[2023-03-16 21:13:50,785] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:13:50,785] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:13:50,785] [INFO] DQC Reference Directory: /var/lib/cwl/stga4e3ca71-648c-4bbc-b826-b1f9bae70a15/dqc_reference
[2023-03-16 21:13:52,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:13:52,533] [INFO] Task started: Prodigal
[2023-03-16 21:13:52,533] [INFO] Running command: cat /var/lib/cwl/stg6c6d4253-19a4-404d-8dc5-2fae38f67f81/OceanDNA-b44405.fa | prodigal -d OceanDNA-b44405/cds.fna -a OceanDNA-b44405/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:14:04,236] [INFO] Task succeeded: Prodigal
[2023-03-16 21:14:04,236] [INFO] Task started: HMMsearch
[2023-03-16 21:14:04,236] [INFO] Running command: hmmsearch --tblout OceanDNA-b44405/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4e3ca71-648c-4bbc-b826-b1f9bae70a15/dqc_reference/reference_markers.hmm OceanDNA-b44405/protein.faa > /dev/null
[2023-03-16 21:14:04,407] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:14:04,407] [INFO] Found 6/6 markers.
[2023-03-16 21:14:04,422] [INFO] Query marker FASTA was written to OceanDNA-b44405/markers.fasta
[2023-03-16 21:14:04,423] [INFO] Task started: Blastn
[2023-03-16 21:14:04,423] [INFO] Running command: blastn -query OceanDNA-b44405/markers.fasta -db /var/lib/cwl/stga4e3ca71-648c-4bbc-b826-b1f9bae70a15/dqc_reference/reference_markers.fasta -out OceanDNA-b44405/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:14:04,944] [INFO] Task succeeded: Blastn
[2023-03-16 21:14:04,945] [INFO] Selected 20 target genomes.
[2023-03-16 21:14:04,945] [INFO] Target genome list was writen to OceanDNA-b44405/target_genomes.txt
[2023-03-16 21:14:04,957] [INFO] Task started: fastANI
[2023-03-16 21:14:04,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6d4253-19a4-404d-8dc5-2fae38f67f81/OceanDNA-b44405.fa --refList OceanDNA-b44405/target_genomes.txt --output OceanDNA-b44405/fastani_result.tsv --threads 1
[2023-03-16 21:14:13,762] [INFO] Task succeeded: fastANI
[2023-03-16 21:14:13,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4e3ca71-648c-4bbc-b826-b1f9bae70a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:14:13,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4e3ca71-648c-4bbc-b826-b1f9bae70a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:14:13,763] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:14:13,763] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:14:13,763] [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 21:14:13,763] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44405/tc_result.tsv
[2023-03-16 21:14:13,763] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:14:13,764] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:14:13,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4e3ca71-648c-4bbc-b826-b1f9bae70a15/dqc_reference/checkm_data
[2023-03-16 21:14:13,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:14:13,769] [INFO] Task started: CheckM
[2023-03-16 21:14:13,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44405/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44405/checkm_input OceanDNA-b44405/checkm_result
[2023-03-16 21:14:45,127] [INFO] Task succeeded: CheckM
[2023-03-16 21:14:45,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:14:45,130] [INFO] ===== Completeness check finished =====
[2023-03-16 21:14:45,130] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:14:45,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44405/markers.fasta)
[2023-03-16 21:14:45,130] [INFO] Task started: Blastn
[2023-03-16 21:14:45,130] [INFO] Running command: blastn -query OceanDNA-b44405/markers.fasta -db /var/lib/cwl/stga4e3ca71-648c-4bbc-b826-b1f9bae70a15/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44405/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:14:45,835] [INFO] Task succeeded: Blastn
[2023-03-16 21:14:45,836] [INFO] Selected 26 target genomes.
[2023-03-16 21:14:45,836] [INFO] Target genome list was writen to OceanDNA-b44405/target_genomes_gtdb.txt
[2023-03-16 21:14:45,860] [INFO] Task started: fastANI
[2023-03-16 21:14:45,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6d4253-19a4-404d-8dc5-2fae38f67f81/OceanDNA-b44405.fa --refList OceanDNA-b44405/target_genomes_gtdb.txt --output OceanDNA-b44405/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:14:56,943] [INFO] Task succeeded: fastANI
[2023-03-16 21:14:56,945] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:14:56,946] [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_002718345.1	s__UBA6522 sp002718345	99.6754	587	682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__UBA6522	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002434915.1	s__UBA6522 sp002434915	77.6971	182	682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__UBA6522	95.0	98.12	97.06	0.85	0.77	3	-
--------------------------------------------------------------------------------
[2023-03-16 21:14:56,946] [INFO] GTDB search result was written to OceanDNA-b44405/result_gtdb.tsv
[2023-03-16 21:14:56,946] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:14:56,946] [INFO] DFAST_QC result json was written to OceanDNA-b44405/dqc_result.json
[2023-03-16 21:14:56,946] [INFO] DFAST_QC completed!
[2023-03-16 21:14:56,947] [INFO] Total running time: 0h1m6s