[2023-03-18 03:45:10,234] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d290aed-5b84-497a-84bb-7f92e5bc1b08/dqc_reference
[2023-03-18 03:45:11,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:11,968] [INFO] Task started: Prodigal
[2023-03-18 03:45:11,968] [INFO] Running command: cat /var/lib/cwl/stg181143dd-5cf6-41ee-9063-830a35c34392/OceanDNA-b43817.fa | prodigal -d OceanDNA-b43817/cds.fna -a OceanDNA-b43817/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:23,648] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:23,648] [INFO] Task started: HMMsearch
[2023-03-18 03:45:23,648] [INFO] Running command: hmmsearch --tblout OceanDNA-b43817/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d290aed-5b84-497a-84bb-7f92e5bc1b08/dqc_reference/reference_markers.hmm OceanDNA-b43817/protein.faa > /dev/null
[2023-03-18 03:45:23,834] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:23,834] [INFO] Found 6/6 markers.
[2023-03-18 03:45:23,848] [INFO] Query marker FASTA was written to OceanDNA-b43817/markers.fasta
[2023-03-18 03:45:23,848] [INFO] Task started: Blastn
[2023-03-18 03:45:23,848] [INFO] Running command: blastn -query OceanDNA-b43817/markers.fasta -db /var/lib/cwl/stg1d290aed-5b84-497a-84bb-7f92e5bc1b08/dqc_reference/reference_markers.fasta -out OceanDNA-b43817/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:24,401] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:24,402] [INFO] Selected 20 target genomes.
[2023-03-18 03:45:24,402] [INFO] Target genome list was writen to OceanDNA-b43817/target_genomes.txt
[2023-03-18 03:45:24,412] [INFO] Task started: fastANI
[2023-03-18 03:45:24,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg181143dd-5cf6-41ee-9063-830a35c34392/OceanDNA-b43817.fa --refList OceanDNA-b43817/target_genomes.txt --output OceanDNA-b43817/fastani_result.tsv --threads 1
[2023-03-18 03:45:34,630] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:34,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d290aed-5b84-497a-84bb-7f92e5bc1b08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:34,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d290aed-5b84-497a-84bb-7f92e5bc1b08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:34,631] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:34,631] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:45:34,631] [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 03:45:34,631] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43817/tc_result.tsv
[2023-03-18 03:45:34,631] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:34,631] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:34,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d290aed-5b84-497a-84bb-7f92e5bc1b08/dqc_reference/checkm_data
[2023-03-18 03:45:34,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:34,638] [INFO] Task started: CheckM
[2023-03-18 03:45:34,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43817/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43817/checkm_input OceanDNA-b43817/checkm_result
[2023-03-18 03:46:07,763] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:07,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:07,867] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:07,868] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:07,868] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43817/markers.fasta)
[2023-03-18 03:46:07,868] [INFO] Task started: Blastn
[2023-03-18 03:46:07,868] [INFO] Running command: blastn -query OceanDNA-b43817/markers.fasta -db /var/lib/cwl/stg1d290aed-5b84-497a-84bb-7f92e5bc1b08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43817/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:08,908] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:08,909] [INFO] Selected 16 target genomes.
[2023-03-18 03:46:08,909] [INFO] Target genome list was writen to OceanDNA-b43817/target_genomes_gtdb.txt
[2023-03-18 03:46:09,013] [INFO] Task started: fastANI
[2023-03-18 03:46:09,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg181143dd-5cf6-41ee-9063-830a35c34392/OceanDNA-b43817.fa --refList OceanDNA-b43817/target_genomes_gtdb.txt --output OceanDNA-b43817/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:15,210] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:15,213] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:46:15,213] [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_004212795.1	s__UBA868 sp002295285	99.3174	558	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.27	99.27	0.84	0.84	2	conclusive
GCA_018672825.1	s__UBA868 sp018672825	92.0633	581	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	99.43	99.28	0.91	0.86	14	-
GCA_016776875.1	s__UBA868 sp016776875	91.7468	433	672	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA868	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:15,214] [INFO] GTDB search result was written to OceanDNA-b43817/result_gtdb.tsv
[2023-03-18 03:46:15,214] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:15,214] [INFO] DFAST_QC result json was written to OceanDNA-b43817/dqc_result.json
[2023-03-18 03:46:15,214] [INFO] DFAST_QC completed!
[2023-03-18 03:46:15,214] [INFO] Total running time: 0h1m5s