[2023-03-19 04:29:38,147] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a5001c2-c4f1-4a8f-974a-b2567b62b3ef/dqc_reference
[2023-03-19 04:29:39,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,833] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,833] [INFO] Running command: cat /var/lib/cwl/stg28d3f8b3-20fa-4118-a84c-77473df8a030/OceanDNA-b45862.fa | prodigal -d OceanDNA-b45862/cds.fna -a OceanDNA-b45862/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:44,784] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:44,784] [INFO] Task started: HMMsearch
[2023-03-19 04:29:44,784] [INFO] Running command: hmmsearch --tblout OceanDNA-b45862/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a5001c2-c4f1-4a8f-974a-b2567b62b3ef/dqc_reference/reference_markers.hmm OceanDNA-b45862/protein.faa > /dev/null
[2023-03-19 04:29:44,931] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:44,931] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28d3f8b3-20fa-4118-a84c-77473df8a030/OceanDNA-b45862.fa]
[2023-03-19 04:29:44,939] [INFO] Query marker FASTA was written to OceanDNA-b45862/markers.fasta
[2023-03-19 04:29:44,940] [INFO] Task started: Blastn
[2023-03-19 04:29:44,940] [INFO] Running command: blastn -query OceanDNA-b45862/markers.fasta -db /var/lib/cwl/stg8a5001c2-c4f1-4a8f-974a-b2567b62b3ef/dqc_reference/reference_markers.fasta -out OceanDNA-b45862/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:46,080] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:46,081] [INFO] Selected 11 target genomes.
[2023-03-19 04:29:46,081] [INFO] Target genome list was writen to OceanDNA-b45862/target_genomes.txt
[2023-03-19 04:29:46,088] [INFO] Task started: fastANI
[2023-03-19 04:29:46,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg28d3f8b3-20fa-4118-a84c-77473df8a030/OceanDNA-b45862.fa --refList OceanDNA-b45862/target_genomes.txt --output OceanDNA-b45862/fastani_result.tsv --threads 1
[2023-03-19 04:29:51,779] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:51,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a5001c2-c4f1-4a8f-974a-b2567b62b3ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:51,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a5001c2-c4f1-4a8f-974a-b2567b62b3ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:51,780] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:51,780] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:29:51,780] [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 04:29:51,780] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45862/tc_result.tsv
[2023-03-19 04:29:51,780] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:51,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:51,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a5001c2-c4f1-4a8f-974a-b2567b62b3ef/dqc_reference/checkm_data
[2023-03-19 04:29:51,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:51,786] [INFO] Task started: CheckM
[2023-03-19 04:29:51,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45862/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45862/checkm_input OceanDNA-b45862/checkm_result
[2023-03-19 04:30:10,549] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:10,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.07%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:10,551] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:10,551] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:10,551] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45862/markers.fasta)
[2023-03-19 04:30:10,552] [INFO] Task started: Blastn
[2023-03-19 04:30:10,552] [INFO] Running command: blastn -query OceanDNA-b45862/markers.fasta -db /var/lib/cwl/stg8a5001c2-c4f1-4a8f-974a-b2567b62b3ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45862/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:10,997] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:10,998] [INFO] Selected 18 target genomes.
[2023-03-19 04:30:10,998] [INFO] Target genome list was writen to OceanDNA-b45862/target_genomes_gtdb.txt
[2023-03-19 04:30:11,041] [INFO] Task started: fastANI
[2023-03-19 04:30:11,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg28d3f8b3-20fa-4118-a84c-77473df8a030/OceanDNA-b45862.fa --refList OceanDNA-b45862/target_genomes_gtdb.txt --output OceanDNA-b45862/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:17,945] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:17,947] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:30:17,947] [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_902516225.1	s__UBA7441 sp902516225	95.6169	107	192	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902603705.1	s__UBA7441 sp902603705	89.8787	98	192	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:17,948] [INFO] GTDB search result was written to OceanDNA-b45862/result_gtdb.tsv
[2023-03-19 04:30:17,948] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:17,948] [INFO] DFAST_QC result json was written to OceanDNA-b45862/dqc_result.json
[2023-03-19 04:30:17,948] [INFO] DFAST_QC completed!
[2023-03-19 04:30:17,948] [INFO] Total running time: 0h0m40s