[2023-03-18 06:37:01,797] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:01,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:01,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg60f9e4fe-4ac6-4427-8423-d2932f7df1e9/dqc_reference
[2023-03-18 06:37:03,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:03,369] [INFO] Task started: Prodigal
[2023-03-18 06:37:03,369] [INFO] Running command: cat /var/lib/cwl/stg85b57568-3b93-46fb-9dd8-3f3b46c5a379/OceanDNA-b20670.fa | prodigal -d OceanDNA-b20670/cds.fna -a OceanDNA-b20670/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:06,282] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:06,283] [INFO] Task started: HMMsearch
[2023-03-18 06:37:06,283] [INFO] Running command: hmmsearch --tblout OceanDNA-b20670/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60f9e4fe-4ac6-4427-8423-d2932f7df1e9/dqc_reference/reference_markers.hmm OceanDNA-b20670/protein.faa > /dev/null
[2023-03-18 06:37:06,457] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:06,458] [INFO] Found 6/6 markers.
[2023-03-18 06:37:06,466] [INFO] Query marker FASTA was written to OceanDNA-b20670/markers.fasta
[2023-03-18 06:37:06,467] [INFO] Task started: Blastn
[2023-03-18 06:37:06,467] [INFO] Running command: blastn -query OceanDNA-b20670/markers.fasta -db /var/lib/cwl/stg60f9e4fe-4ac6-4427-8423-d2932f7df1e9/dqc_reference/reference_markers.fasta -out OceanDNA-b20670/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:07,796] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:07,796] [INFO] Selected 14 target genomes.
[2023-03-18 06:37:07,797] [INFO] Target genome list was writen to OceanDNA-b20670/target_genomes.txt
[2023-03-18 06:37:07,805] [INFO] Task started: fastANI
[2023-03-18 06:37:07,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b57568-3b93-46fb-9dd8-3f3b46c5a379/OceanDNA-b20670.fa --refList OceanDNA-b20670/target_genomes.txt --output OceanDNA-b20670/fastani_result.tsv --threads 1
[2023-03-18 06:37:14,162] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:14,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60f9e4fe-4ac6-4427-8423-d2932f7df1e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:14,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60f9e4fe-4ac6-4427-8423-d2932f7df1e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:14,163] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:14,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:37:14,163] [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 06:37:14,163] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20670/tc_result.tsv
[2023-03-18 06:37:14,163] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:14,163] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:14,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60f9e4fe-4ac6-4427-8423-d2932f7df1e9/dqc_reference/checkm_data
[2023-03-18 06:37:14,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:14,169] [INFO] Task started: CheckM
[2023-03-18 06:37:14,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20670/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20670/checkm_input OceanDNA-b20670/checkm_result
[2023-03-18 06:37:27,962] [INFO] Task succeeded: CheckM
[2023-03-18 06:37:27,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.68%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:37:27,963] [INFO] ===== Completeness check finished =====
[2023-03-18 06:37:27,963] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:37:27,964] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20670/markers.fasta)
[2023-03-18 06:37:27,964] [INFO] Task started: Blastn
[2023-03-18 06:37:27,964] [INFO] Running command: blastn -query OceanDNA-b20670/markers.fasta -db /var/lib/cwl/stg60f9e4fe-4ac6-4427-8423-d2932f7df1e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20670/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:28,616] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:28,617] [INFO] Selected 16 target genomes.
[2023-03-18 06:37:28,617] [INFO] Target genome list was writen to OceanDNA-b20670/target_genomes_gtdb.txt
[2023-03-18 06:37:28,729] [INFO] Task started: fastANI
[2023-03-18 06:37:28,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b57568-3b93-46fb-9dd8-3f3b46c5a379/OceanDNA-b20670.fa --refList OceanDNA-b20670/target_genomes_gtdb.txt --output OceanDNA-b20670/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:37:35,352] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:35,354] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:37:35,354] [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_002703645.1	s__TMED161 sp002703645	78.8498	101	167	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:37:35,354] [INFO] GTDB search result was written to OceanDNA-b20670/result_gtdb.tsv
[2023-03-18 06:37:35,355] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:37:35,355] [INFO] DFAST_QC result json was written to OceanDNA-b20670/dqc_result.json
[2023-03-18 06:37:35,355] [INFO] DFAST_QC completed!
[2023-03-18 06:37:35,355] [INFO] Total running time: 0h0m34s