[2023-03-18 00:15:08,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:15:08,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:15:08,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg809d5180-6606-4f46-90d8-55e1e3958d69/dqc_reference
[2023-03-18 00:15:09,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:15:09,467] [INFO] Task started: Prodigal
[2023-03-18 00:15:09,467] [INFO] Running command: cat /var/lib/cwl/stgd6918f0c-00e8-49cd-a7fc-db8dce8b9714/OceanDNA-b25175.fa | prodigal -d OceanDNA-b25175/cds.fna -a OceanDNA-b25175/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:15:12,248] [INFO] Task succeeded: Prodigal
[2023-03-18 00:15:12,249] [INFO] Task started: HMMsearch
[2023-03-18 00:15:12,249] [INFO] Running command: hmmsearch --tblout OceanDNA-b25175/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg809d5180-6606-4f46-90d8-55e1e3958d69/dqc_reference/reference_markers.hmm OceanDNA-b25175/protein.faa > /dev/null
[2023-03-18 00:15:12,414] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:15:12,414] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6918f0c-00e8-49cd-a7fc-db8dce8b9714/OceanDNA-b25175.fa]
[2023-03-18 00:15:12,423] [INFO] Query marker FASTA was written to OceanDNA-b25175/markers.fasta
[2023-03-18 00:15:12,424] [INFO] Task started: Blastn
[2023-03-18 00:15:12,424] [INFO] Running command: blastn -query OceanDNA-b25175/markers.fasta -db /var/lib/cwl/stg809d5180-6606-4f46-90d8-55e1e3958d69/dqc_reference/reference_markers.fasta -out OceanDNA-b25175/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:12,982] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:12,982] [INFO] Selected 15 target genomes.
[2023-03-18 00:15:12,983] [INFO] Target genome list was writen to OceanDNA-b25175/target_genomes.txt
[2023-03-18 00:15:12,991] [INFO] Task started: fastANI
[2023-03-18 00:15:12,991] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6918f0c-00e8-49cd-a7fc-db8dce8b9714/OceanDNA-b25175.fa --refList OceanDNA-b25175/target_genomes.txt --output OceanDNA-b25175/fastani_result.tsv --threads 1
[2023-03-18 00:15:19,998] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:19,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg809d5180-6606-4f46-90d8-55e1e3958d69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:15:19,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg809d5180-6606-4f46-90d8-55e1e3958d69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:15:19,999] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:15:19,999] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:15:19,999] [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 00:15:20,002] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25175/tc_result.tsv
[2023-03-18 00:15:20,002] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:15:20,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:15:20,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg809d5180-6606-4f46-90d8-55e1e3958d69/dqc_reference/checkm_data
[2023-03-18 00:15:20,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:15:20,008] [INFO] Task started: CheckM
[2023-03-18 00:15:20,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25175/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25175/checkm_input OceanDNA-b25175/checkm_result
[2023-03-18 00:15:33,577] [INFO] Task succeeded: CheckM
[2023-03-18 00:15:33,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 00:15:33,588] [INFO] ===== Completeness check finished =====
[2023-03-18 00:15:33,588] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:15:33,588] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25175/markers.fasta)
[2023-03-18 00:15:33,588] [INFO] Task started: Blastn
[2023-03-18 00:15:33,588] [INFO] Running command: blastn -query OceanDNA-b25175/markers.fasta -db /var/lib/cwl/stg809d5180-6606-4f46-90d8-55e1e3958d69/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25175/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:34,332] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:34,337] [INFO] Selected 23 target genomes.
[2023-03-18 00:15:34,337] [INFO] Target genome list was writen to OceanDNA-b25175/target_genomes_gtdb.txt
[2023-03-18 00:15:34,362] [INFO] Task started: fastANI
[2023-03-18 00:15:34,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6918f0c-00e8-49cd-a7fc-db8dce8b9714/OceanDNA-b25175.fa --refList OceanDNA-b25175/target_genomes_gtdb.txt --output OceanDNA-b25175/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:15:38,642] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:38,645] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:15:38,646] [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_902544525.1	s__CACCCN01 sp902544525	97.3483	158	172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	95.77	95.63	0.82	0.80	3	conclusive
GCA_905182445.1	s__CACCCN01 sp905182445	78.2031	68	172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777745.1	s__CACCCN01 sp016777745	77.8475	57	172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	99.44	99.44	0.52	0.52	2	-
GCA_905182345.1	s__CACCCN01 sp905182345	77.7125	64	172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CACCCN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:15:38,646] [INFO] GTDB search result was written to OceanDNA-b25175/result_gtdb.tsv
[2023-03-18 00:15:38,646] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:15:38,647] [INFO] DFAST_QC result json was written to OceanDNA-b25175/dqc_result.json
[2023-03-18 00:15:38,647] [INFO] DFAST_QC completed!
[2023-03-18 00:15:38,647] [INFO] Total running time: 0h0m30s