[2023-03-15 10:49:28,604] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,605] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg24f2c053-a95e-40c6-9b15-e0fd4d17e0eb/dqc_reference
[2023-03-15 10:49:29,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,729] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,729] [INFO] Running command: cat /var/lib/cwl/stg5ee5fb56-be20-47ed-9f00-b56c73e06395/OceanDNA-b22623.fa | prodigal -d OceanDNA-b22623/cds.fna -a OceanDNA-b22623/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:38,089] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:38,090] [INFO] Task started: HMMsearch
[2023-03-15 10:49:38,090] [INFO] Running command: hmmsearch --tblout OceanDNA-b22623/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24f2c053-a95e-40c6-9b15-e0fd4d17e0eb/dqc_reference/reference_markers.hmm OceanDNA-b22623/protein.faa > /dev/null
[2023-03-15 10:49:38,275] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:38,276] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5ee5fb56-be20-47ed-9f00-b56c73e06395/OceanDNA-b22623.fa]
[2023-03-15 10:49:38,295] [INFO] Query marker FASTA was written to OceanDNA-b22623/markers.fasta
[2023-03-15 10:49:38,295] [INFO] Task started: Blastn
[2023-03-15 10:49:38,295] [INFO] Running command: blastn -query OceanDNA-b22623/markers.fasta -db /var/lib/cwl/stg24f2c053-a95e-40c6-9b15-e0fd4d17e0eb/dqc_reference/reference_markers.fasta -out OceanDNA-b22623/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:38,859] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:38,860] [INFO] Selected 9 target genomes.
[2023-03-15 10:49:38,861] [INFO] Target genome list was writen to OceanDNA-b22623/target_genomes.txt
[2023-03-15 10:49:38,867] [INFO] Task started: fastANI
[2023-03-15 10:49:38,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ee5fb56-be20-47ed-9f00-b56c73e06395/OceanDNA-b22623.fa --refList OceanDNA-b22623/target_genomes.txt --output OceanDNA-b22623/fastani_result.tsv --threads 1
[2023-03-15 10:49:45,712] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:45,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24f2c053-a95e-40c6-9b15-e0fd4d17e0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:45,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24f2c053-a95e-40c6-9b15-e0fd4d17e0eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:45,712] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:45,713] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:45,713] [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 10:49:45,713] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22623/tc_result.tsv
[2023-03-15 10:49:45,713] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:45,713] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:45,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24f2c053-a95e-40c6-9b15-e0fd4d17e0eb/dqc_reference/checkm_data
[2023-03-15 10:49:45,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:45,720] [INFO] Task started: CheckM
[2023-03-15 10:49:45,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22623/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22623/checkm_input OceanDNA-b22623/checkm_result
[2023-03-15 10:50:12,848] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:12,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:12,852] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:12,852] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:12,852] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22623/markers.fasta)
[2023-03-15 10:50:12,853] [INFO] Task started: Blastn
[2023-03-15 10:50:12,853] [INFO] Running command: blastn -query OceanDNA-b22623/markers.fasta -db /var/lib/cwl/stg24f2c053-a95e-40c6-9b15-e0fd4d17e0eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22623/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:13,545] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:13,547] [INFO] Selected 11 target genomes.
[2023-03-15 10:50:13,547] [INFO] Target genome list was writen to OceanDNA-b22623/target_genomes_gtdb.txt
[2023-03-15 10:50:13,562] [INFO] Task started: fastANI
[2023-03-15 10:50:13,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ee5fb56-be20-47ed-9f00-b56c73e06395/OceanDNA-b22623.fa --refList OceanDNA-b22623/target_genomes_gtdb.txt --output OceanDNA-b22623/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:19,130] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:19,132] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:50:19,132] [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_018401745.1	s__M30B53 sp018401745	96.0673	116	180	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	96.02	95.94	0.68	0.66	3	conclusive
--------------------------------------------------------------------------------
[2023-03-15 10:50:19,133] [INFO] GTDB search result was written to OceanDNA-b22623/result_gtdb.tsv
[2023-03-15 10:50:19,133] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:19,134] [INFO] DFAST_QC result json was written to OceanDNA-b22623/dqc_result.json
[2023-03-15 10:50:19,134] [INFO] DFAST_QC completed!
[2023-03-15 10:50:19,134] [INFO] Total running time: 0h0m51s