[2023-03-16 13:03:54,687] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:03:54,687] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:03:54,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ced7904-f900-4993-a163-b129d04b6152/dqc_reference
[2023-03-16 13:03:55,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:03:55,980] [INFO] Task started: Prodigal
[2023-03-16 13:03:55,980] [INFO] Running command: cat /var/lib/cwl/stge5501c61-7257-4f10-a73f-66eb610d50d0/OceanDNA-b18515.fa | prodigal -d OceanDNA-b18515/cds.fna -a OceanDNA-b18515/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:04:02,137] [INFO] Task succeeded: Prodigal
[2023-03-16 13:04:02,137] [INFO] Task started: HMMsearch
[2023-03-16 13:04:02,137] [INFO] Running command: hmmsearch --tblout OceanDNA-b18515/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ced7904-f900-4993-a163-b129d04b6152/dqc_reference/reference_markers.hmm OceanDNA-b18515/protein.faa > /dev/null
[2023-03-16 13:04:02,273] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:04:02,274] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5501c61-7257-4f10-a73f-66eb610d50d0/OceanDNA-b18515.fa]
[2023-03-16 13:04:02,287] [INFO] Query marker FASTA was written to OceanDNA-b18515/markers.fasta
[2023-03-16 13:04:02,287] [INFO] Task started: Blastn
[2023-03-16 13:04:02,287] [INFO] Running command: blastn -query OceanDNA-b18515/markers.fasta -db /var/lib/cwl/stg4ced7904-f900-4993-a163-b129d04b6152/dqc_reference/reference_markers.fasta -out OceanDNA-b18515/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:04:02,768] [INFO] Task succeeded: Blastn
[2023-03-16 13:04:02,769] [INFO] Selected 12 target genomes.
[2023-03-16 13:04:02,769] [INFO] Target genome list was writen to OceanDNA-b18515/target_genomes.txt
[2023-03-16 13:04:02,779] [INFO] Task started: fastANI
[2023-03-16 13:04:02,779] [INFO] Running command: fastANI --query /var/lib/cwl/stge5501c61-7257-4f10-a73f-66eb610d50d0/OceanDNA-b18515.fa --refList OceanDNA-b18515/target_genomes.txt --output OceanDNA-b18515/fastani_result.tsv --threads 1
[2023-03-16 13:04:07,414] [INFO] Task succeeded: fastANI
[2023-03-16 13:04:07,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ced7904-f900-4993-a163-b129d04b6152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:04:07,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ced7904-f900-4993-a163-b129d04b6152/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:04:07,415] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:04:07,415] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 13:04:07,415] [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 13:04:07,415] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18515/tc_result.tsv
[2023-03-16 13:04:07,416] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:04:07,416] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:04:07,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ced7904-f900-4993-a163-b129d04b6152/dqc_reference/checkm_data
[2023-03-16 13:04:07,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:04:07,422] [INFO] Task started: CheckM
[2023-03-16 13:04:07,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18515/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18515/checkm_input OceanDNA-b18515/checkm_result
[2023-03-16 13:04:30,967] [INFO] Task succeeded: CheckM
[2023-03-16 13:04:30,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.21%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 13:04:30,969] [INFO] ===== Completeness check finished =====
[2023-03-16 13:04:30,969] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:04:30,969] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18515/markers.fasta)
[2023-03-16 13:04:30,970] [INFO] Task started: Blastn
[2023-03-16 13:04:30,970] [INFO] Running command: blastn -query OceanDNA-b18515/markers.fasta -db /var/lib/cwl/stg4ced7904-f900-4993-a163-b129d04b6152/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18515/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:04:32,017] [INFO] Task succeeded: Blastn
[2023-03-16 13:04:32,018] [INFO] Selected 17 target genomes.
[2023-03-16 13:04:32,018] [INFO] Target genome list was writen to OceanDNA-b18515/target_genomes_gtdb.txt
[2023-03-16 13:04:32,516] [INFO] Task started: fastANI
[2023-03-16 13:04:32,517] [INFO] Running command: fastANI --query /var/lib/cwl/stge5501c61-7257-4f10-a73f-66eb610d50d0/OceanDNA-b18515.fa --refList OceanDNA-b18515/target_genomes_gtdb.txt --output OceanDNA-b18515/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:04:43,217] [INFO] Task succeeded: fastANI
[2023-03-16 13:04:43,220] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:04:43,220] [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_012964215.1	s__GCA-002701945 sp012964215	89.5837	251	330	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	98.56	98.56	0.81	0.81	2	-
GCA_004124535.1	s__UBA2126 sp004124535	88.6893	147	330	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__UBA2126	95.0	97.80	97.80	0.52	0.52	2	-
--------------------------------------------------------------------------------
[2023-03-16 13:04:43,220] [INFO] GTDB search result was written to OceanDNA-b18515/result_gtdb.tsv
[2023-03-16 13:04:43,220] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:04:43,221] [INFO] DFAST_QC result json was written to OceanDNA-b18515/dqc_result.json
[2023-03-16 13:04:43,221] [INFO] DFAST_QC completed!
[2023-03-16 13:04:43,221] [INFO] Total running time: 0h0m49s