[2023-03-16 04:05:20,414] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,414] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg237cd2d2-5eae-4c84-816f-cda62eac239e/dqc_reference
[2023-03-16 04:05:22,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,127] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,127] [INFO] Running command: cat /var/lib/cwl/stga85ecee1-cdd8-4c35-a75a-b7a763efa530/OceanDNA-b16213.fa | prodigal -d OceanDNA-b16213/cds.fna -a OceanDNA-b16213/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:39,576] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:39,576] [INFO] Task started: HMMsearch
[2023-03-16 04:05:39,576] [INFO] Running command: hmmsearch --tblout OceanDNA-b16213/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg237cd2d2-5eae-4c84-816f-cda62eac239e/dqc_reference/reference_markers.hmm OceanDNA-b16213/protein.faa > /dev/null
[2023-03-16 04:05:39,788] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:39,789] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga85ecee1-cdd8-4c35-a75a-b7a763efa530/OceanDNA-b16213.fa]
[2023-03-16 04:05:39,812] [INFO] Query marker FASTA was written to OceanDNA-b16213/markers.fasta
[2023-03-16 04:05:39,813] [INFO] Task started: Blastn
[2023-03-16 04:05:39,813] [INFO] Running command: blastn -query OceanDNA-b16213/markers.fasta -db /var/lib/cwl/stg237cd2d2-5eae-4c84-816f-cda62eac239e/dqc_reference/reference_markers.fasta -out OceanDNA-b16213/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:40,312] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:40,313] [INFO] Selected 17 target genomes.
[2023-03-16 04:05:40,313] [INFO] Target genome list was writen to OceanDNA-b16213/target_genomes.txt
[2023-03-16 04:05:40,322] [INFO] Task started: fastANI
[2023-03-16 04:05:40,322] [INFO] Running command: fastANI --query /var/lib/cwl/stga85ecee1-cdd8-4c35-a75a-b7a763efa530/OceanDNA-b16213.fa --refList OceanDNA-b16213/target_genomes.txt --output OceanDNA-b16213/fastani_result.tsv --threads 1
[2023-03-16 04:05:50,162] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:50,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg237cd2d2-5eae-4c84-816f-cda62eac239e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:50,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg237cd2d2-5eae-4c84-816f-cda62eac239e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:50,162] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:50,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:05:50,163] [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 04:05:50,163] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16213/tc_result.tsv
[2023-03-16 04:05:50,163] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:50,163] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:50,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg237cd2d2-5eae-4c84-816f-cda62eac239e/dqc_reference/checkm_data
[2023-03-16 04:05:50,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:50,171] [INFO] Task started: CheckM
[2023-03-16 04:05:50,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16213/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16213/checkm_input OceanDNA-b16213/checkm_result
[2023-03-16 04:06:35,680] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:35,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:35,684] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:35,684] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:35,684] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16213/markers.fasta)
[2023-03-16 04:06:35,684] [INFO] Task started: Blastn
[2023-03-16 04:06:35,684] [INFO] Running command: blastn -query OceanDNA-b16213/markers.fasta -db /var/lib/cwl/stg237cd2d2-5eae-4c84-816f-cda62eac239e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16213/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:36,334] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:36,335] [INFO] Selected 14 target genomes.
[2023-03-16 04:06:36,335] [INFO] Target genome list was writen to OceanDNA-b16213/target_genomes_gtdb.txt
[2023-03-16 04:06:36,348] [INFO] Task started: fastANI
[2023-03-16 04:06:36,348] [INFO] Running command: fastANI --query /var/lib/cwl/stga85ecee1-cdd8-4c35-a75a-b7a763efa530/OceanDNA-b16213.fa --refList OceanDNA-b16213/target_genomes_gtdb.txt --output OceanDNA-b16213/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:47,760] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:47,764] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:47,764] [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
GCF_000155595.1	s__Phormidesmis sp000155595	80.7635	799	1097	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	80.4016	750	1097	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	76.3219	164	1097	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242035.1	s__Phormidesmis foveolarum	76.2327	137	1097	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:47,764] [INFO] GTDB search result was written to OceanDNA-b16213/result_gtdb.tsv
[2023-03-16 04:06:47,765] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:47,765] [INFO] DFAST_QC result json was written to OceanDNA-b16213/dqc_result.json
[2023-03-16 04:06:47,765] [INFO] DFAST_QC completed!
[2023-03-16 04:06:47,765] [INFO] Total running time: 0h1m27s