[2023-03-14 12:29:45,293] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:29:45,297] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:29:45,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg291304d0-afaf-4392-a190-ef08ba85732b/dqc_reference
[2023-03-14 12:29:46,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:29:46,424] [INFO] Task started: Prodigal
[2023-03-14 12:29:46,424] [INFO] Running command: cat /var/lib/cwl/stg7912a4e5-45ef-4048-848e-2ee8f1ad9f43/OceanDNA-b23856.fa | prodigal -d OceanDNA-b23856/cds.fna -a OceanDNA-b23856/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:29:53,002] [INFO] Task succeeded: Prodigal
[2023-03-14 12:29:53,003] [INFO] Task started: HMMsearch
[2023-03-14 12:29:53,003] [INFO] Running command: hmmsearch --tblout OceanDNA-b23856/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg291304d0-afaf-4392-a190-ef08ba85732b/dqc_reference/reference_markers.hmm OceanDNA-b23856/protein.faa > /dev/null
[2023-03-14 12:29:53,178] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:29:53,179] [INFO] Found 6/6 markers.
[2023-03-14 12:29:53,191] [INFO] Query marker FASTA was written to OceanDNA-b23856/markers.fasta
[2023-03-14 12:29:53,193] [INFO] Task started: Blastn
[2023-03-14 12:29:53,193] [INFO] Running command: blastn -query OceanDNA-b23856/markers.fasta -db /var/lib/cwl/stg291304d0-afaf-4392-a190-ef08ba85732b/dqc_reference/reference_markers.fasta -out OceanDNA-b23856/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:29:53,766] [INFO] Task succeeded: Blastn
[2023-03-14 12:29:53,767] [INFO] Selected 18 target genomes.
[2023-03-14 12:29:53,767] [INFO] Target genome list was writen to OceanDNA-b23856/target_genomes.txt
[2023-03-14 12:29:53,803] [INFO] Task started: fastANI
[2023-03-14 12:29:53,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg7912a4e5-45ef-4048-848e-2ee8f1ad9f43/OceanDNA-b23856.fa --refList OceanDNA-b23856/target_genomes.txt --output OceanDNA-b23856/fastani_result.tsv --threads 1
[2023-03-14 12:30:01,715] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:01,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg291304d0-afaf-4392-a190-ef08ba85732b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:30:01,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg291304d0-afaf-4392-a190-ef08ba85732b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:30:01,716] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:30:01,716] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:30:01,716] [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
--------------------------------------------------------------------------------
[2023-03-14 12:30:01,716] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23856/tc_result.tsv
[2023-03-14 12:30:01,717] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:30:01,717] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:30:01,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg291304d0-afaf-4392-a190-ef08ba85732b/dqc_reference/checkm_data
[2023-03-14 12:30:01,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:30:01,730] [INFO] Task started: CheckM
[2023-03-14 12:30:01,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23856/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23856/checkm_input OceanDNA-b23856/checkm_result
[2023-03-14 12:30:23,932] [INFO] Task succeeded: CheckM
[2023-03-14 12:30:23,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:30:23,938] [INFO] ===== Completeness check finished =====
[2023-03-14 12:30:23,938] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:30:23,939] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23856/markers.fasta)
[2023-03-14 12:30:23,940] [INFO] Task started: Blastn
[2023-03-14 12:30:23,940] [INFO] Running command: blastn -query OceanDNA-b23856/markers.fasta -db /var/lib/cwl/stg291304d0-afaf-4392-a190-ef08ba85732b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23856/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:30:24,835] [INFO] Task succeeded: Blastn
[2023-03-14 12:30:24,839] [INFO] Selected 20 target genomes.
[2023-03-14 12:30:24,839] [INFO] Target genome list was writen to OceanDNA-b23856/target_genomes_gtdb.txt
[2023-03-14 12:30:24,867] [INFO] Task started: fastANI
[2023-03-14 12:30:24,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg7912a4e5-45ef-4048-848e-2ee8f1ad9f43/OceanDNA-b23856.fa --refList OceanDNA-b23856/target_genomes_gtdb.txt --output OceanDNA-b23856/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:30:30,712] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:30,715] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:30:30,715] [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_018645985.1	s__Hellea sp018645985	98.3278	307	401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hellea	95.0	98.93	98.88	0.76	0.74	3	conclusive
GCA_905477785.1	s__Hellea sp905477785	82.5592	319	401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hellea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:30:30,719] [INFO] GTDB search result was written to OceanDNA-b23856/result_gtdb.tsv
[2023-03-14 12:30:30,724] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:30:30,728] [INFO] DFAST_QC result json was written to OceanDNA-b23856/dqc_result.json
[2023-03-14 12:30:30,729] [INFO] DFAST_QC completed!
[2023-03-14 12:30:30,729] [INFO] Total running time: 0h0m45s