[2023-03-15 08:11:06,163] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:11:06,168] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:11:06,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d8ac33a-ef51-4591-90b4-2d73a1aea3c5/dqc_reference
[2023-03-15 08:11:07,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:11:07,330] [INFO] Task started: Prodigal
[2023-03-15 08:11:07,330] [INFO] Running command: cat /var/lib/cwl/stgbf111e06-1b90-45cd-9abf-2700dc8938fc/OceanDNA-b43651.fa | prodigal -d OceanDNA-b43651/cds.fna -a OceanDNA-b43651/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:11:17,358] [INFO] Task succeeded: Prodigal
[2023-03-15 08:11:17,358] [INFO] Task started: HMMsearch
[2023-03-15 08:11:17,358] [INFO] Running command: hmmsearch --tblout OceanDNA-b43651/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d8ac33a-ef51-4591-90b4-2d73a1aea3c5/dqc_reference/reference_markers.hmm OceanDNA-b43651/protein.faa > /dev/null
[2023-03-15 08:11:17,563] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:11:17,564] [INFO] Found 6/6 markers.
[2023-03-15 08:11:17,610] [INFO] Query marker FASTA was written to OceanDNA-b43651/markers.fasta
[2023-03-15 08:11:17,611] [INFO] Task started: Blastn
[2023-03-15 08:11:17,611] [INFO] Running command: blastn -query OceanDNA-b43651/markers.fasta -db /var/lib/cwl/stg5d8ac33a-ef51-4591-90b4-2d73a1aea3c5/dqc_reference/reference_markers.fasta -out OceanDNA-b43651/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:11:18,218] [INFO] Task succeeded: Blastn
[2023-03-15 08:11:18,219] [INFO] Selected 33 target genomes.
[2023-03-15 08:11:18,219] [INFO] Target genome list was writen to OceanDNA-b43651/target_genomes.txt
[2023-03-15 08:11:18,240] [INFO] Task started: fastANI
[2023-03-15 08:11:18,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf111e06-1b90-45cd-9abf-2700dc8938fc/OceanDNA-b43651.fa --refList OceanDNA-b43651/target_genomes.txt --output OceanDNA-b43651/fastani_result.tsv --threads 1
[2023-03-15 08:11:36,684] [INFO] Task succeeded: fastANI
[2023-03-15 08:11:36,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d8ac33a-ef51-4591-90b4-2d73a1aea3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:11:36,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d8ac33a-ef51-4591-90b4-2d73a1aea3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:11:36,685] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:11:36,685] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:11:36,685] [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 08:11:36,700] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43651/tc_result.tsv
[2023-03-15 08:11:36,713] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:11:36,713] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:11:36,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d8ac33a-ef51-4591-90b4-2d73a1aea3c5/dqc_reference/checkm_data
[2023-03-15 08:11:36,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:11:36,729] [INFO] Task started: CheckM
[2023-03-15 08:11:36,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43651/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43651/checkm_input OceanDNA-b43651/checkm_result
[2023-03-15 08:12:07,732] [INFO] Task succeeded: CheckM
[2023-03-15 08:12:07,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:12:07,829] [INFO] ===== Completeness check finished =====
[2023-03-15 08:12:07,829] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:12:07,829] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43651/markers.fasta)
[2023-03-15 08:12:07,830] [INFO] Task started: Blastn
[2023-03-15 08:12:07,830] [INFO] Running command: blastn -query OceanDNA-b43651/markers.fasta -db /var/lib/cwl/stg5d8ac33a-ef51-4591-90b4-2d73a1aea3c5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43651/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:12:08,740] [INFO] Task succeeded: Blastn
[2023-03-15 08:12:08,742] [INFO] Selected 31 target genomes.
[2023-03-15 08:12:08,742] [INFO] Target genome list was writen to OceanDNA-b43651/target_genomes_gtdb.txt
[2023-03-15 08:12:08,766] [INFO] Task started: fastANI
[2023-03-15 08:12:08,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf111e06-1b90-45cd-9abf-2700dc8938fc/OceanDNA-b43651.fa --refList OceanDNA-b43651/target_genomes_gtdb.txt --output OceanDNA-b43651/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:12:23,849] [INFO] Task succeeded: fastANI
[2023-03-15 08:12:23,853] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:12:23,853] [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_012960345.1	s__UBA11791 sp012960345	97.3186	431	490	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	99.31	99.31	0.83	0.83	2	conclusive
GCA_002714255.1	s__UBA11791 sp002714255	93.5322	300	490	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	98.20	98.17	0.64	0.59	4	-
GCA_905612355.1	s__UBA11791 sp905612355	92.1088	270	490	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA11791	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:12:23,853] [INFO] GTDB search result was written to OceanDNA-b43651/result_gtdb.tsv
[2023-03-15 08:12:23,854] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:12:23,854] [INFO] DFAST_QC result json was written to OceanDNA-b43651/dqc_result.json
[2023-03-15 08:12:23,855] [INFO] DFAST_QC completed!
[2023-03-15 08:12:23,855] [INFO] Total running time: 0h1m18s