[2023-03-17 23:01:26,550] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:01:26,564] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:01:26,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg169d9da0-a71a-46d5-82d3-f4e55e3a03cd/dqc_reference
[2023-03-17 23:01:28,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:01:28,781] [INFO] Task started: Prodigal
[2023-03-17 23:01:28,781] [INFO] Running command: cat /var/lib/cwl/stg8605a517-b220-4c9f-8bf0-ac85791960b5/OceanDNA-b16216.fa | prodigal -d OceanDNA-b16216/cds.fna -a OceanDNA-b16216/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:01:49,392] [INFO] Task succeeded: Prodigal
[2023-03-17 23:01:49,393] [INFO] Task started: HMMsearch
[2023-03-17 23:01:49,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b16216/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg169d9da0-a71a-46d5-82d3-f4e55e3a03cd/dqc_reference/reference_markers.hmm OceanDNA-b16216/protein.faa > /dev/null
[2023-03-17 23:01:49,618] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:01:49,619] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8605a517-b220-4c9f-8bf0-ac85791960b5/OceanDNA-b16216.fa]
[2023-03-17 23:01:49,654] [INFO] Query marker FASTA was written to OceanDNA-b16216/markers.fasta
[2023-03-17 23:01:49,655] [INFO] Task started: Blastn
[2023-03-17 23:01:49,655] [INFO] Running command: blastn -query OceanDNA-b16216/markers.fasta -db /var/lib/cwl/stg169d9da0-a71a-46d5-82d3-f4e55e3a03cd/dqc_reference/reference_markers.fasta -out OceanDNA-b16216/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:01:50,166] [INFO] Task succeeded: Blastn
[2023-03-17 23:01:50,170] [INFO] Selected 15 target genomes.
[2023-03-17 23:01:50,170] [INFO] Target genome list was writen to OceanDNA-b16216/target_genomes.txt
[2023-03-17 23:01:50,178] [INFO] Task started: fastANI
[2023-03-17 23:01:50,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg8605a517-b220-4c9f-8bf0-ac85791960b5/OceanDNA-b16216.fa --refList OceanDNA-b16216/target_genomes.txt --output OceanDNA-b16216/fastani_result.tsv --threads 1
[2023-03-17 23:02:01,263] [INFO] Task succeeded: fastANI
[2023-03-17 23:02:01,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg169d9da0-a71a-46d5-82d3-f4e55e3a03cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:02:01,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg169d9da0-a71a-46d5-82d3-f4e55e3a03cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:02:01,264] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:02:01,264] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:02:01,264] [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
--------------------------------------------------------------------------------
[2023-03-17 23:02:01,267] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16216/tc_result.tsv
[2023-03-17 23:02:01,268] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:02:01,269] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:02:01,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg169d9da0-a71a-46d5-82d3-f4e55e3a03cd/dqc_reference/checkm_data
[2023-03-17 23:02:01,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:02:01,418] [INFO] Task started: CheckM
[2023-03-17 23:02:01,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16216/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16216/checkm_input OceanDNA-b16216/checkm_result
[2023-03-17 23:02:54,980] [INFO] Task succeeded: CheckM
[2023-03-17 23:02:54,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:02:54,996] [INFO] ===== Completeness check finished =====
[2023-03-17 23:02:54,996] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:02:54,996] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16216/markers.fasta)
[2023-03-17 23:02:54,997] [INFO] Task started: Blastn
[2023-03-17 23:02:54,997] [INFO] Running command: blastn -query OceanDNA-b16216/markers.fasta -db /var/lib/cwl/stg169d9da0-a71a-46d5-82d3-f4e55e3a03cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16216/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:02:55,694] [INFO] Task succeeded: Blastn
[2023-03-17 23:02:55,706] [INFO] Selected 14 target genomes.
[2023-03-17 23:02:55,706] [INFO] Target genome list was writen to OceanDNA-b16216/target_genomes_gtdb.txt
[2023-03-17 23:02:55,722] [INFO] Task started: fastANI
[2023-03-17 23:02:55,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg8605a517-b220-4c9f-8bf0-ac85791960b5/OceanDNA-b16216.fa --refList OceanDNA-b16216/target_genomes_gtdb.txt --output OceanDNA-b16216/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:03:07,119] [INFO] Task succeeded: fastANI
[2023-03-17 23:03:07,123] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:03:07,123] [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_002286735.1	s__Phormidesmis sp002286735	76.6423	147	1260	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	76.5091	151	1260	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	76.3858	149	1260	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	76.2856	180	1260	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155595.1	s__Phormidesmis sp000155595	76.0765	121	1260	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:03:07,123] [INFO] GTDB search result was written to OceanDNA-b16216/result_gtdb.tsv
[2023-03-17 23:03:07,123] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:03:07,124] [INFO] DFAST_QC result json was written to OceanDNA-b16216/dqc_result.json
[2023-03-17 23:03:07,124] [INFO] DFAST_QC completed!
[2023-03-17 23:03:07,124] [INFO] Total running time: 0h1m41s