[2023-03-18 23:11:06,909] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,909] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8796bf8-42fb-4ef6-993d-4e8e95565834/dqc_reference
[2023-03-18 23:11:08,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,107] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,108] [INFO] Running command: cat /var/lib/cwl/stgefa40df8-74ff-4dcd-885d-09374444c88f/OceanDNA-b40523.fa | prodigal -d OceanDNA-b40523/cds.fna -a OceanDNA-b40523/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:23,651] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:23,652] [INFO] Task started: HMMsearch
[2023-03-18 23:11:23,652] [INFO] Running command: hmmsearch --tblout OceanDNA-b40523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8796bf8-42fb-4ef6-993d-4e8e95565834/dqc_reference/reference_markers.hmm OceanDNA-b40523/protein.faa > /dev/null
[2023-03-18 23:11:23,922] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:23,922] [INFO] Found 6/6 markers.
[2023-03-18 23:11:23,939] [INFO] Query marker FASTA was written to OceanDNA-b40523/markers.fasta
[2023-03-18 23:11:23,939] [INFO] Task started: Blastn
[2023-03-18 23:11:23,939] [INFO] Running command: blastn -query OceanDNA-b40523/markers.fasta -db /var/lib/cwl/stgb8796bf8-42fb-4ef6-993d-4e8e95565834/dqc_reference/reference_markers.fasta -out OceanDNA-b40523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:24,549] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:24,549] [INFO] Selected 30 target genomes.
[2023-03-18 23:11:24,550] [INFO] Target genome list was writen to OceanDNA-b40523/target_genomes.txt
[2023-03-18 23:11:24,566] [INFO] Task started: fastANI
[2023-03-18 23:11:24,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa40df8-74ff-4dcd-885d-09374444c88f/OceanDNA-b40523.fa --refList OceanDNA-b40523/target_genomes.txt --output OceanDNA-b40523/fastani_result.tsv --threads 1
[2023-03-18 23:11:44,108] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:44,109] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8796bf8-42fb-4ef6-993d-4e8e95565834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:44,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8796bf8-42fb-4ef6-993d-4e8e95565834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:44,109] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:44,109] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:44,109] [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
--------------------------------------------------------------------------------
[2023-03-18 23:11:44,204] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40523/tc_result.tsv
[2023-03-18 23:11:44,204] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:44,204] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:44,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8796bf8-42fb-4ef6-993d-4e8e95565834/dqc_reference/checkm_data
[2023-03-18 23:11:44,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:44,243] [INFO] Task started: CheckM
[2023-03-18 23:11:44,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40523/checkm_input OceanDNA-b40523/checkm_result
[2023-03-18 23:12:25,713] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:25,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:25,715] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:25,715] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:25,716] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40523/markers.fasta)
[2023-03-18 23:12:25,716] [INFO] Task started: Blastn
[2023-03-18 23:12:25,716] [INFO] Running command: blastn -query OceanDNA-b40523/markers.fasta -db /var/lib/cwl/stgb8796bf8-42fb-4ef6-993d-4e8e95565834/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:26,721] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:26,722] [INFO] Selected 23 target genomes.
[2023-03-18 23:12:26,722] [INFO] Target genome list was writen to OceanDNA-b40523/target_genomes_gtdb.txt
[2023-03-18 23:12:26,741] [INFO] Task started: fastANI
[2023-03-18 23:12:26,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa40df8-74ff-4dcd-885d-09374444c88f/OceanDNA-b40523.fa --refList OceanDNA-b40523/target_genomes_gtdb.txt --output OceanDNA-b40523/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:39,217] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:39,220] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:12:39,220] [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_002414385.1	s__UBA5109 sp002414385	99.16	818	870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5109	95.0	99.32	99.09	0.94	0.90	5	conclusive
GCA_002746215.1	s__UBA5109 sp002746215	76.756	98	870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5109	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:39,220] [INFO] GTDB search result was written to OceanDNA-b40523/result_gtdb.tsv
[2023-03-18 23:12:39,220] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:39,220] [INFO] DFAST_QC result json was written to OceanDNA-b40523/dqc_result.json
[2023-03-18 23:12:39,221] [INFO] DFAST_QC completed!
[2023-03-18 23:12:39,221] [INFO] Total running time: 0h1m32s