[2023-03-16 07:34:40,373] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,373] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg2232ee44-9ec3-4b97-83bd-2d0ec1800060/dqc_reference
[2023-03-16 07:34:41,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:41,796] [INFO] Task started: Prodigal
[2023-03-16 07:34:41,796] [INFO] Running command: cat /var/lib/cwl/stgfc0fbd75-8a44-479b-bc4f-0993d8dcea1a/OceanDNA-b3418.fa | prodigal -d OceanDNA-b3418/cds.fna -a OceanDNA-b3418/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:34:46,331] [INFO] Task succeeded: Prodigal
[2023-03-16 07:34:46,332] [INFO] Task started: HMMsearch
[2023-03-16 07:34:46,332] [INFO] Running command: hmmsearch --tblout OceanDNA-b3418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2232ee44-9ec3-4b97-83bd-2d0ec1800060/dqc_reference/reference_markers.hmm OceanDNA-b3418/protein.faa > /dev/null
[2023-03-16 07:34:46,453] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:34:46,454] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfc0fbd75-8a44-479b-bc4f-0993d8dcea1a/OceanDNA-b3418.fa]
[2023-03-16 07:34:46,465] [INFO] Query marker FASTA was written to OceanDNA-b3418/markers.fasta
[2023-03-16 07:34:46,466] [INFO] Task started: Blastn
[2023-03-16 07:34:46,466] [INFO] Running command: blastn -query OceanDNA-b3418/markers.fasta -db /var/lib/cwl/stg2232ee44-9ec3-4b97-83bd-2d0ec1800060/dqc_reference/reference_markers.fasta -out OceanDNA-b3418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:34:47,108] [INFO] Task succeeded: Blastn
[2023-03-16 07:34:47,109] [INFO] Selected 18 target genomes.
[2023-03-16 07:34:47,109] [INFO] Target genome list was writen to OceanDNA-b3418/target_genomes.txt
[2023-03-16 07:34:47,260] [INFO] Task started: fastANI
[2023-03-16 07:34:47,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0fbd75-8a44-479b-bc4f-0993d8dcea1a/OceanDNA-b3418.fa --refList OceanDNA-b3418/target_genomes.txt --output OceanDNA-b3418/fastani_result.tsv --threads 1
[2023-03-16 07:34:59,189] [INFO] Task succeeded: fastANI
[2023-03-16 07:34:59,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2232ee44-9ec3-4b97-83bd-2d0ec1800060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:34:59,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2232ee44-9ec3-4b97-83bd-2d0ec1800060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:34:59,189] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:34:59,190] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:34:59,190] [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 07:34:59,190] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3418/tc_result.tsv
[2023-03-16 07:34:59,190] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:34:59,190] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:34:59,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2232ee44-9ec3-4b97-83bd-2d0ec1800060/dqc_reference/checkm_data
[2023-03-16 07:34:59,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:34:59,289] [INFO] Task started: CheckM
[2023-03-16 07:34:59,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3418/checkm_input OceanDNA-b3418/checkm_result
[2023-03-16 07:35:16,568] [INFO] Task succeeded: CheckM
[2023-03-16 07:35:16,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:35:16,571] [INFO] ===== Completeness check finished =====
[2023-03-16 07:35:16,571] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:35:16,571] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3418/markers.fasta)
[2023-03-16 07:35:16,573] [INFO] Task started: Blastn
[2023-03-16 07:35:16,573] [INFO] Running command: blastn -query OceanDNA-b3418/markers.fasta -db /var/lib/cwl/stg2232ee44-9ec3-4b97-83bd-2d0ec1800060/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:17,113] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:17,115] [INFO] Selected 8 target genomes.
[2023-03-16 07:35:17,115] [INFO] Target genome list was writen to OceanDNA-b3418/target_genomes_gtdb.txt
[2023-03-16 07:35:17,478] [INFO] Task started: fastANI
[2023-03-16 07:35:17,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0fbd75-8a44-479b-bc4f-0993d8dcea1a/OceanDNA-b3418.fa --refList OceanDNA-b3418/target_genomes_gtdb.txt --output OceanDNA-b3418/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:35:20,530] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:20,534] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:35:20,534] [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_016650125.1	s__67-14 sp016650125	80.9778	93	155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712175.1	s__67-14 sp016712175	80.3056	81	155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304845.1	s__67-14 sp017304845	79.6264	65	155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897355.1	s__67-14 sp001897355	79.0749	95	155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.98	99.98	0.99	0.99	2	-
GCA_016649615.1	s__67-14 sp016649615	78.3362	66	155	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:35:20,536] [INFO] GTDB search result was written to OceanDNA-b3418/result_gtdb.tsv
[2023-03-16 07:35:20,538] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:35:20,539] [INFO] DFAST_QC result json was written to OceanDNA-b3418/dqc_result.json
[2023-03-16 07:35:20,539] [INFO] DFAST_QC completed!
[2023-03-16 07:35:20,539] [INFO] Total running time: 0h0m40s