[2023-03-15 13:03:53,432] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg308f7b12-a90e-4bfa-a1d6-0d63cf697945/dqc_reference
[2023-03-15 13:03:54,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,756] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,756] [INFO] Running command: cat /var/lib/cwl/stga8dd38f3-1e5d-4a3b-ab5c-97d4622caff3/OceanDNA-b37060.fa | prodigal -d OceanDNA-b37060/cds.fna -a OceanDNA-b37060/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:09,110] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:09,111] [INFO] Task started: HMMsearch
[2023-03-15 13:04:09,111] [INFO] Running command: hmmsearch --tblout OceanDNA-b37060/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg308f7b12-a90e-4bfa-a1d6-0d63cf697945/dqc_reference/reference_markers.hmm OceanDNA-b37060/protein.faa > /dev/null
[2023-03-15 13:04:09,345] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:09,345] [INFO] Found 6/6 markers.
[2023-03-15 13:04:09,363] [INFO] Query marker FASTA was written to OceanDNA-b37060/markers.fasta
[2023-03-15 13:04:09,364] [INFO] Task started: Blastn
[2023-03-15 13:04:09,364] [INFO] Running command: blastn -query OceanDNA-b37060/markers.fasta -db /var/lib/cwl/stg308f7b12-a90e-4bfa-a1d6-0d63cf697945/dqc_reference/reference_markers.fasta -out OceanDNA-b37060/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:09,971] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:09,972] [INFO] Selected 35 target genomes.
[2023-03-15 13:04:09,972] [INFO] Target genome list was writen to OceanDNA-b37060/target_genomes.txt
[2023-03-15 13:04:10,039] [INFO] Task started: fastANI
[2023-03-15 13:04:10,040] [INFO] Running command: fastANI --query /var/lib/cwl/stga8dd38f3-1e5d-4a3b-ab5c-97d4622caff3/OceanDNA-b37060.fa --refList OceanDNA-b37060/target_genomes.txt --output OceanDNA-b37060/fastani_result.tsv --threads 1
[2023-03-15 13:04:34,514] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:34,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg308f7b12-a90e-4bfa-a1d6-0d63cf697945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:34,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg308f7b12-a90e-4bfa-a1d6-0d63cf697945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:34,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:34,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:34,515] [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
--------------------------------------------------------------------------------
[2023-03-15 13:04:34,515] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37060/tc_result.tsv
[2023-03-15 13:04:34,518] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:34,518] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:34,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg308f7b12-a90e-4bfa-a1d6-0d63cf697945/dqc_reference/checkm_data
[2023-03-15 13:04:34,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:34,525] [INFO] Task started: CheckM
[2023-03-15 13:04:34,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37060/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37060/checkm_input OceanDNA-b37060/checkm_result
[2023-03-15 13:05:13,183] [INFO] Task succeeded: CheckM
[2023-03-15 13:05:13,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:05:13,186] [INFO] ===== Completeness check finished =====
[2023-03-15 13:05:13,186] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:05:13,186] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37060/markers.fasta)
[2023-03-15 13:05:13,186] [INFO] Task started: Blastn
[2023-03-15 13:05:13,186] [INFO] Running command: blastn -query OceanDNA-b37060/markers.fasta -db /var/lib/cwl/stg308f7b12-a90e-4bfa-a1d6-0d63cf697945/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37060/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:05:14,180] [INFO] Task succeeded: Blastn
[2023-03-15 13:05:14,180] [INFO] Selected 21 target genomes.
[2023-03-15 13:05:14,181] [INFO] Target genome list was writen to OceanDNA-b37060/target_genomes_gtdb.txt
[2023-03-15 13:05:14,347] [INFO] Task started: fastANI
[2023-03-15 13:05:14,347] [INFO] Running command: fastANI --query /var/lib/cwl/stga8dd38f3-1e5d-4a3b-ab5c-97d4622caff3/OceanDNA-b37060.fa --refList OceanDNA-b37060/target_genomes_gtdb.txt --output OceanDNA-b37060/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:26,921] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:26,925] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:05:26,925] [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_002348825.1	s__UBA4421 sp002348825	99.1461	654	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.36	99.22	0.85	0.84	3	conclusive
GCA_002725095.1	s__UBA4421 sp002725095	81.8495	410	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.07	99.07	0.73	0.73	2	-
GCA_002684495.1	s__UBA4421 sp002684495	77.6459	303	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690405.1	s__UBA4421 sp002690405	77.5859	284	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.88	98.84	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:26,925] [INFO] GTDB search result was written to OceanDNA-b37060/result_gtdb.tsv
[2023-03-15 13:05:26,925] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:26,926] [INFO] DFAST_QC result json was written to OceanDNA-b37060/dqc_result.json
[2023-03-15 13:05:26,926] [INFO] DFAST_QC completed!
[2023-03-15 13:05:26,926] [INFO] Total running time: 0h1m33s