[2023-03-15 05:53:02,353] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:53:02,354] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:53:02,354] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdeee5ef-03fc-4c0f-b64e-9f639d2d2483/dqc_reference
[2023-03-15 05:53:03,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:53:03,478] [INFO] Task started: Prodigal
[2023-03-15 05:53:03,479] [INFO] Running command: cat /var/lib/cwl/stgb951bb2a-bc8b-4e0a-8c79-25ecd2c34a71/OceanDNA-b26075.fa | prodigal -d OceanDNA-b26075/cds.fna -a OceanDNA-b26075/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:53:14,969] [INFO] Task succeeded: Prodigal
[2023-03-15 05:53:14,969] [INFO] Task started: HMMsearch
[2023-03-15 05:53:14,969] [INFO] Running command: hmmsearch --tblout OceanDNA-b26075/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdeee5ef-03fc-4c0f-b64e-9f639d2d2483/dqc_reference/reference_markers.hmm OceanDNA-b26075/protein.faa > /dev/null
[2023-03-15 05:53:15,148] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:53:15,149] [INFO] Found 6/6 markers.
[2023-03-15 05:53:15,341] [INFO] Query marker FASTA was written to OceanDNA-b26075/markers.fasta
[2023-03-15 05:53:15,342] [INFO] Task started: Blastn
[2023-03-15 05:53:15,342] [INFO] Running command: blastn -query OceanDNA-b26075/markers.fasta -db /var/lib/cwl/stgbdeee5ef-03fc-4c0f-b64e-9f639d2d2483/dqc_reference/reference_markers.fasta -out OceanDNA-b26075/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:15,923] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:15,925] [INFO] Selected 25 target genomes.
[2023-03-15 05:53:15,926] [INFO] Target genome list was writen to OceanDNA-b26075/target_genomes.txt
[2023-03-15 05:53:15,942] [INFO] Task started: fastANI
[2023-03-15 05:53:15,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgb951bb2a-bc8b-4e0a-8c79-25ecd2c34a71/OceanDNA-b26075.fa --refList OceanDNA-b26075/target_genomes.txt --output OceanDNA-b26075/fastani_result.tsv --threads 1
[2023-03-15 05:53:28,332] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:28,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdeee5ef-03fc-4c0f-b64e-9f639d2d2483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:53:28,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdeee5ef-03fc-4c0f-b64e-9f639d2d2483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:53:28,332] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:53:28,333] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:53:28,333] [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 05:53:28,334] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26075/tc_result.tsv
[2023-03-15 05:53:28,334] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:53:28,334] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:53:28,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdeee5ef-03fc-4c0f-b64e-9f639d2d2483/dqc_reference/checkm_data
[2023-03-15 05:53:28,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:53:28,341] [INFO] Task started: CheckM
[2023-03-15 05:53:28,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26075/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26075/checkm_input OceanDNA-b26075/checkm_result
[2023-03-15 05:54:00,558] [INFO] Task succeeded: CheckM
[2023-03-15 05:54:00,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:54:00,561] [INFO] ===== Completeness check finished =====
[2023-03-15 05:54:00,561] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:54:00,561] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26075/markers.fasta)
[2023-03-15 05:54:00,562] [INFO] Task started: Blastn
[2023-03-15 05:54:00,562] [INFO] Running command: blastn -query OceanDNA-b26075/markers.fasta -db /var/lib/cwl/stgbdeee5ef-03fc-4c0f-b64e-9f639d2d2483/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26075/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:54:01,504] [INFO] Task succeeded: Blastn
[2023-03-15 05:54:01,509] [INFO] Selected 24 target genomes.
[2023-03-15 05:54:01,509] [INFO] Target genome list was writen to OceanDNA-b26075/target_genomes_gtdb.txt
[2023-03-15 05:54:01,533] [INFO] Task started: fastANI
[2023-03-15 05:54:01,533] [INFO] Running command: fastANI --query /var/lib/cwl/stgb951bb2a-bc8b-4e0a-8c79-25ecd2c34a71/OceanDNA-b26075.fa --refList OceanDNA-b26075/target_genomes_gtdb.txt --output OceanDNA-b26075/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:54:09,993] [INFO] Task succeeded: fastANI
[2023-03-15 05:54:09,996] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:54:09,996] [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_016780775.1	s__JADHLI01 sp016780775	87.3662	567	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__JADHLI01	95.0	99.93	99.93	0.97	0.97	2	-
GCA_000238815.2	s__HIMB100 sp000238815	77.2757	94	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524805.1	s__WTJO01 sp011524805	75.9831	82	657	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__WTJO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:54:09,998] [INFO] GTDB search result was written to OceanDNA-b26075/result_gtdb.tsv
[2023-03-15 05:54:10,002] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:54:10,005] [INFO] DFAST_QC result json was written to OceanDNA-b26075/dqc_result.json
[2023-03-15 05:54:10,005] [INFO] DFAST_QC completed!
[2023-03-15 05:54:10,005] [INFO] Total running time: 0h1m8s