[2023-03-19 02:16:59,711] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:16:59,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:16:59,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg67b631f1-dfcf-4f25-ac10-cef9f5f2a737/dqc_reference
[2023-03-19 02:17:00,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:17:00,831] [INFO] Task started: Prodigal
[2023-03-19 02:17:00,831] [INFO] Running command: cat /var/lib/cwl/stg4ec6bc04-8b5a-43be-9f1b-3616c1af8f70/OceanDNA-b1747.fa | prodigal -d OceanDNA-b1747/cds.fna -a OceanDNA-b1747/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:17:07,673] [INFO] Task succeeded: Prodigal
[2023-03-19 02:17:07,674] [INFO] Task started: HMMsearch
[2023-03-19 02:17:07,674] [INFO] Running command: hmmsearch --tblout OceanDNA-b1747/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67b631f1-dfcf-4f25-ac10-cef9f5f2a737/dqc_reference/reference_markers.hmm OceanDNA-b1747/protein.faa > /dev/null
[2023-03-19 02:17:07,829] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:17:07,829] [INFO] Found 6/6 markers.
[2023-03-19 02:17:07,844] [INFO] Query marker FASTA was written to OceanDNA-b1747/markers.fasta
[2023-03-19 02:17:07,845] [INFO] Task started: Blastn
[2023-03-19 02:17:07,845] [INFO] Running command: blastn -query OceanDNA-b1747/markers.fasta -db /var/lib/cwl/stg67b631f1-dfcf-4f25-ac10-cef9f5f2a737/dqc_reference/reference_markers.fasta -out OceanDNA-b1747/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:08,363] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:08,363] [INFO] Selected 20 target genomes.
[2023-03-19 02:17:08,364] [INFO] Target genome list was writen to OceanDNA-b1747/target_genomes.txt
[2023-03-19 02:17:08,373] [INFO] Task started: fastANI
[2023-03-19 02:17:08,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec6bc04-8b5a-43be-9f1b-3616c1af8f70/OceanDNA-b1747.fa --refList OceanDNA-b1747/target_genomes.txt --output OceanDNA-b1747/fastani_result.tsv --threads 1
[2023-03-19 02:17:22,435] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:22,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67b631f1-dfcf-4f25-ac10-cef9f5f2a737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:17:22,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67b631f1-dfcf-4f25-ac10-cef9f5f2a737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:17:22,436] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:17:22,436] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:17:22,436] [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 02:17:22,441] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1747/tc_result.tsv
[2023-03-19 02:17:22,443] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:17:22,444] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:17:22,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67b631f1-dfcf-4f25-ac10-cef9f5f2a737/dqc_reference/checkm_data
[2023-03-19 02:17:22,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:17:22,450] [INFO] Task started: CheckM
[2023-03-19 02:17:22,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1747/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1747/checkm_input OceanDNA-b1747/checkm_result
[2023-03-19 02:17:45,407] [INFO] Task succeeded: CheckM
[2023-03-19 02:17:45,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:17:45,409] [INFO] ===== Completeness check finished =====
[2023-03-19 02:17:45,409] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:17:45,410] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1747/markers.fasta)
[2023-03-19 02:17:45,411] [INFO] Task started: Blastn
[2023-03-19 02:17:45,411] [INFO] Running command: blastn -query OceanDNA-b1747/markers.fasta -db /var/lib/cwl/stg67b631f1-dfcf-4f25-ac10-cef9f5f2a737/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1747/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:46,077] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:46,078] [INFO] Selected 18 target genomes.
[2023-03-19 02:17:46,078] [INFO] Target genome list was writen to OceanDNA-b1747/target_genomes_gtdb.txt
[2023-03-19 02:17:46,101] [INFO] Task started: fastANI
[2023-03-19 02:17:46,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec6bc04-8b5a-43be-9f1b-3616c1af8f70/OceanDNA-b1747.fa --refList OceanDNA-b1747/target_genomes_gtdb.txt --output OceanDNA-b1747/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:17:53,767] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:53,770] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:17:53,770] [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_009937405.1	s__UBA11606 sp009937405	96.5061	139	152	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.36	99.36	0.86	0.86	2	conclusive
GCA_018699415.1	s__UBA11606 sp018699415	86.8207	134	152	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.44	99.44	0.86	0.85	3	-
GCA_016845585.1	s__UBA11606 sp016845585	78.547	88	152	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:17:53,771] [INFO] GTDB search result was written to OceanDNA-b1747/result_gtdb.tsv
[2023-03-19 02:17:53,771] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:17:53,771] [INFO] DFAST_QC result json was written to OceanDNA-b1747/dqc_result.json
[2023-03-19 02:17:53,771] [INFO] DFAST_QC completed!
[2023-03-19 02:17:53,771] [INFO] Total running time: 0h0m54s