[2023-03-16 15:26:08,856] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,856] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc3c51cb-ffb9-455e-84c6-006aa40e6434/dqc_reference
[2023-03-16 15:26:11,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:11,536] [INFO] Task started: Prodigal
[2023-03-16 15:26:11,537] [INFO] Running command: cat /var/lib/cwl/stg817c16f5-43d2-4ef2-89f9-6cb9a2c70311/OceanDNA-b42253.fa | prodigal -d OceanDNA-b42253/cds.fna -a OceanDNA-b42253/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:15,632] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:15,632] [INFO] Task started: HMMsearch
[2023-03-16 15:26:15,632] [INFO] Running command: hmmsearch --tblout OceanDNA-b42253/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc3c51cb-ffb9-455e-84c6-006aa40e6434/dqc_reference/reference_markers.hmm OceanDNA-b42253/protein.faa > /dev/null
[2023-03-16 15:26:15,861] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:15,862] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg817c16f5-43d2-4ef2-89f9-6cb9a2c70311/OceanDNA-b42253.fa]
[2023-03-16 15:26:15,870] [INFO] Query marker FASTA was written to OceanDNA-b42253/markers.fasta
[2023-03-16 15:26:15,870] [INFO] Task started: Blastn
[2023-03-16 15:26:15,870] [INFO] Running command: blastn -query OceanDNA-b42253/markers.fasta -db /var/lib/cwl/stgcc3c51cb-ffb9-455e-84c6-006aa40e6434/dqc_reference/reference_markers.fasta -out OceanDNA-b42253/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:20,238] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:20,239] [INFO] Selected 15 target genomes.
[2023-03-16 15:26:20,239] [INFO] Target genome list was writen to OceanDNA-b42253/target_genomes.txt
[2023-03-16 15:26:20,253] [INFO] Task started: fastANI
[2023-03-16 15:26:20,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg817c16f5-43d2-4ef2-89f9-6cb9a2c70311/OceanDNA-b42253.fa --refList OceanDNA-b42253/target_genomes.txt --output OceanDNA-b42253/fastani_result.tsv --threads 1
[2023-03-16 15:26:26,741] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:26,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc3c51cb-ffb9-455e-84c6-006aa40e6434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:26,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc3c51cb-ffb9-455e-84c6-006aa40e6434/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:26,742] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:26:26,742] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 15:26:26,742] [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 15:26:26,742] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42253/tc_result.tsv
[2023-03-16 15:26:26,742] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:26,743] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:26,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc3c51cb-ffb9-455e-84c6-006aa40e6434/dqc_reference/checkm_data
[2023-03-16 15:26:26,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:26,747] [INFO] Task started: CheckM
[2023-03-16 15:26:26,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42253/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42253/checkm_input OceanDNA-b42253/checkm_result
[2023-03-16 15:26:51,965] [INFO] Task succeeded: CheckM
[2023-03-16 15:26:51,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 15:26:51,967] [INFO] ===== Completeness check finished =====
[2023-03-16 15:26:51,967] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:26:51,968] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42253/markers.fasta)
[2023-03-16 15:26:51,969] [INFO] Task started: Blastn
[2023-03-16 15:26:51,969] [INFO] Running command: blastn -query OceanDNA-b42253/markers.fasta -db /var/lib/cwl/stgcc3c51cb-ffb9-455e-84c6-006aa40e6434/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42253/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:52,986] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:52,987] [INFO] Selected 11 target genomes.
[2023-03-16 15:26:52,987] [INFO] Target genome list was writen to OceanDNA-b42253/target_genomes_gtdb.txt
[2023-03-16 15:26:53,324] [INFO] Task started: fastANI
[2023-03-16 15:26:53,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg817c16f5-43d2-4ef2-89f9-6cb9a2c70311/OceanDNA-b42253.fa --refList OceanDNA-b42253/target_genomes_gtdb.txt --output OceanDNA-b42253/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:26:55,377] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:55,383] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 15:26:55,384] [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_902520725.1	s__SAR86A sp902520725	96.216	190	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	99.82	99.82	0.73	0.73	2	conclusive
GCA_902517425.1	s__SAR86A sp902517425	86.9654	176	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520495.1	s__SAR86A sp902520495	80.2541	159	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558095.1	s__SAR86A sp902558095	79.5854	144	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559345.1	s__SAR86A sp902559345	79.5303	123	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169105.1	s__SAR86A sp002169105	79.2473	91	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517505.1	s__SAR86A sp902517505	79.1211	111	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.73	97.59	0.82	0.80	3	-
GCA_902556105.1	s__SAR86A sp902556105	78.9691	116	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560315.1	s__SAR86A sp902560315	78.9089	131	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	95.47	95.47	0.82	0.82	2	-
GCA_002721465.1	s__SAR86A sp002721465	78.3858	79	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.78	96.78	0.69	0.69	2	-
--------------------------------------------------------------------------------
[2023-03-16 15:26:55,384] [INFO] GTDB search result was written to OceanDNA-b42253/result_gtdb.tsv
[2023-03-16 15:26:55,384] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:26:55,385] [INFO] DFAST_QC result json was written to OceanDNA-b42253/dqc_result.json
[2023-03-16 15:26:55,385] [INFO] DFAST_QC completed!
[2023-03-16 15:26:55,385] [INFO] Total running time: 0h0m47s