[2023-03-16 10:20:34,794] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,794] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg360ae18e-736d-47d6-a1fc-5e147391be11/dqc_reference
[2023-03-16 10:20:35,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,978] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,979] [INFO] Running command: cat /var/lib/cwl/stg0a30656b-056f-412d-8411-5e943c21f6b9/OceanDNA-b26419.fa | prodigal -d OceanDNA-b26419/cds.fna -a OceanDNA-b26419/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:41,922] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:41,922] [INFO] Task started: HMMsearch
[2023-03-16 10:20:41,922] [INFO] Running command: hmmsearch --tblout OceanDNA-b26419/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg360ae18e-736d-47d6-a1fc-5e147391be11/dqc_reference/reference_markers.hmm OceanDNA-b26419/protein.faa > /dev/null
[2023-03-16 10:20:42,156] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:42,156] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0a30656b-056f-412d-8411-5e943c21f6b9/OceanDNA-b26419.fa]
[2023-03-16 10:20:42,169] [INFO] Query marker FASTA was written to OceanDNA-b26419/markers.fasta
[2023-03-16 10:20:42,169] [INFO] Task started: Blastn
[2023-03-16 10:20:42,169] [INFO] Running command: blastn -query OceanDNA-b26419/markers.fasta -db /var/lib/cwl/stg360ae18e-736d-47d6-a1fc-5e147391be11/dqc_reference/reference_markers.fasta -out OceanDNA-b26419/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:42,652] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:42,653] [INFO] Selected 19 target genomes.
[2023-03-16 10:20:42,653] [INFO] Target genome list was writen to OceanDNA-b26419/target_genomes.txt
[2023-03-16 10:20:42,670] [INFO] Task started: fastANI
[2023-03-16 10:20:42,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a30656b-056f-412d-8411-5e943c21f6b9/OceanDNA-b26419.fa --refList OceanDNA-b26419/target_genomes.txt --output OceanDNA-b26419/fastani_result.tsv --threads 1
[2023-03-16 10:20:57,170] [INFO] Task succeeded: fastANI
[2023-03-16 10:20:57,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg360ae18e-736d-47d6-a1fc-5e147391be11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:20:57,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg360ae18e-736d-47d6-a1fc-5e147391be11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:20:57,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:20:57,171] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:20:57,171] [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 10:20:57,171] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26419/tc_result.tsv
[2023-03-16 10:20:57,171] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:20:57,171] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:20:57,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg360ae18e-736d-47d6-a1fc-5e147391be11/dqc_reference/checkm_data
[2023-03-16 10:20:57,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:20:57,178] [INFO] Task started: CheckM
[2023-03-16 10:20:57,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26419/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26419/checkm_input OceanDNA-b26419/checkm_result
[2023-03-16 10:21:18,084] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:18,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:18,086] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:18,087] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:18,087] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26419/markers.fasta)
[2023-03-16 10:21:18,088] [INFO] Task started: Blastn
[2023-03-16 10:21:18,088] [INFO] Running command: blastn -query OceanDNA-b26419/markers.fasta -db /var/lib/cwl/stg360ae18e-736d-47d6-a1fc-5e147391be11/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26419/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:18,602] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:18,603] [INFO] Selected 9 target genomes.
[2023-03-16 10:21:18,603] [INFO] Target genome list was writen to OceanDNA-b26419/target_genomes_gtdb.txt
[2023-03-16 10:21:18,611] [INFO] Task started: fastANI
[2023-03-16 10:21:18,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a30656b-056f-412d-8411-5e943c21f6b9/OceanDNA-b26419.fa --refList OceanDNA-b26419/target_genomes_gtdb.txt --output OceanDNA-b26419/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:22,257] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:22,261] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:21:22,261] [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_018624035.1	s__UBA8309 sp018624035	92.4362	118	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920665.1	s__UBA8309 sp009920665	89.7294	122	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	80.5992	75	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	79.5819	61	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:22,261] [INFO] GTDB search result was written to OceanDNA-b26419/result_gtdb.tsv
[2023-03-16 10:21:22,262] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:22,263] [INFO] DFAST_QC result json was written to OceanDNA-b26419/dqc_result.json
[2023-03-16 10:21:22,263] [INFO] DFAST_QC completed!
[2023-03-16 10:21:22,263] [INFO] Total running time: 0h0m47s