[2023-03-18 02:48:49,405] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:49,406] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:49,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d7c6842-963d-439e-8638-1fe6ac2ede0e/dqc_reference
[2023-03-18 02:48:50,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:50,549] [INFO] Task started: Prodigal
[2023-03-18 02:48:50,549] [INFO] Running command: cat /var/lib/cwl/stg02f6edef-6e3f-44f8-8cf2-8e07a1269557/OceanDNA-b32666.fa | prodigal -d OceanDNA-b32666/cds.fna -a OceanDNA-b32666/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:48:55,831] [INFO] Task succeeded: Prodigal
[2023-03-18 02:48:55,831] [INFO] Task started: HMMsearch
[2023-03-18 02:48:55,831] [INFO] Running command: hmmsearch --tblout OceanDNA-b32666/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d7c6842-963d-439e-8638-1fe6ac2ede0e/dqc_reference/reference_markers.hmm OceanDNA-b32666/protein.faa > /dev/null
[2023-03-18 02:48:56,004] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:48:56,004] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg02f6edef-6e3f-44f8-8cf2-8e07a1269557/OceanDNA-b32666.fa]
[2023-03-18 02:48:56,015] [INFO] Query marker FASTA was written to OceanDNA-b32666/markers.fasta
[2023-03-18 02:48:56,015] [INFO] Task started: Blastn
[2023-03-18 02:48:56,015] [INFO] Running command: blastn -query OceanDNA-b32666/markers.fasta -db /var/lib/cwl/stg7d7c6842-963d-439e-8638-1fe6ac2ede0e/dqc_reference/reference_markers.fasta -out OceanDNA-b32666/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:48:56,568] [INFO] Task succeeded: Blastn
[2023-03-18 02:48:56,569] [INFO] Selected 20 target genomes.
[2023-03-18 02:48:56,569] [INFO] Target genome list was writen to OceanDNA-b32666/target_genomes.txt
[2023-03-18 02:48:56,581] [INFO] Task started: fastANI
[2023-03-18 02:48:56,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f6edef-6e3f-44f8-8cf2-8e07a1269557/OceanDNA-b32666.fa --refList OceanDNA-b32666/target_genomes.txt --output OceanDNA-b32666/fastani_result.tsv --threads 1
[2023-03-18 02:49:11,161] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:11,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d7c6842-963d-439e-8638-1fe6ac2ede0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:49:11,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d7c6842-963d-439e-8638-1fe6ac2ede0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:49:11,162] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:49:11,162] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:49:11,162] [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 02:49:11,162] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32666/tc_result.tsv
[2023-03-18 02:49:11,162] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:49:11,162] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:49:11,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d7c6842-963d-439e-8638-1fe6ac2ede0e/dqc_reference/checkm_data
[2023-03-18 02:49:11,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:49:11,168] [INFO] Task started: CheckM
[2023-03-18 02:49:11,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32666/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32666/checkm_input OceanDNA-b32666/checkm_result
[2023-03-18 02:49:30,738] [INFO] Task succeeded: CheckM
[2023-03-18 02:49:30,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:49:30,740] [INFO] ===== Completeness check finished =====
[2023-03-18 02:49:30,741] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:49:30,741] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32666/markers.fasta)
[2023-03-18 02:49:30,742] [INFO] Task started: Blastn
[2023-03-18 02:49:30,742] [INFO] Running command: blastn -query OceanDNA-b32666/markers.fasta -db /var/lib/cwl/stg7d7c6842-963d-439e-8638-1fe6ac2ede0e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32666/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:31,456] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:31,457] [INFO] Selected 20 target genomes.
[2023-03-18 02:49:31,457] [INFO] Target genome list was writen to OceanDNA-b32666/target_genomes_gtdb.txt
[2023-03-18 02:49:31,568] [INFO] Task started: fastANI
[2023-03-18 02:49:31,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f6edef-6e3f-44f8-8cf2-8e07a1269557/OceanDNA-b32666.fa --refList OceanDNA-b32666/target_genomes_gtdb.txt --output OceanDNA-b32666/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:49:45,235] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:45,237] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:49:45,237] [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_016869335.1	s__VGEJ01 sp016869335	76.7794	55	206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVV01;f__SHVV01;g__VGEJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:49:45,237] [INFO] GTDB search result was written to OceanDNA-b32666/result_gtdb.tsv
[2023-03-18 02:49:45,237] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:49:45,238] [INFO] DFAST_QC result json was written to OceanDNA-b32666/dqc_result.json
[2023-03-18 02:49:45,238] [INFO] DFAST_QC completed!
[2023-03-18 02:49:45,238] [INFO] Total running time: 0h0m56s