[2023-03-17 05:59:11,061] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,061] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg819bc1ab-64e9-49c5-903e-61525d913077/dqc_reference
[2023-03-17 05:59:12,174] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,175] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,176] [INFO] Running command: cat /var/lib/cwl/stg91e61cab-4f36-4998-adab-788f4faf9935/OceanDNA-b31227.fa | prodigal -d OceanDNA-b31227/cds.fna -a OceanDNA-b31227/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:19,941] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:19,941] [INFO] Task started: HMMsearch
[2023-03-17 05:59:19,941] [INFO] Running command: hmmsearch --tblout OceanDNA-b31227/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg819bc1ab-64e9-49c5-903e-61525d913077/dqc_reference/reference_markers.hmm OceanDNA-b31227/protein.faa > /dev/null
[2023-03-17 05:59:20,090] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:20,091] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg91e61cab-4f36-4998-adab-788f4faf9935/OceanDNA-b31227.fa]
[2023-03-17 05:59:20,105] [INFO] Query marker FASTA was written to OceanDNA-b31227/markers.fasta
[2023-03-17 05:59:20,105] [INFO] Task started: Blastn
[2023-03-17 05:59:20,105] [INFO] Running command: blastn -query OceanDNA-b31227/markers.fasta -db /var/lib/cwl/stg819bc1ab-64e9-49c5-903e-61525d913077/dqc_reference/reference_markers.fasta -out OceanDNA-b31227/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:20,612] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:20,907] [INFO] Selected 22 target genomes.
[2023-03-17 05:59:20,907] [INFO] Target genome list was writen to OceanDNA-b31227/target_genomes.txt
[2023-03-17 05:59:20,917] [INFO] Task started: fastANI
[2023-03-17 05:59:20,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg91e61cab-4f36-4998-adab-788f4faf9935/OceanDNA-b31227.fa --refList OceanDNA-b31227/target_genomes.txt --output OceanDNA-b31227/fastani_result.tsv --threads 1
[2023-03-17 05:59:35,510] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:35,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg819bc1ab-64e9-49c5-903e-61525d913077/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:35,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg819bc1ab-64e9-49c5-903e-61525d913077/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:35,511] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:35,511] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:59:35,511] [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
--------------------------------------------------------------------------------
[2023-03-17 05:59:35,511] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31227/tc_result.tsv
[2023-03-17 05:59:35,511] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:35,511] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:35,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg819bc1ab-64e9-49c5-903e-61525d913077/dqc_reference/checkm_data
[2023-03-17 05:59:35,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:35,518] [INFO] Task started: CheckM
[2023-03-17 05:59:35,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31227/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31227/checkm_input OceanDNA-b31227/checkm_result
[2023-03-17 06:00:00,218] [INFO] Task succeeded: CheckM
[2023-03-17 06:00:00,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.81%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:00:00,221] [INFO] ===== Completeness check finished =====
[2023-03-17 06:00:00,221] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:00:00,221] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31227/markers.fasta)
[2023-03-17 06:00:00,221] [INFO] Task started: Blastn
[2023-03-17 06:00:00,221] [INFO] Running command: blastn -query OceanDNA-b31227/markers.fasta -db /var/lib/cwl/stg819bc1ab-64e9-49c5-903e-61525d913077/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31227/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:00:00,868] [INFO] Task succeeded: Blastn
[2023-03-17 06:00:00,869] [INFO] Selected 20 target genomes.
[2023-03-17 06:00:00,869] [INFO] Target genome list was writen to OceanDNA-b31227/target_genomes_gtdb.txt
[2023-03-17 06:00:01,021] [INFO] Task started: fastANI
[2023-03-17 06:00:01,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg91e61cab-4f36-4998-adab-788f4faf9935/OceanDNA-b31227.fa --refList OceanDNA-b31227/target_genomes_gtdb.txt --output OceanDNA-b31227/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:00:12,681] [INFO] Task succeeded: fastANI
[2023-03-17 06:00:12,684] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:00:12,684] [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_002378125.1	s__UBA3470 sp002378125	84.1364	297	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA3470	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709525.1	s__UBA3470 sp002709525	82.6034	287	370	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA3470	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:00:12,684] [INFO] GTDB search result was written to OceanDNA-b31227/result_gtdb.tsv
[2023-03-17 06:00:12,684] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:00:12,685] [INFO] DFAST_QC result json was written to OceanDNA-b31227/dqc_result.json
[2023-03-17 06:00:12,685] [INFO] DFAST_QC completed!
[2023-03-17 06:00:12,685] [INFO] Total running time: 0h1m2s