[2023-03-16 00:43:24,409] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:43:24,412] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:43:24,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e04c789-918d-4efc-a290-ef79857a2f5c/dqc_reference
[2023-03-16 00:43:25,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:43:25,533] [INFO] Task started: Prodigal
[2023-03-16 00:43:25,533] [INFO] Running command: cat /var/lib/cwl/stgbca20dfa-4445-43a0-804a-e0db53a58e46/OceanDNA-b33543.fa | prodigal -d OceanDNA-b33543/cds.fna -a OceanDNA-b33543/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:43:40,347] [INFO] Task succeeded: Prodigal
[2023-03-16 00:43:40,347] [INFO] Task started: HMMsearch
[2023-03-16 00:43:40,348] [INFO] Running command: hmmsearch --tblout OceanDNA-b33543/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e04c789-918d-4efc-a290-ef79857a2f5c/dqc_reference/reference_markers.hmm OceanDNA-b33543/protein.faa > /dev/null
[2023-03-16 00:43:40,548] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:43:40,549] [INFO] Found 6/6 markers.
[2023-03-16 00:43:40,593] [INFO] Query marker FASTA was written to OceanDNA-b33543/markers.fasta
[2023-03-16 00:43:40,594] [INFO] Task started: Blastn
[2023-03-16 00:43:40,594] [INFO] Running command: blastn -query OceanDNA-b33543/markers.fasta -db /var/lib/cwl/stg3e04c789-918d-4efc-a290-ef79857a2f5c/dqc_reference/reference_markers.fasta -out OceanDNA-b33543/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:43:41,208] [INFO] Task succeeded: Blastn
[2023-03-16 00:43:41,221] [INFO] Selected 28 target genomes.
[2023-03-16 00:43:41,221] [INFO] Target genome list was writen to OceanDNA-b33543/target_genomes.txt
[2023-03-16 00:43:41,267] [INFO] Task started: fastANI
[2023-03-16 00:43:41,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca20dfa-4445-43a0-804a-e0db53a58e46/OceanDNA-b33543.fa --refList OceanDNA-b33543/target_genomes.txt --output OceanDNA-b33543/fastani_result.tsv --threads 1
[2023-03-16 00:43:57,347] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:57,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e04c789-918d-4efc-a290-ef79857a2f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:43:57,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e04c789-918d-4efc-a290-ef79857a2f5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:43:57,350] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:43:57,350] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:43:57,350] [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
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	76.7245	54	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:43:57,356] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33543/tc_result.tsv
[2023-03-16 00:43:57,367] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:43:57,367] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:43:57,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e04c789-918d-4efc-a290-ef79857a2f5c/dqc_reference/checkm_data
[2023-03-16 00:43:57,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:43:57,418] [INFO] Task started: CheckM
[2023-03-16 00:43:57,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33543/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33543/checkm_input OceanDNA-b33543/checkm_result
[2023-03-16 00:44:38,032] [INFO] Task succeeded: CheckM
[2023-03-16 00:44:38,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:44:38,108] [INFO] ===== Completeness check finished =====
[2023-03-16 00:44:38,108] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:44:38,109] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33543/markers.fasta)
[2023-03-16 00:44:38,110] [INFO] Task started: Blastn
[2023-03-16 00:44:38,110] [INFO] Running command: blastn -query OceanDNA-b33543/markers.fasta -db /var/lib/cwl/stg3e04c789-918d-4efc-a290-ef79857a2f5c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33543/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:44:39,144] [INFO] Task succeeded: Blastn
[2023-03-16 00:44:39,154] [INFO] Selected 24 target genomes.
[2023-03-16 00:44:39,154] [INFO] Target genome list was writen to OceanDNA-b33543/target_genomes_gtdb.txt
[2023-03-16 00:44:39,181] [INFO] Task started: fastANI
[2023-03-16 00:44:39,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca20dfa-4445-43a0-804a-e0db53a58e46/OceanDNA-b33543.fa --refList OceanDNA-b33543/target_genomes_gtdb.txt --output OceanDNA-b33543/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:44:53,526] [INFO] Task succeeded: fastANI
[2023-03-16 00:44:53,528] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:44:53,529] [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_017857895.1	s__Algicoccus sp017857895	88.772	587	766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Algicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737415.1	s__NBD-18 sp002737415	76.556	50	766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:44:53,532] [INFO] GTDB search result was written to OceanDNA-b33543/result_gtdb.tsv
[2023-03-16 00:44:53,536] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:44:53,540] [INFO] DFAST_QC result json was written to OceanDNA-b33543/dqc_result.json
[2023-03-16 00:44:53,541] [INFO] DFAST_QC completed!
[2023-03-16 00:44:53,541] [INFO] Total running time: 0h1m29s