,410] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:13,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bb1cc34-0b59-4825-bbf8-1347504243e0/dqc_reference
[2023-03-19 02:05:14,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:14,505] [INFO] Task started: Prodigal
[2023-03-19 02:05:14,505] [INFO] Running command: cat /var/lib/cwl/stg1d7a8607-f683-44d9-9e83-a6dac0d6f8ca/OceanDNA-b5590.fa | prodigal -d OceanDNA-b5590/cds.fna -a OceanDNA-b5590/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:33,187] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:33,187] [INFO] Task started: HMMsearch
[2023-03-19 02:05:33,187] [INFO] Running command: hmmsearch --tblout OceanDNA-b5590/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bb1cc34-0b59-4825-bbf8-1347504243e0/dqc_reference/reference_markers.hmm OceanDNA-b5590/protein.faa > /dev/null
[2023-03-19 02:05:33,388] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:33,389] [INFO] Found 6/6 markers.
[2023-03-19 02:05:33,403] [INFO] Query marker FASTA was written to OceanDNA-b5590/markers.fasta
[2023-03-19 02:05:33,404] [INFO] Task started: Blastn
[2023-03-19 02:05:33,404] [INFO] Running command: blastn -query OceanDNA-b5590/markers.fasta -db /var/lib/cwl/stg7bb1cc34-0b59-4825-bbf8-1347504243e0/dqc_reference/reference_markers.fasta -out OceanDNA-b5590/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:34,004] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:34,005] [INFO] Selected 23 target genomes.
[2023-03-19 02:05:34,006] [INFO] Target genome list was writen to OceanDNA-b5590/target_genomes.txt
[2023-03-19 02:05:34,024] [INFO] Task started: fastANI
[2023-03-19 02:05:34,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7a8607-f683-44d9-9e83-a6dac0d6f8ca/OceanDNA-b5590.fa --refList OceanDNA-b5590/target_genomes.txt --output OceanDNA-b5590/fastani_result.tsv --threads 1
[2023-03-19 02:05:49,772] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:49,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bb1cc34-0b59-4825-bbf8-1347504243e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:49,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bb1cc34-0b59-4825-bbf8-1347504243e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:49,773] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:49,773] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:49,773] [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
--------------------------------------------------------------------------------
[2023-03-19 02:05:49,773] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5590/tc_result.tsv
[2023-03-19 02:05:49,773] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:49,773] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:49,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bb1cc34-0b59-4825-bbf8-1347504243e0/dqc_reference/checkm_data
[2023-03-19 02:05:49,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:49,780] [INFO] Task started: CheckM
[2023-03-19 02:05:49,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5590/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5590/checkm_input OceanDNA-b5590/checkm_result
[2023-03-19 02:06:40,021] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:40,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:40,024] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:40,024] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:40,024] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5590/markers.fasta)
[2023-03-19 02:06:40,025] [INFO] Task started: Blastn
[2023-03-19 02:06:40,025] [INFO] Running command: blastn -query OceanDNA-b5590/markers.fasta -db /var/lib/cwl/stg7bb1cc34-0b59-4825-bbf8-1347504243e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5590/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:40,993] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:40,994] [INFO] Selected 27 target genomes.
[2023-03-19 02:06:40,994] [INFO] Target genome list was writen to OceanDNA-b5590/target_genomes_gtdb.txt
[2023-03-19 02:06:41,546] [INFO] Task started: fastANI
[2023-03-19 02:06:41,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7a8607-f683-44d9-9e83-a6dac0d6f8ca/OceanDNA-b5590.fa --refList OceanDNA-b5590/target_genomes_gtdb.txt --output OceanDNA-b5590/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:06:55,013] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:55,015] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:06:55,016] [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_009921445.1	s__RFXV01 sp009921445	89.1547	460	687	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__RFXV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:06:55,016] [INFO] GTDB search result was written to OceanDNA-b5590/result_gtdb.tsv
[2023-03-19 02:06:55,016] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:06:55,016] [INFO] DFAST_QC result json was written to OceanDNA-b5590/dqc_result.json
[2023-03-19 02:06:55,016] [INFO] DFAST_QC completed!
[2023-03-19 02:06:55,016] [INFO] Total running time: 0h1m42s