[2023-03-18 03:09:33,542] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg71c79943-011e-45ee-b0d8-7915b8feadf2/dqc_reference
[2023-03-18 03:09:34,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stgcbe289b2-e4f0-4807-a2d4-41ef30a59ed4/OceanDNA-b42084.fa | prodigal -d OceanDNA-b42084/cds.fna -a OceanDNA-b42084/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:39,645] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:39,645] [INFO] Task started: HMMsearch
[2023-03-18 03:09:39,645] [INFO] Running command: hmmsearch --tblout OceanDNA-b42084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71c79943-011e-45ee-b0d8-7915b8feadf2/dqc_reference/reference_markers.hmm OceanDNA-b42084/protein.faa > /dev/null
[2023-03-18 03:09:39,820] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:39,821] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcbe289b2-e4f0-4807-a2d4-41ef30a59ed4/OceanDNA-b42084.fa]
[2023-03-18 03:09:39,828] [INFO] Query marker FASTA was written to OceanDNA-b42084/markers.fasta
[2023-03-18 03:09:39,828] [INFO] Task started: Blastn
[2023-03-18 03:09:39,828] [INFO] Running command: blastn -query OceanDNA-b42084/markers.fasta -db /var/lib/cwl/stg71c79943-011e-45ee-b0d8-7915b8feadf2/dqc_reference/reference_markers.fasta -out OceanDNA-b42084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:40,341] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:40,342] [INFO] Selected 13 target genomes.
[2023-03-18 03:09:40,342] [INFO] Target genome list was writen to OceanDNA-b42084/target_genomes.txt
[2023-03-18 03:09:40,349] [INFO] Task started: fastANI
[2023-03-18 03:09:40,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe289b2-e4f0-4807-a2d4-41ef30a59ed4/OceanDNA-b42084.fa --refList OceanDNA-b42084/target_genomes.txt --output OceanDNA-b42084/fastani_result.tsv --threads 1
[2023-03-18 03:09:46,419] [INFO] Task succeeded: fastANI
[2023-03-18 03:09:46,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71c79943-011e-45ee-b0d8-7915b8feadf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:09:46,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71c79943-011e-45ee-b0d8-7915b8feadf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:09:46,420] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:09:46,420] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:09:46,420] [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 03:09:46,420] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42084/tc_result.tsv
[2023-03-18 03:09:46,420] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:09:46,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:09:46,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71c79943-011e-45ee-b0d8-7915b8feadf2/dqc_reference/checkm_data
[2023-03-18 03:09:46,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:09:46,429] [INFO] Task started: CheckM
[2023-03-18 03:09:46,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42084/checkm_input OceanDNA-b42084/checkm_result
[2023-03-18 03:10:04,892] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:04,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:04,894] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:04,894] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:04,894] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42084/markers.fasta)
[2023-03-18 03:10:04,894] [INFO] Task started: Blastn
[2023-03-18 03:10:04,894] [INFO] Running command: blastn -query OceanDNA-b42084/markers.fasta -db /var/lib/cwl/stg71c79943-011e-45ee-b0d8-7915b8feadf2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:05,729] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:05,729] [INFO] Selected 8 target genomes.
[2023-03-18 03:10:05,730] [INFO] Target genome list was writen to OceanDNA-b42084/target_genomes_gtdb.txt
[2023-03-18 03:10:05,755] [INFO] Task started: fastANI
[2023-03-18 03:10:05,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe289b2-e4f0-4807-a2d4-41ef30a59ed4/OceanDNA-b42084.fa --refList OceanDNA-b42084/target_genomes_gtdb.txt --output OceanDNA-b42084/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:07,898] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:07,904] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:10:07,904] [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_902599315.1	s__D2472 sp902599315	96.6559	292	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	97.18	96.37	0.89	0.86	3	conclusive
GCA_902515775.1	s__D2472 sp902515775	94.5034	253	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541245.1	s__D2472 sp902541245	93.6088	180	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528215.1	s__D2472 sp902528215	92.6326	237	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	85.8778	227	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_902515455.1	s__D2472 sp902515455	85.4463	192	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627055.1	s__D2472 sp902627055	85.1017	243	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331545.1	s__D2472 sp003331545	78.666	105	316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:07,904] [INFO] GTDB search result was written to OceanDNA-b42084/result_gtdb.tsv
[2023-03-18 03:10:07,904] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:07,905] [INFO] DFAST_QC result json was written to OceanDNA-b42084/dqc_result.json
[2023-03-18 03:10:07,905] [INFO] DFAST_QC completed!
[2023-03-18 03:10:07,905] [INFO] Total running time: 0h0m34s