[2023-03-17 09:05:02,523] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,523] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg09d10a94-b145-448f-88b2-ee1081de0700/dqc_reference
[2023-03-17 09:05:03,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,734] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,734] [INFO] Running command: cat /var/lib/cwl/stg72ca561b-27d0-4e0a-8155-5e12bc9ca443/OceanDNA-b10968.fa | prodigal -d OceanDNA-b10968/cds.fna -a OceanDNA-b10968/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:16,765] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:16,766] [INFO] Task started: HMMsearch
[2023-03-17 09:05:16,766] [INFO] Running command: hmmsearch --tblout OceanDNA-b10968/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09d10a94-b145-448f-88b2-ee1081de0700/dqc_reference/reference_markers.hmm OceanDNA-b10968/protein.faa > /dev/null
[2023-03-17 09:05:16,942] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:16,943] [INFO] Found 6/6 markers.
[2023-03-17 09:05:16,954] [INFO] Query marker FASTA was written to OceanDNA-b10968/markers.fasta
[2023-03-17 09:05:16,954] [INFO] Task started: Blastn
[2023-03-17 09:05:16,954] [INFO] Running command: blastn -query OceanDNA-b10968/markers.fasta -db /var/lib/cwl/stg09d10a94-b145-448f-88b2-ee1081de0700/dqc_reference/reference_markers.fasta -out OceanDNA-b10968/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:17,533] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:17,533] [INFO] Selected 27 target genomes.
[2023-03-17 09:05:17,534] [INFO] Target genome list was writen to OceanDNA-b10968/target_genomes.txt
[2023-03-17 09:05:17,582] [INFO] Task started: fastANI
[2023-03-17 09:05:17,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ca561b-27d0-4e0a-8155-5e12bc9ca443/OceanDNA-b10968.fa --refList OceanDNA-b10968/target_genomes.txt --output OceanDNA-b10968/fastani_result.tsv --threads 1
[2023-03-17 09:05:33,358] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:33,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09d10a94-b145-448f-88b2-ee1081de0700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:33,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09d10a94-b145-448f-88b2-ee1081de0700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:33,359] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:33,359] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:33,359] [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 09:05:33,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10968/tc_result.tsv
[2023-03-17 09:05:33,359] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:33,359] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:33,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09d10a94-b145-448f-88b2-ee1081de0700/dqc_reference/checkm_data
[2023-03-17 09:05:33,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:33,365] [INFO] Task started: CheckM
[2023-03-17 09:05:33,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10968/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10968/checkm_input OceanDNA-b10968/checkm_result
[2023-03-17 09:06:10,368] [INFO] Task succeeded: CheckM
[2023-03-17 09:06:10,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:06:10,370] [INFO] ===== Completeness check finished =====
[2023-03-17 09:06:10,370] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:06:10,370] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10968/markers.fasta)
[2023-03-17 09:06:10,371] [INFO] Task started: Blastn
[2023-03-17 09:06:10,371] [INFO] Running command: blastn -query OceanDNA-b10968/markers.fasta -db /var/lib/cwl/stg09d10a94-b145-448f-88b2-ee1081de0700/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10968/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:06:11,349] [INFO] Task succeeded: Blastn
[2023-03-17 09:06:11,350] [INFO] Selected 28 target genomes.
[2023-03-17 09:06:11,350] [INFO] Target genome list was writen to OceanDNA-b10968/target_genomes_gtdb.txt
[2023-03-17 09:06:11,580] [INFO] Task started: fastANI
[2023-03-17 09:06:11,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ca561b-27d0-4e0a-8155-5e12bc9ca443/OceanDNA-b10968.fa --refList OceanDNA-b10968/target_genomes_gtdb.txt --output OceanDNA-b10968/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:06:22,629] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:22,633] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:06:22,633] [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_011526275.1	s__UBA7428 sp011526275	77.3366	104	561	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526285.1	s__UBA7428 sp011526285	76.7593	114	561	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526265.1	s__UBA7428 sp011526265	76.6599	79	561	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478905.1	s__UBA7428 sp905478905	76.5093	95	561	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_011526335.1	s__UBA7428 sp011526335	76.3613	67	561	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:06:22,633] [INFO] GTDB search result was written to OceanDNA-b10968/result_gtdb.tsv
[2023-03-17 09:06:22,633] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:06:22,634] [INFO] DFAST_QC result json was written to OceanDNA-b10968/dqc_result.json
[2023-03-17 09:06:22,634] [INFO] DFAST_QC completed!
[2023-03-17 09:06:22,634] [INFO] Total running time: 0h1m20s