[2023-03-18 01:54:18,000] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:18,000] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:18,000] [INFO] DQC Reference Directory: /var/lib/cwl/stg61577380-891d-4952-b58e-2536f59b3610/dqc_reference
[2023-03-18 01:54:19,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:19,134] [INFO] Task started: Prodigal
[2023-03-18 01:54:19,134] [INFO] Running command: cat /var/lib/cwl/stg0db6b705-a04a-4a84-9c65-839856779fe0/OceanDNA-b40257.fa | prodigal -d OceanDNA-b40257/cds.fna -a OceanDNA-b40257/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:28,712] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:28,712] [INFO] Task started: HMMsearch
[2023-03-18 01:54:28,712] [INFO] Running command: hmmsearch --tblout OceanDNA-b40257/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61577380-891d-4952-b58e-2536f59b3610/dqc_reference/reference_markers.hmm OceanDNA-b40257/protein.faa > /dev/null
[2023-03-18 01:54:28,878] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:28,879] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0db6b705-a04a-4a84-9c65-839856779fe0/OceanDNA-b40257.fa]
[2023-03-18 01:54:28,893] [INFO] Query marker FASTA was written to OceanDNA-b40257/markers.fasta
[2023-03-18 01:54:28,894] [INFO] Task started: Blastn
[2023-03-18 01:54:28,894] [INFO] Running command: blastn -query OceanDNA-b40257/markers.fasta -db /var/lib/cwl/stg61577380-891d-4952-b58e-2536f59b3610/dqc_reference/reference_markers.fasta -out OceanDNA-b40257/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:29,438] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:29,439] [INFO] Selected 23 target genomes.
[2023-03-18 01:54:29,439] [INFO] Target genome list was writen to OceanDNA-b40257/target_genomes.txt
[2023-03-18 01:54:29,449] [INFO] Task started: fastANI
[2023-03-18 01:54:29,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg0db6b705-a04a-4a84-9c65-839856779fe0/OceanDNA-b40257.fa --refList OceanDNA-b40257/target_genomes.txt --output OceanDNA-b40257/fastani_result.tsv --threads 1
[2023-03-18 01:54:43,358] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:43,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61577380-891d-4952-b58e-2536f59b3610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:43,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61577380-891d-4952-b58e-2536f59b3610/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:43,359] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:43,359] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:54:43,359] [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 01:54:43,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40257/tc_result.tsv
[2023-03-18 01:54:43,359] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:43,359] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:43,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61577380-891d-4952-b58e-2536f59b3610/dqc_reference/checkm_data
[2023-03-18 01:54:43,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:43,366] [INFO] Task started: CheckM
[2023-03-18 01:54:43,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40257/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40257/checkm_input OceanDNA-b40257/checkm_result
[2023-03-18 01:55:11,517] [INFO] Task succeeded: CheckM
[2023-03-18 01:55:11,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:55:11,519] [INFO] ===== Completeness check finished =====
[2023-03-18 01:55:11,519] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:55:11,520] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40257/markers.fasta)
[2023-03-18 01:55:11,521] [INFO] Task started: Blastn
[2023-03-18 01:55:11,521] [INFO] Running command: blastn -query OceanDNA-b40257/markers.fasta -db /var/lib/cwl/stg61577380-891d-4952-b58e-2536f59b3610/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40257/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:55:12,260] [INFO] Task succeeded: Blastn
[2023-03-18 01:55:12,261] [INFO] Selected 24 target genomes.
[2023-03-18 01:55:12,261] [INFO] Target genome list was writen to OceanDNA-b40257/target_genomes_gtdb.txt
[2023-03-18 01:55:12,338] [INFO] Task started: fastANI
[2023-03-18 01:55:12,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg0db6b705-a04a-4a84-9c65-839856779fe0/OceanDNA-b40257.fa --refList OceanDNA-b40257/target_genomes_gtdb.txt --output OceanDNA-b40257/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:55:24,709] [INFO] Task succeeded: fastANI
[2023-03-18 01:55:24,712] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:55:24,712] [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_018401885.1	s__UBA9145 sp018401885	77.1803	82	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.27	98.07	0.94	0.93	3	-
GCA_001438145.1	s__UBA9145 sp001438145	77.0722	91	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.16	96.74	0.82	0.76	25	-
GCA_017853205.1	s__UBA9145 sp003482475	76.7271	84	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.11	98.58	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-18 01:55:24,712] [INFO] GTDB search result was written to OceanDNA-b40257/result_gtdb.tsv
[2023-03-18 01:55:24,712] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:55:24,713] [INFO] DFAST_QC result json was written to OceanDNA-b40257/dqc_result.json
[2023-03-18 01:55:24,713] [INFO] DFAST_QC completed!
[2023-03-18 01:55:24,713] [INFO] Total running time: 0h1m7s