[2023-03-17 03:50:15,855] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:15,855] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:15,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a76aa87-1772-4df2-bbfb-7b4a39881f18/dqc_reference
[2023-03-17 03:50:17,133] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:17,134] [INFO] Task started: Prodigal
[2023-03-17 03:50:17,134] [INFO] Running command: cat /var/lib/cwl/stg0f8969c4-6a92-4ff5-8d39-e2d795d963f3/OceanDNA-b9056.fa | prodigal -d OceanDNA-b9056/cds.fna -a OceanDNA-b9056/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:22,912] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:22,912] [INFO] Task started: HMMsearch
[2023-03-17 03:50:22,912] [INFO] Running command: hmmsearch --tblout OceanDNA-b9056/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a76aa87-1772-4df2-bbfb-7b4a39881f18/dqc_reference/reference_markers.hmm OceanDNA-b9056/protein.faa > /dev/null
[2023-03-17 03:50:23,073] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:23,073] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0f8969c4-6a92-4ff5-8d39-e2d795d963f3/OceanDNA-b9056.fa]
[2023-03-17 03:50:23,083] [INFO] Query marker FASTA was written to OceanDNA-b9056/markers.fasta
[2023-03-17 03:50:23,084] [INFO] Task started: Blastn
[2023-03-17 03:50:23,084] [INFO] Running command: blastn -query OceanDNA-b9056/markers.fasta -db /var/lib/cwl/stg6a76aa87-1772-4df2-bbfb-7b4a39881f18/dqc_reference/reference_markers.fasta -out OceanDNA-b9056/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:23,536] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:23,537] [INFO] Selected 23 target genomes.
[2023-03-17 03:50:23,538] [INFO] Target genome list was writen to OceanDNA-b9056/target_genomes.txt
[2023-03-17 03:50:23,557] [INFO] Task started: fastANI
[2023-03-17 03:50:23,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8969c4-6a92-4ff5-8d39-e2d795d963f3/OceanDNA-b9056.fa --refList OceanDNA-b9056/target_genomes.txt --output OceanDNA-b9056/fastani_result.tsv --threads 1
[2023-03-17 03:50:36,684] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:36,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a76aa87-1772-4df2-bbfb-7b4a39881f18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:36,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a76aa87-1772-4df2-bbfb-7b4a39881f18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:36,684] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:36,684] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:50:36,685] [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 03:50:36,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9056/tc_result.tsv
[2023-03-17 03:50:36,685] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:36,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:36,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a76aa87-1772-4df2-bbfb-7b4a39881f18/dqc_reference/checkm_data
[2023-03-17 03:50:36,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:36,690] [INFO] Task started: CheckM
[2023-03-17 03:50:36,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9056/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9056/checkm_input OceanDNA-b9056/checkm_result
[2023-03-17 03:50:58,021] [INFO] Task succeeded: CheckM
[2023-03-17 03:50:58,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:50:58,023] [INFO] ===== Completeness check finished =====
[2023-03-17 03:50:58,023] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:50:58,023] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9056/markers.fasta)
[2023-03-17 03:50:58,023] [INFO] Task started: Blastn
[2023-03-17 03:50:58,023] [INFO] Running command: blastn -query OceanDNA-b9056/markers.fasta -db /var/lib/cwl/stg6a76aa87-1772-4df2-bbfb-7b4a39881f18/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9056/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:58,456] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:58,457] [INFO] Selected 18 target genomes.
[2023-03-17 03:50:58,457] [INFO] Target genome list was writen to OceanDNA-b9056/target_genomes_gtdb.txt
[2023-03-17 03:50:58,826] [INFO] Task started: fastANI
[2023-03-17 03:50:58,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f8969c4-6a92-4ff5-8d39-e2d795d963f3/OceanDNA-b9056.fa --refList OceanDNA-b9056/target_genomes_gtdb.txt --output OceanDNA-b9056/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:05,177] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:05,180] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:51:05,180] [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_017852075.1	s__MS024-2A sp017852075	98.9155	146	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	conclusive
GCA_002292265.1	s__MS024-2A sp002292265	79.7025	114	149	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:05,180] [INFO] GTDB search result was written to OceanDNA-b9056/result_gtdb.tsv
[2023-03-17 03:51:05,180] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:05,181] [INFO] DFAST_QC result json was written to OceanDNA-b9056/dqc_result.json
[2023-03-17 03:51:05,181] [INFO] DFAST_QC completed!
[2023-03-17 03:51:05,181] [INFO] Total running time: 0h0m49s