[2023-03-18 22:28:07,930] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:28:07,934] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:28:07,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg57492cb1-b465-451b-938d-f4f8e9a9cb2e/dqc_reference
[2023-03-18 22:28:09,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:28:09,040] [INFO] Task started: Prodigal
[2023-03-18 22:28:09,040] [INFO] Running command: cat /var/lib/cwl/stgce82760d-55f4-4953-8f65-ce0bcc70da2f/OceanDNA-b21417.fa | prodigal -d OceanDNA-b21417/cds.fna -a OceanDNA-b21417/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:28:15,744] [INFO] Task succeeded: Prodigal
[2023-03-18 22:28:15,745] [INFO] Task started: HMMsearch
[2023-03-18 22:28:15,745] [INFO] Running command: hmmsearch --tblout OceanDNA-b21417/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57492cb1-b465-451b-938d-f4f8e9a9cb2e/dqc_reference/reference_markers.hmm OceanDNA-b21417/protein.faa > /dev/null
[2023-03-18 22:28:15,927] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:28:15,927] [INFO] Found 6/6 markers.
[2023-03-18 22:28:15,980] [INFO] Query marker FASTA was written to OceanDNA-b21417/markers.fasta
[2023-03-18 22:28:15,982] [INFO] Task started: Blastn
[2023-03-18 22:28:15,982] [INFO] Running command: blastn -query OceanDNA-b21417/markers.fasta -db /var/lib/cwl/stg57492cb1-b465-451b-938d-f4f8e9a9cb2e/dqc_reference/reference_markers.fasta -out OceanDNA-b21417/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:28:16,631] [INFO] Task succeeded: Blastn
[2023-03-18 22:28:16,637] [INFO] Selected 12 target genomes.
[2023-03-18 22:28:16,637] [INFO] Target genome list was writen to OceanDNA-b21417/target_genomes.txt
[2023-03-18 22:28:16,644] [INFO] Task started: fastANI
[2023-03-18 22:28:16,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgce82760d-55f4-4953-8f65-ce0bcc70da2f/OceanDNA-b21417.fa --refList OceanDNA-b21417/target_genomes.txt --output OceanDNA-b21417/fastani_result.tsv --threads 1
[2023-03-18 22:28:23,347] [INFO] Task succeeded: fastANI
[2023-03-18 22:28:23,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57492cb1-b465-451b-938d-f4f8e9a9cb2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:28:23,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57492cb1-b465-451b-938d-f4f8e9a9cb2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:28:23,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:28:23,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:28:23,348] [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
--------------------------------------------------------------------------------
[2023-03-18 22:28:23,353] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21417/tc_result.tsv
[2023-03-18 22:28:23,364] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:28:23,364] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:28:23,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57492cb1-b465-451b-938d-f4f8e9a9cb2e/dqc_reference/checkm_data
[2023-03-18 22:28:23,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:28:23,666] [INFO] Task started: CheckM
[2023-03-18 22:28:23,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21417/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21417/checkm_input OceanDNA-b21417/checkm_result
[2023-03-18 22:28:46,285] [INFO] Task succeeded: CheckM
[2023-03-18 22:28:46,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:28:46,359] [INFO] ===== Completeness check finished =====
[2023-03-18 22:28:46,359] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:28:46,360] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21417/markers.fasta)
[2023-03-18 22:28:46,361] [INFO] Task started: Blastn
[2023-03-18 22:28:46,361] [INFO] Running command: blastn -query OceanDNA-b21417/markers.fasta -db /var/lib/cwl/stg57492cb1-b465-451b-938d-f4f8e9a9cb2e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21417/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:28:47,060] [INFO] Task succeeded: Blastn
[2023-03-18 22:28:47,074] [INFO] Selected 18 target genomes.
[2023-03-18 22:28:47,075] [INFO] Target genome list was writen to OceanDNA-b21417/target_genomes_gtdb.txt
[2023-03-18 22:28:47,099] [INFO] Task started: fastANI
[2023-03-18 22:28:47,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgce82760d-55f4-4953-8f65-ce0bcc70da2f/OceanDNA-b21417.fa --refList OceanDNA-b21417/target_genomes_gtdb.txt --output OceanDNA-b21417/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:28:51,296] [INFO] Task succeeded: fastANI
[2023-03-18 22:28:51,299] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:28:51,299] [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_018646705.1	s__BM521 sp018646705	99.9443	277	309	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__BM521	95.0	99.84	99.84	0.87	0.87	2	conclusive
GCA_002869205.1	s__BM521 sp002869205	81.4362	185	309	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__BM521	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003482855.1	s__UBA11699 sp003482855	75.9446	63	309	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__UBA11699	95.0	99.86	99.86	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:28:51,305] [INFO] GTDB search result was written to OceanDNA-b21417/result_gtdb.tsv
[2023-03-18 22:28:51,317] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:28:51,324] [INFO] DFAST_QC result json was written to OceanDNA-b21417/dqc_result.json
[2023-03-18 22:28:51,324] [INFO] DFAST_QC completed!
[2023-03-18 22:28:51,324] [INFO] Total running time: 0h0m43s