[2023-03-16 04:35:06,173] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:35:06,173] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:35:06,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b178aa3-267f-4917-88ca-283b9dde3f97/dqc_reference
[2023-03-16 04:35:07,256] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:35:07,257] [INFO] Task started: Prodigal
[2023-03-16 04:35:07,257] [INFO] Running command: cat /var/lib/cwl/stgdc44f988-5ccc-4456-b720-1618364f2d91/OceanDNA-b36995.fa | prodigal -d OceanDNA-b36995/cds.fna -a OceanDNA-b36995/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:35:22,155] [INFO] Task succeeded: Prodigal
[2023-03-16 04:35:22,155] [INFO] Task started: HMMsearch
[2023-03-16 04:35:22,155] [INFO] Running command: hmmsearch --tblout OceanDNA-b36995/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b178aa3-267f-4917-88ca-283b9dde3f97/dqc_reference/reference_markers.hmm OceanDNA-b36995/protein.faa > /dev/null
[2023-03-16 04:35:22,357] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:35:22,358] [INFO] Found 6/6 markers.
[2023-03-16 04:35:22,381] [INFO] Query marker FASTA was written to OceanDNA-b36995/markers.fasta
[2023-03-16 04:35:22,382] [INFO] Task started: Blastn
[2023-03-16 04:35:22,382] [INFO] Running command: blastn -query OceanDNA-b36995/markers.fasta -db /var/lib/cwl/stg1b178aa3-267f-4917-88ca-283b9dde3f97/dqc_reference/reference_markers.fasta -out OceanDNA-b36995/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:35:22,976] [INFO] Task succeeded: Blastn
[2023-03-16 04:35:22,976] [INFO] Selected 35 target genomes.
[2023-03-16 04:35:22,977] [INFO] Target genome list was writen to OceanDNA-b36995/target_genomes.txt
[2023-03-16 04:35:22,993] [INFO] Task started: fastANI
[2023-03-16 04:35:22,993] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc44f988-5ccc-4456-b720-1618364f2d91/OceanDNA-b36995.fa --refList OceanDNA-b36995/target_genomes.txt --output OceanDNA-b36995/fastani_result.tsv --threads 1
[2023-03-16 04:35:43,884] [INFO] Task succeeded: fastANI
[2023-03-16 04:35:43,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b178aa3-267f-4917-88ca-283b9dde3f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:35:43,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b178aa3-267f-4917-88ca-283b9dde3f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:35:43,885] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:35:43,885] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:35:43,885] [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
--------------------------------------------------------------------------------
[2023-03-16 04:35:43,886] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36995/tc_result.tsv
[2023-03-16 04:35:43,886] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:35:43,886] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:35:43,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b178aa3-267f-4917-88ca-283b9dde3f97/dqc_reference/checkm_data
[2023-03-16 04:35:43,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:35:43,894] [INFO] Task started: CheckM
[2023-03-16 04:35:43,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36995/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36995/checkm_input OceanDNA-b36995/checkm_result
[2023-03-16 04:36:23,975] [INFO] Task succeeded: CheckM
[2023-03-16 04:36:23,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:36:23,977] [INFO] ===== Completeness check finished =====
[2023-03-16 04:36:23,978] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:36:23,978] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36995/markers.fasta)
[2023-03-16 04:36:23,979] [INFO] Task started: Blastn
[2023-03-16 04:36:23,979] [INFO] Running command: blastn -query OceanDNA-b36995/markers.fasta -db /var/lib/cwl/stg1b178aa3-267f-4917-88ca-283b9dde3f97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36995/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:36:24,953] [INFO] Task succeeded: Blastn
[2023-03-16 04:36:24,954] [INFO] Selected 15 target genomes.
[2023-03-16 04:36:24,954] [INFO] Target genome list was writen to OceanDNA-b36995/target_genomes_gtdb.txt
[2023-03-16 04:36:24,971] [INFO] Task started: fastANI
[2023-03-16 04:36:24,971] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc44f988-5ccc-4456-b720-1618364f2d91/OceanDNA-b36995.fa --refList OceanDNA-b36995/target_genomes_gtdb.txt --output OceanDNA-b36995/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:36:34,646] [INFO] Task succeeded: fastANI
[2023-03-16 04:36:34,651] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:36:34,651] [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_009886205.1	s__UBA4421 sp009886205	98.2515	722	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.44	96.05	0.88	0.79	9	conclusive
GCA_002336645.1	s__UBA4421 sp002336645	83.6403	558	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182095.1	s__UBA4421 sp905182095	81.203	476	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182905.1	s__UBA4421 sp002390555	78.9546	386	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.65	99.65	0.88	0.88	2	-
GCA_002704225.1	s__UBA4421 sp002704225	75.9765	52	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.56	99.05	0.92	0.86	4	-
GCA_009936775.1	s__UBA4421 sp009936775	75.8727	61	848	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:36:34,657] [INFO] GTDB search result was written to OceanDNA-b36995/result_gtdb.tsv
[2023-03-16 04:36:34,657] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:36:34,658] [INFO] DFAST_QC result json was written to OceanDNA-b36995/dqc_result.json
[2023-03-16 04:36:34,658] [INFO] DFAST_QC completed!
[2023-03-16 04:36:34,658] [INFO] Total running time: 0h1m28s