[2023-03-15 13:45:07,860] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg6616f4b1-b2fa-49cf-bde9-3d9a012c83ba/dqc_reference
[2023-03-15 13:45:09,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,270] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,270] [INFO] Running command: cat /var/lib/cwl/stg286301b2-63f5-41a6-98d4-6f389ebbeb21/OceanDNA-b34274.fa | prodigal -d OceanDNA-b34274/cds.fna -a OceanDNA-b34274/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:14,624] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:14,624] [INFO] Task started: HMMsearch
[2023-03-15 13:45:14,624] [INFO] Running command: hmmsearch --tblout OceanDNA-b34274/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6616f4b1-b2fa-49cf-bde9-3d9a012c83ba/dqc_reference/reference_markers.hmm OceanDNA-b34274/protein.faa > /dev/null
[2023-03-15 13:45:14,778] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:14,778] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg286301b2-63f5-41a6-98d4-6f389ebbeb21/OceanDNA-b34274.fa]
[2023-03-15 13:45:14,792] [INFO] Query marker FASTA was written to OceanDNA-b34274/markers.fasta
[2023-03-15 13:45:14,794] [INFO] Task started: Blastn
[2023-03-15 13:45:14,794] [INFO] Running command: blastn -query OceanDNA-b34274/markers.fasta -db /var/lib/cwl/stg6616f4b1-b2fa-49cf-bde9-3d9a012c83ba/dqc_reference/reference_markers.fasta -out OceanDNA-b34274/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:15,474] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:15,475] [INFO] Selected 19 target genomes.
[2023-03-15 13:45:15,475] [INFO] Target genome list was writen to OceanDNA-b34274/target_genomes.txt
[2023-03-15 13:45:15,488] [INFO] Task started: fastANI
[2023-03-15 13:45:15,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg286301b2-63f5-41a6-98d4-6f389ebbeb21/OceanDNA-b34274.fa --refList OceanDNA-b34274/target_genomes.txt --output OceanDNA-b34274/fastani_result.tsv --threads 1
[2023-03-15 13:45:27,201] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:27,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6616f4b1-b2fa-49cf-bde9-3d9a012c83ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:27,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6616f4b1-b2fa-49cf-bde9-3d9a012c83ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:27,202] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:45:27,202] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:45:27,202] [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 13:45:27,202] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34274/tc_result.tsv
[2023-03-15 13:45:27,202] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:27,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:27,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6616f4b1-b2fa-49cf-bde9-3d9a012c83ba/dqc_reference/checkm_data
[2023-03-15 13:45:27,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:27,211] [INFO] Task started: CheckM
[2023-03-15 13:45:27,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34274/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34274/checkm_input OceanDNA-b34274/checkm_result
[2023-03-15 13:45:46,641] [INFO] Task succeeded: CheckM
[2023-03-15 13:45:46,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:45:46,644] [INFO] ===== Completeness check finished =====
[2023-03-15 13:45:46,644] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:45:46,644] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34274/markers.fasta)
[2023-03-15 13:45:46,645] [INFO] Task started: Blastn
[2023-03-15 13:45:46,645] [INFO] Running command: blastn -query OceanDNA-b34274/markers.fasta -db /var/lib/cwl/stg6616f4b1-b2fa-49cf-bde9-3d9a012c83ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34274/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:47,096] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:47,098] [INFO] Selected 19 target genomes.
[2023-03-15 13:45:47,098] [INFO] Target genome list was writen to OceanDNA-b34274/target_genomes_gtdb.txt
[2023-03-15 13:45:47,117] [INFO] Task started: fastANI
[2023-03-15 13:45:47,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg286301b2-63f5-41a6-98d4-6f389ebbeb21/OceanDNA-b34274.fa --refList OceanDNA-b34274/target_genomes_gtdb.txt --output OceanDNA-b34274/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:45:59,042] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:59,045] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:45:59,045] [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_014898095.1	s__Thalassotalea sp014898095	79.6541	116	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	77.2182	51	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:45:59,045] [INFO] GTDB search result was written to OceanDNA-b34274/result_gtdb.tsv
[2023-03-15 13:45:59,046] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:45:59,046] [INFO] DFAST_QC result json was written to OceanDNA-b34274/dqc_result.json
[2023-03-15 13:45:59,047] [INFO] DFAST_QC completed!
[2023-03-15 13:45:59,047] [INFO] Total running time: 0h0m51s