[2023-03-15 20:34:28,421] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:28,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:28,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgc03ef86a-5922-40eb-8c4d-0d4f2781ecf5/dqc_reference
[2023-03-15 20:34:29,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:29,546] [INFO] Task started: Prodigal
[2023-03-15 20:34:29,546] [INFO] Running command: cat /var/lib/cwl/stg186f48e5-86df-4a8d-bba5-dfd3972fc2c5/OceanDNA-b32792.fa | prodigal -d OceanDNA-b32792/cds.fna -a OceanDNA-b32792/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:35,207] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:35,208] [INFO] Task started: HMMsearch
[2023-03-15 20:34:35,208] [INFO] Running command: hmmsearch --tblout OceanDNA-b32792/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc03ef86a-5922-40eb-8c4d-0d4f2781ecf5/dqc_reference/reference_markers.hmm OceanDNA-b32792/protein.faa > /dev/null
[2023-03-15 20:34:35,390] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:35,391] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg186f48e5-86df-4a8d-bba5-dfd3972fc2c5/OceanDNA-b32792.fa]
[2023-03-15 20:34:35,398] [INFO] Query marker FASTA was written to OceanDNA-b32792/markers.fasta
[2023-03-15 20:34:35,398] [INFO] Task started: Blastn
[2023-03-15 20:34:35,398] [INFO] Running command: blastn -query OceanDNA-b32792/markers.fasta -db /var/lib/cwl/stgc03ef86a-5922-40eb-8c4d-0d4f2781ecf5/dqc_reference/reference_markers.fasta -out OceanDNA-b32792/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:35,958] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:35,959] [INFO] Selected 13 target genomes.
[2023-03-15 20:34:35,959] [INFO] Target genome list was writen to OceanDNA-b32792/target_genomes.txt
[2023-03-15 20:34:35,966] [INFO] Task started: fastANI
[2023-03-15 20:34:35,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg186f48e5-86df-4a8d-bba5-dfd3972fc2c5/OceanDNA-b32792.fa --refList OceanDNA-b32792/target_genomes.txt --output OceanDNA-b32792/fastani_result.tsv --threads 1
[2023-03-15 20:34:42,537] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:42,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc03ef86a-5922-40eb-8c4d-0d4f2781ecf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:42,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc03ef86a-5922-40eb-8c4d-0d4f2781ecf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:42,537] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:42,537] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:34:42,537] [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 20:34:42,538] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32792/tc_result.tsv
[2023-03-15 20:34:42,538] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:42,538] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:42,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc03ef86a-5922-40eb-8c4d-0d4f2781ecf5/dqc_reference/checkm_data
[2023-03-15 20:34:42,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:42,542] [INFO] Task started: CheckM
[2023-03-15 20:34:42,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32792/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32792/checkm_input OceanDNA-b32792/checkm_result
[2023-03-15 20:35:02,330] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:02,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:02,331] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:02,331] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:02,332] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32792/markers.fasta)
[2023-03-15 20:35:02,332] [INFO] Task started: Blastn
[2023-03-15 20:35:02,332] [INFO] Running command: blastn -query OceanDNA-b32792/markers.fasta -db /var/lib/cwl/stgc03ef86a-5922-40eb-8c4d-0d4f2781ecf5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32792/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:03,234] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:03,234] [INFO] Selected 20 target genomes.
[2023-03-15 20:35:03,235] [INFO] Target genome list was writen to OceanDNA-b32792/target_genomes_gtdb.txt
[2023-03-15 20:35:03,727] [INFO] Task started: fastANI
[2023-03-15 20:35:03,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg186f48e5-86df-4a8d-bba5-dfd3972fc2c5/OceanDNA-b32792.fa --refList OceanDNA-b32792/target_genomes_gtdb.txt --output OceanDNA-b32792/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:11,043] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:11,045] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:35:11,046] [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_002500565.1	s__UBA7879 sp002500565	99.955	309	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7879;f__UBA7879;g__UBA7879	95.0	99.85	99.85	0.87	0.87	2	conclusive
GCA_002869105.1	s__UBA7879 sp002869105	76.5453	84	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7879;f__UBA7879;g__UBA7879	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:11,046] [INFO] GTDB search result was written to OceanDNA-b32792/result_gtdb.tsv
[2023-03-15 20:35:11,046] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:11,046] [INFO] DFAST_QC result json was written to OceanDNA-b32792/dqc_result.json
[2023-03-15 20:35:11,046] [INFO] DFAST_QC completed!
[2023-03-15 20:35:11,046] [INFO] Total running time: 0h0m43s