[2023-03-18 01:14:00,922] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:14:00,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:14:00,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bd39d48-bd50-46a5-b1f4-4a7484243ab6/dqc_reference
[2023-03-18 01:14:02,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:14:02,073] [INFO] Task started: Prodigal
[2023-03-18 01:14:02,073] [INFO] Running command: cat /var/lib/cwl/stg3b438d76-768b-482d-8e0c-d963b49749c9/OceanDNA-b16231.fa | prodigal -d OceanDNA-b16231/cds.fna -a OceanDNA-b16231/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:14:21,901] [INFO] Task succeeded: Prodigal
[2023-03-18 01:14:21,901] [INFO] Task started: HMMsearch
[2023-03-18 01:14:21,901] [INFO] Running command: hmmsearch --tblout OceanDNA-b16231/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bd39d48-bd50-46a5-b1f4-4a7484243ab6/dqc_reference/reference_markers.hmm OceanDNA-b16231/protein.faa > /dev/null
[2023-03-18 01:14:22,117] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:14:22,118] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3b438d76-768b-482d-8e0c-d963b49749c9/OceanDNA-b16231.fa]
[2023-03-18 01:14:22,141] [INFO] Query marker FASTA was written to OceanDNA-b16231/markers.fasta
[2023-03-18 01:14:22,142] [INFO] Task started: Blastn
[2023-03-18 01:14:22,143] [INFO] Running command: blastn -query OceanDNA-b16231/markers.fasta -db /var/lib/cwl/stg8bd39d48-bd50-46a5-b1f4-4a7484243ab6/dqc_reference/reference_markers.fasta -out OceanDNA-b16231/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:14:22,659] [INFO] Task succeeded: Blastn
[2023-03-18 01:14:22,660] [INFO] Selected 24 target genomes.
[2023-03-18 01:14:22,660] [INFO] Target genome list was writen to OceanDNA-b16231/target_genomes.txt
[2023-03-18 01:14:22,675] [INFO] Task started: fastANI
[2023-03-18 01:14:22,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b438d76-768b-482d-8e0c-d963b49749c9/OceanDNA-b16231.fa --refList OceanDNA-b16231/target_genomes.txt --output OceanDNA-b16231/fastani_result.tsv --threads 1
[2023-03-18 01:14:36,154] [INFO] Task succeeded: fastANI
[2023-03-18 01:14:36,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bd39d48-bd50-46a5-b1f4-4a7484243ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:14:36,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bd39d48-bd50-46a5-b1f4-4a7484243ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:14:36,155] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:14:36,155] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:14:36,155] [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 01:14:36,155] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16231/tc_result.tsv
[2023-03-18 01:14:36,155] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:14:36,156] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:14:36,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bd39d48-bd50-46a5-b1f4-4a7484243ab6/dqc_reference/checkm_data
[2023-03-18 01:14:36,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:14:36,172] [INFO] Task started: CheckM
[2023-03-18 01:14:36,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16231/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16231/checkm_input OceanDNA-b16231/checkm_result
[2023-03-18 01:15:26,274] [INFO] Task succeeded: CheckM
[2023-03-18 01:15:26,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:15:26,277] [INFO] ===== Completeness check finished =====
[2023-03-18 01:15:26,277] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:15:26,278] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16231/markers.fasta)
[2023-03-18 01:15:26,279] [INFO] Task started: Blastn
[2023-03-18 01:15:26,279] [INFO] Running command: blastn -query OceanDNA-b16231/markers.fasta -db /var/lib/cwl/stg8bd39d48-bd50-46a5-b1f4-4a7484243ab6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16231/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:15:27,053] [INFO] Task succeeded: Blastn
[2023-03-18 01:15:27,054] [INFO] Selected 19 target genomes.
[2023-03-18 01:15:27,054] [INFO] Target genome list was writen to OceanDNA-b16231/target_genomes_gtdb.txt
[2023-03-18 01:15:27,088] [INFO] Task started: fastANI
[2023-03-18 01:15:27,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b438d76-768b-482d-8e0c-d963b49749c9/OceanDNA-b16231.fa --refList OceanDNA-b16231/target_genomes_gtdb.txt --output OceanDNA-b16231/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:15:42,676] [INFO] Task succeeded: fastANI
[2023-03-18 01:15:42,681] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:15:42,681] [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_003242035.1	s__Phormidesmis foveolarum	78.6456	450	1189	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286735.1	s__Phormidesmis sp002286735	76.6791	227	1189	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314865.1	s__Phormidesmis priestleyi_B	76.4402	209	1189	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207105.1	s__Phormidesmis sp015207105	76.4314	163	1189	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033015.1	s__Phormidesmis sp012033015	76.4007	151	1189	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242115.1	s__Phormidesmis priestleyi_A	76.3703	177	1189	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010671975.1	s__SIO4C1 sp010671975	75.5653	61	1189	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__SIO4C1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:15:42,681] [INFO] GTDB search result was written to OceanDNA-b16231/result_gtdb.tsv
[2023-03-18 01:15:42,681] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:15:42,682] [INFO] DFAST_QC result json was written to OceanDNA-b16231/dqc_result.json
[2023-03-18 01:15:42,682] [INFO] DFAST_QC completed!
[2023-03-18 01:15:42,682] [INFO] Total running time: 0h1m42s