[2023-03-15 17:24:01,292] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,296] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,296] [INFO] DQC Reference Directory: /var/lib/cwl/stgddf492c0-a21e-4e94-bbeb-cb0900865e13/dqc_reference
[2023-03-15 17:24:02,625] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,625] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,625] [INFO] Running command: cat /var/lib/cwl/stgea7bdd5d-fa04-4264-a029-7e263e98def1/OceanDNA-b16222.fa | prodigal -d OceanDNA-b16222/cds.fna -a OceanDNA-b16222/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:29,096] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:29,096] [INFO] Task started: HMMsearch
[2023-03-15 17:24:29,097] [INFO] Running command: hmmsearch --tblout OceanDNA-b16222/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddf492c0-a21e-4e94-bbeb-cb0900865e13/dqc_reference/reference_markers.hmm OceanDNA-b16222/protein.faa > /dev/null
[2023-03-15 17:24:29,378] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:29,379] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgea7bdd5d-fa04-4264-a029-7e263e98def1/OceanDNA-b16222.fa]
[2023-03-15 17:24:29,408] [INFO] Query marker FASTA was written to OceanDNA-b16222/markers.fasta
[2023-03-15 17:24:29,409] [INFO] Task started: Blastn
[2023-03-15 17:24:29,409] [INFO] Running command: blastn -query OceanDNA-b16222/markers.fasta -db /var/lib/cwl/stgddf492c0-a21e-4e94-bbeb-cb0900865e13/dqc_reference/reference_markers.fasta -out OceanDNA-b16222/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:30,006] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:30,007] [INFO] Selected 26 target genomes.
[2023-03-15 17:24:30,007] [INFO] Target genome list was writen to OceanDNA-b16222/target_genomes.txt
[2023-03-15 17:24:30,028] [INFO] Task started: fastANI
[2023-03-15 17:24:30,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgea7bdd5d-fa04-4264-a029-7e263e98def1/OceanDNA-b16222.fa --refList OceanDNA-b16222/target_genomes.txt --output OceanDNA-b16222/fastani_result.tsv --threads 1
[2023-03-15 17:24:48,900] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:48,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddf492c0-a21e-4e94-bbeb-cb0900865e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:48,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddf492c0-a21e-4e94-bbeb-cb0900865e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:48,901] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:48,901] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:24:48,901] [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
--------------------------------------------------------------------------------
[2023-03-15 17:24:48,902] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16222/tc_result.tsv
[2023-03-15 17:24:48,902] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:48,902] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:48,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddf492c0-a21e-4e94-bbeb-cb0900865e13/dqc_reference/checkm_data
[2023-03-15 17:24:48,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:48,911] [INFO] Task started: CheckM
[2023-03-15 17:24:48,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16222/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16222/checkm_input OceanDNA-b16222/checkm_result
[2023-03-15 17:25:48,353] [INFO] Task succeeded: CheckM
[2023-03-15 17:25:48,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:25:48,357] [INFO] ===== Completeness check finished =====
[2023-03-15 17:25:48,357] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:25:48,357] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16222/markers.fasta)
[2023-03-15 17:25:48,358] [INFO] Task started: Blastn
[2023-03-15 17:25:48,358] [INFO] Running command: blastn -query OceanDNA-b16222/markers.fasta -db /var/lib/cwl/stgddf492c0-a21e-4e94-bbeb-cb0900865e13/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16222/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:49,374] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:49,375] [INFO] Selected 27 target genomes.
[2023-03-15 17:25:49,375] [INFO] Target genome list was writen to OceanDNA-b16222/target_genomes_gtdb.txt
[2023-03-15 17:25:49,398] [INFO] Task started: fastANI
[2023-03-15 17:25:49,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgea7bdd5d-fa04-4264-a029-7e263e98def1/OceanDNA-b16222.fa --refList OceanDNA-b16222/target_genomes_gtdb.txt --output OceanDNA-b16222/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:26:12,941] [INFO] Task succeeded: fastANI
[2023-03-15 17:26:12,946] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:26:12,946] [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	79.0542	595	1484	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	76.6444	162	1484	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	76.4835	232	1484	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	76.3094	154	1484	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	76.2789	201	1484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317045.1	s__PCC-7407 sp000317045	75.7758	56	1484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-7407;f__PCC-7407;g__PCC-7407	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763385.1	s__Nodosilinea sp000763385	75.546	64	1484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695775.1	s__Nodosilinea sp014695775	75.4287	59	1484	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	100.00	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-03-15 17:26:12,947] [INFO] GTDB search result was written to OceanDNA-b16222/result_gtdb.tsv
[2023-03-15 17:26:12,947] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:26:12,947] [INFO] DFAST_QC result json was written to OceanDNA-b16222/dqc_result.json
[2023-03-15 17:26:12,947] [INFO] DFAST_QC completed!
[2023-03-15 17:26:12,948] [INFO] Total running time: 0h2m12s