[2023-03-19 02:51:48,256] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:51:48,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:51:48,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg8dc910bf-b146-4d8a-9ae4-5163d39a1c45/dqc_reference
[2023-03-19 02:51:49,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:51:49,356] [INFO] Task started: Prodigal
[2023-03-19 02:51:49,356] [INFO] Running command: cat /var/lib/cwl/stg78672313-4963-4faa-98b2-8df91e9fa2b9/OceanDNA-b36070.fa | prodigal -d OceanDNA-b36070/cds.fna -a OceanDNA-b36070/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:51:54,217] [INFO] Task succeeded: Prodigal
[2023-03-19 02:51:54,217] [INFO] Task started: HMMsearch
[2023-03-19 02:51:54,217] [INFO] Running command: hmmsearch --tblout OceanDNA-b36070/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8dc910bf-b146-4d8a-9ae4-5163d39a1c45/dqc_reference/reference_markers.hmm OceanDNA-b36070/protein.faa > /dev/null
[2023-03-19 02:51:54,361] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:51:54,362] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78672313-4963-4faa-98b2-8df91e9fa2b9/OceanDNA-b36070.fa]
[2023-03-19 02:51:54,371] [INFO] Query marker FASTA was written to OceanDNA-b36070/markers.fasta
[2023-03-19 02:51:54,372] [INFO] Task started: Blastn
[2023-03-19 02:51:54,372] [INFO] Running command: blastn -query OceanDNA-b36070/markers.fasta -db /var/lib/cwl/stg8dc910bf-b146-4d8a-9ae4-5163d39a1c45/dqc_reference/reference_markers.fasta -out OceanDNA-b36070/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:51:54,978] [INFO] Task succeeded: Blastn
[2023-03-19 02:51:55,014] [INFO] Selected 26 target genomes.
[2023-03-19 02:51:55,014] [INFO] Target genome list was writen to OceanDNA-b36070/target_genomes.txt
[2023-03-19 02:51:55,030] [INFO] Task started: fastANI
[2023-03-19 02:51:55,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg78672313-4963-4faa-98b2-8df91e9fa2b9/OceanDNA-b36070.fa --refList OceanDNA-b36070/target_genomes.txt --output OceanDNA-b36070/fastani_result.tsv --threads 1
[2023-03-19 02:52:10,508] [INFO] Task succeeded: fastANI
[2023-03-19 02:52:10,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8dc910bf-b146-4d8a-9ae4-5163d39a1c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:52:10,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8dc910bf-b146-4d8a-9ae4-5163d39a1c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:52:10,509] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:52:10,509] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:52:10,509] [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
--------------------------------------------------------------------------------
[2023-03-19 02:52:10,509] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36070/tc_result.tsv
[2023-03-19 02:52:10,509] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:52:10,510] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:52:10,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8dc910bf-b146-4d8a-9ae4-5163d39a1c45/dqc_reference/checkm_data
[2023-03-19 02:52:10,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:52:10,551] [INFO] Task started: CheckM
[2023-03-19 02:52:10,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36070/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36070/checkm_input OceanDNA-b36070/checkm_result
[2023-03-19 02:52:28,885] [INFO] Task succeeded: CheckM
[2023-03-19 02:52:28,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:52:28,925] [INFO] ===== Completeness check finished =====
[2023-03-19 02:52:28,925] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:52:28,925] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36070/markers.fasta)
[2023-03-19 02:52:28,926] [INFO] Task started: Blastn
[2023-03-19 02:52:28,926] [INFO] Running command: blastn -query OceanDNA-b36070/markers.fasta -db /var/lib/cwl/stg8dc910bf-b146-4d8a-9ae4-5163d39a1c45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36070/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:52:29,742] [INFO] Task succeeded: Blastn
[2023-03-19 02:52:29,743] [INFO] Selected 25 target genomes.
[2023-03-19 02:52:29,743] [INFO] Target genome list was writen to OceanDNA-b36070/target_genomes_gtdb.txt
[2023-03-19 02:52:29,772] [INFO] Task started: fastANI
[2023-03-19 02:52:29,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg78672313-4963-4faa-98b2-8df91e9fa2b9/OceanDNA-b36070.fa --refList OceanDNA-b36070/target_genomes_gtdb.txt --output OceanDNA-b36070/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:52:44,543] [INFO] Task succeeded: fastANI
[2023-03-19 02:52:44,545] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:52:44,545] [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_002311315.1	s__UBA1147 sp002311315	92.0572	232	249	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__UBA2778;g__UBA1147	95.0	98.77	98.77	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:52:44,545] [INFO] GTDB search result was written to OceanDNA-b36070/result_gtdb.tsv
[2023-03-19 02:52:44,545] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:52:44,546] [INFO] DFAST_QC result json was written to OceanDNA-b36070/dqc_result.json
[2023-03-19 02:52:44,546] [INFO] DFAST_QC completed!
[2023-03-19 02:52:44,546] [INFO] Total running time: 0h0m56s