[2023-03-18 23:22:48,513] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:22:48,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:22:48,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg30056429-dd38-4fe7-a1e0-0c761e5a2448/dqc_reference
[2023-03-18 23:22:49,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:22:49,618] [INFO] Task started: Prodigal
[2023-03-18 23:22:49,619] [INFO] Running command: cat /var/lib/cwl/stg94823be5-74ba-4e57-b478-abd4cc3a9c24/OceanDNA-b25263.fa | prodigal -d OceanDNA-b25263/cds.fna -a OceanDNA-b25263/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:22:54,070] [INFO] Task succeeded: Prodigal
[2023-03-18 23:22:54,070] [INFO] Task started: HMMsearch
[2023-03-18 23:22:54,070] [INFO] Running command: hmmsearch --tblout OceanDNA-b25263/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30056429-dd38-4fe7-a1e0-0c761e5a2448/dqc_reference/reference_markers.hmm OceanDNA-b25263/protein.faa > /dev/null
[2023-03-18 23:22:54,208] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:22:54,209] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg94823be5-74ba-4e57-b478-abd4cc3a9c24/OceanDNA-b25263.fa]
[2023-03-18 23:22:54,218] [INFO] Query marker FASTA was written to OceanDNA-b25263/markers.fasta
[2023-03-18 23:22:54,218] [INFO] Task started: Blastn
[2023-03-18 23:22:54,218] [INFO] Running command: blastn -query OceanDNA-b25263/markers.fasta -db /var/lib/cwl/stg30056429-dd38-4fe7-a1e0-0c761e5a2448/dqc_reference/reference_markers.fasta -out OceanDNA-b25263/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:22:54,714] [INFO] Task succeeded: Blastn
[2023-03-18 23:22:54,716] [INFO] Selected 16 target genomes.
[2023-03-18 23:22:54,716] [INFO] Target genome list was writen to OceanDNA-b25263/target_genomes.txt
[2023-03-18 23:22:54,726] [INFO] Task started: fastANI
[2023-03-18 23:22:54,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg94823be5-74ba-4e57-b478-abd4cc3a9c24/OceanDNA-b25263.fa --refList OceanDNA-b25263/target_genomes.txt --output OceanDNA-b25263/fastani_result.tsv --threads 1
[2023-03-18 23:23:01,745] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:01,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30056429-dd38-4fe7-a1e0-0c761e5a2448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:23:01,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30056429-dd38-4fe7-a1e0-0c761e5a2448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:23:01,745] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:23:01,745] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:23:01,745] [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 23:23:01,746] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25263/tc_result.tsv
[2023-03-18 23:23:01,746] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:23:01,746] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:23:01,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30056429-dd38-4fe7-a1e0-0c761e5a2448/dqc_reference/checkm_data
[2023-03-18 23:23:01,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:23:01,752] [INFO] Task started: CheckM
[2023-03-18 23:23:01,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25263/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25263/checkm_input OceanDNA-b25263/checkm_result
[2023-03-18 23:23:18,752] [INFO] Task succeeded: CheckM
[2023-03-18 23:23:18,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 5.07%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:23:18,755] [INFO] ===== Completeness check finished =====
[2023-03-18 23:23:18,755] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:23:18,755] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25263/markers.fasta)
[2023-03-18 23:23:18,756] [INFO] Task started: Blastn
[2023-03-18 23:23:18,756] [INFO] Running command: blastn -query OceanDNA-b25263/markers.fasta -db /var/lib/cwl/stg30056429-dd38-4fe7-a1e0-0c761e5a2448/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25263/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:19,435] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:19,436] [INFO] Selected 15 target genomes.
[2023-03-18 23:23:19,436] [INFO] Target genome list was writen to OceanDNA-b25263/target_genomes_gtdb.txt
[2023-03-18 23:23:19,443] [INFO] Task started: fastANI
[2023-03-18 23:23:19,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg94823be5-74ba-4e57-b478-abd4cc3a9c24/OceanDNA-b25263.fa --refList OceanDNA-b25263/target_genomes_gtdb.txt --output OceanDNA-b25263/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:23:22,116] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:22,120] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:23:22,120] [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_905182445.1	s__CACCCN01 sp905182445	96.1688	170	285	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	conclusive
GCA_905182145.1	s__CACCCN01 sp905182145	85.6988	175	285	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	84.9911	114	285	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	79.7431	178	285	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_902544525.1	s__CACCCN01 sp902544525	78.821	156	285	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	-
--------------------------------------------------------------------------------
[2023-03-18 23:23:22,121] [INFO] GTDB search result was written to OceanDNA-b25263/result_gtdb.tsv
[2023-03-18 23:23:22,121] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:23:22,122] [INFO] DFAST_QC result json was written to OceanDNA-b25263/dqc_result.json
[2023-03-18 23:23:22,123] [INFO] DFAST_QC completed!
[2023-03-18 23:23:22,123] [INFO] Total running time: 0h0m34s