[2023-03-18 06:37:17,658] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:17,659] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:17,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cca4fd9-4da3-429d-a93a-1d3aa7d4a63b/dqc_reference
[2023-03-18 06:37:18,720] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:18,721] [INFO] Task started: Prodigal
[2023-03-18 06:37:18,721] [INFO] Running command: cat /var/lib/cwl/stg0172869e-3450-4e61-b172-d151e49815ca/OceanDNA-b36951.fa | prodigal -d OceanDNA-b36951/cds.fna -a OceanDNA-b36951/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:27,864] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:27,865] [INFO] Task started: HMMsearch
[2023-03-18 06:37:27,865] [INFO] Running command: hmmsearch --tblout OceanDNA-b36951/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cca4fd9-4da3-429d-a93a-1d3aa7d4a63b/dqc_reference/reference_markers.hmm OceanDNA-b36951/protein.faa > /dev/null
[2023-03-18 06:37:28,019] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:28,020] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0172869e-3450-4e61-b172-d151e49815ca/OceanDNA-b36951.fa]
[2023-03-18 06:37:28,034] [INFO] Query marker FASTA was written to OceanDNA-b36951/markers.fasta
[2023-03-18 06:37:28,034] [INFO] Task started: Blastn
[2023-03-18 06:37:28,034] [INFO] Running command: blastn -query OceanDNA-b36951/markers.fasta -db /var/lib/cwl/stg1cca4fd9-4da3-429d-a93a-1d3aa7d4a63b/dqc_reference/reference_markers.fasta -out OceanDNA-b36951/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:28,589] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:28,590] [INFO] Selected 34 target genomes.
[2023-03-18 06:37:28,590] [INFO] Target genome list was writen to OceanDNA-b36951/target_genomes.txt
[2023-03-18 06:37:28,604] [INFO] Task started: fastANI
[2023-03-18 06:37:28,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg0172869e-3450-4e61-b172-d151e49815ca/OceanDNA-b36951.fa --refList OceanDNA-b36951/target_genomes.txt --output OceanDNA-b36951/fastani_result.tsv --threads 1
[2023-03-18 06:37:49,875] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:49,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cca4fd9-4da3-429d-a93a-1d3aa7d4a63b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:49,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cca4fd9-4da3-429d-a93a-1d3aa7d4a63b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:49,876] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:49,876] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:37:49,876] [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 06:37:49,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36951/tc_result.tsv
[2023-03-18 06:37:49,876] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:49,876] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:49,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cca4fd9-4da3-429d-a93a-1d3aa7d4a63b/dqc_reference/checkm_data
[2023-03-18 06:37:49,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:49,907] [INFO] Task started: CheckM
[2023-03-18 06:37:49,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36951/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36951/checkm_input OceanDNA-b36951/checkm_result
[2023-03-18 06:38:17,446] [INFO] Task succeeded: CheckM
[2023-03-18 06:38:17,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:38:17,448] [INFO] ===== Completeness check finished =====
[2023-03-18 06:38:17,449] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:38:17,449] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36951/markers.fasta)
[2023-03-18 06:38:17,449] [INFO] Task started: Blastn
[2023-03-18 06:38:17,449] [INFO] Running command: blastn -query OceanDNA-b36951/markers.fasta -db /var/lib/cwl/stg1cca4fd9-4da3-429d-a93a-1d3aa7d4a63b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36951/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:38:18,271] [INFO] Task succeeded: Blastn
[2023-03-18 06:38:18,272] [INFO] Selected 29 target genomes.
[2023-03-18 06:38:18,272] [INFO] Target genome list was writen to OceanDNA-b36951/target_genomes_gtdb.txt
[2023-03-18 06:38:18,438] [INFO] Task started: fastANI
[2023-03-18 06:38:18,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg0172869e-3450-4e61-b172-d151e49815ca/OceanDNA-b36951.fa --refList OceanDNA-b36951/target_genomes_gtdb.txt --output OceanDNA-b36951/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:38:33,117] [INFO] Task succeeded: fastANI
[2023-03-18 06:38:33,123] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:38:33,123] [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_016779425.1	s__UBA4421 sp016779425	77.0773	56	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	97.24	97.24	0.58	0.58	2	-
GCA_009936895.1	s__UBA4421 sp009936895	77.0064	65	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731575.1	s__UBA4421 sp002731575	76.848	77	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.29	99.29	0.71	0.71	2	-
GCA_002704225.1	s__UBA4421 sp002704225	76.7864	100	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.56	99.05	0.92	0.86	4	-
GCA_012269545.1	s__UBA4421 sp012269545	76.6353	91	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613475.1	s__UBA4421 sp902613475	76.4723	57	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528515.1	s__UBA4421 sp902528515	76.3378	58	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726925.1	s__UBA4421 sp002726925	76.2173	63	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.34	98.19	0.75	0.72	3	-
--------------------------------------------------------------------------------
[2023-03-18 06:38:33,123] [INFO] GTDB search result was written to OceanDNA-b36951/result_gtdb.tsv
[2023-03-18 06:38:33,123] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:38:33,124] [INFO] DFAST_QC result json was written to OceanDNA-b36951/dqc_result.json
[2023-03-18 06:38:33,124] [INFO] DFAST_QC completed!
[2023-03-18 06:38:33,124] [INFO] Total running time: 0h1m15s