[2023-03-16 04:24:46,339] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,339] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe3e2723-87e9-47e1-abe8-815657336e30/dqc_reference
[2023-03-16 04:24:48,118] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,118] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,118] [INFO] Running command: cat /var/lib/cwl/stg3fea6a8b-b0fb-4d8c-bb3a-b4d3bf2e10d2/OceanDNA-b25279.fa | prodigal -d OceanDNA-b25279/cds.fna -a OceanDNA-b25279/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:24:52,777] [INFO] Task succeeded: Prodigal
[2023-03-16 04:24:52,777] [INFO] Task started: HMMsearch
[2023-03-16 04:24:52,777] [INFO] Running command: hmmsearch --tblout OceanDNA-b25279/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe3e2723-87e9-47e1-abe8-815657336e30/dqc_reference/reference_markers.hmm OceanDNA-b25279/protein.faa > /dev/null
[2023-03-16 04:24:52,977] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:24:52,978] [INFO] Found 6/6 markers.
[2023-03-16 04:24:52,985] [INFO] Query marker FASTA was written to OceanDNA-b25279/markers.fasta
[2023-03-16 04:24:52,985] [INFO] Task started: Blastn
[2023-03-16 04:24:52,985] [INFO] Running command: blastn -query OceanDNA-b25279/markers.fasta -db /var/lib/cwl/stgbe3e2723-87e9-47e1-abe8-815657336e30/dqc_reference/reference_markers.fasta -out OceanDNA-b25279/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:24:53,629] [INFO] Task succeeded: Blastn
[2023-03-16 04:24:53,629] [INFO] Selected 16 target genomes.
[2023-03-16 04:24:53,630] [INFO] Target genome list was writen to OceanDNA-b25279/target_genomes.txt
[2023-03-16 04:24:53,638] [INFO] Task started: fastANI
[2023-03-16 04:24:53,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fea6a8b-b0fb-4d8c-bb3a-b4d3bf2e10d2/OceanDNA-b25279.fa --refList OceanDNA-b25279/target_genomes.txt --output OceanDNA-b25279/fastani_result.tsv --threads 1
[2023-03-16 04:24:59,792] [INFO] Task succeeded: fastANI
[2023-03-16 04:24:59,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe3e2723-87e9-47e1-abe8-815657336e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:24:59,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe3e2723-87e9-47e1-abe8-815657336e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:24:59,793] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:24:59,793] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:24:59,793] [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 04:24:59,793] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25279/tc_result.tsv
[2023-03-16 04:24:59,793] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:24:59,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:24:59,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe3e2723-87e9-47e1-abe8-815657336e30/dqc_reference/checkm_data
[2023-03-16 04:24:59,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:24:59,799] [INFO] Task started: CheckM
[2023-03-16 04:24:59,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25279/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25279/checkm_input OceanDNA-b25279/checkm_result
[2023-03-16 04:25:17,836] [INFO] Task succeeded: CheckM
[2023-03-16 04:25:17,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:25:17,838] [INFO] ===== Completeness check finished =====
[2023-03-16 04:25:17,838] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:25:17,838] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25279/markers.fasta)
[2023-03-16 04:25:17,839] [INFO] Task started: Blastn
[2023-03-16 04:25:17,839] [INFO] Running command: blastn -query OceanDNA-b25279/markers.fasta -db /var/lib/cwl/stgbe3e2723-87e9-47e1-abe8-815657336e30/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25279/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:18,609] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:18,610] [INFO] Selected 27 target genomes.
[2023-03-16 04:25:18,610] [INFO] Target genome list was writen to OceanDNA-b25279/target_genomes_gtdb.txt
[2023-03-16 04:25:18,686] [INFO] Task started: fastANI
[2023-03-16 04:25:18,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fea6a8b-b0fb-4d8c-bb3a-b4d3bf2e10d2/OceanDNA-b25279.fa --refList OceanDNA-b25279/target_genomes_gtdb.txt --output OceanDNA-b25279/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:25:23,779] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:23,782] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:25:23,782] [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_902518955.1	s__CABYIR01 sp902518955	77.4696	77	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CABYIR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902584815.1	s__CABYIR01 sp902584815	76.8904	88	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CABYIR01	95.0	97.27	95.18	0.69	0.61	8	-
GCA_003282485.1	s__AG-422-B15 sp003282485	75.9303	53	302	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:25:23,782] [INFO] GTDB search result was written to OceanDNA-b25279/result_gtdb.tsv
[2023-03-16 04:25:23,782] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:25:23,783] [INFO] DFAST_QC result json was written to OceanDNA-b25279/dqc_result.json
[2023-03-16 04:25:23,783] [INFO] DFAST_QC completed!
[2023-03-16 04:25:23,783] [INFO] Total running time: 0h0m37s