[2023-03-18 22:25:04,315] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:25:04,315] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:25:04,315] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc274a32-68b8-45bd-a08c-5731a3c0844e/dqc_reference
[2023-03-18 22:25:05,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:25:05,391] [INFO] Task started: Prodigal
[2023-03-18 22:25:05,391] [INFO] Running command: cat /var/lib/cwl/stg741bebd0-80f3-4722-a22a-8bb584eb2671/OceanDNA-b20682.fa | prodigal -d OceanDNA-b20682/cds.fna -a OceanDNA-b20682/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:25:08,511] [INFO] Task succeeded: Prodigal
[2023-03-18 22:25:08,512] [INFO] Task started: HMMsearch
[2023-03-18 22:25:08,512] [INFO] Running command: hmmsearch --tblout OceanDNA-b20682/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc274a32-68b8-45bd-a08c-5731a3c0844e/dqc_reference/reference_markers.hmm OceanDNA-b20682/protein.faa > /dev/null
[2023-03-18 22:25:08,643] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:25:08,643] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg741bebd0-80f3-4722-a22a-8bb584eb2671/OceanDNA-b20682.fa]
[2023-03-18 22:25:08,654] [INFO] Query marker FASTA was written to OceanDNA-b20682/markers.fasta
[2023-03-18 22:25:08,654] [INFO] Task started: Blastn
[2023-03-18 22:25:08,655] [INFO] Running command: blastn -query OceanDNA-b20682/markers.fasta -db /var/lib/cwl/stgbc274a32-68b8-45bd-a08c-5731a3c0844e/dqc_reference/reference_markers.fasta -out OceanDNA-b20682/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:09,149] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:09,150] [INFO] Selected 10 target genomes.
[2023-03-18 22:25:09,150] [INFO] Target genome list was writen to OceanDNA-b20682/target_genomes.txt
[2023-03-18 22:25:09,157] [INFO] Task started: fastANI
[2023-03-18 22:25:09,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg741bebd0-80f3-4722-a22a-8bb584eb2671/OceanDNA-b20682.fa --refList OceanDNA-b20682/target_genomes.txt --output OceanDNA-b20682/fastani_result.tsv --threads 1
[2023-03-18 22:25:14,004] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:14,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc274a32-68b8-45bd-a08c-5731a3c0844e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:25:14,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc274a32-68b8-45bd-a08c-5731a3c0844e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:25:14,005] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:25:14,005] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:25:14,005] [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 22:25:14,005] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20682/tc_result.tsv
[2023-03-18 22:25:14,005] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:25:14,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:25:14,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc274a32-68b8-45bd-a08c-5731a3c0844e/dqc_reference/checkm_data
[2023-03-18 22:25:14,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:25:14,011] [INFO] Task started: CheckM
[2023-03-18 22:25:14,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20682/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20682/checkm_input OceanDNA-b20682/checkm_result
[2023-03-18 22:25:28,739] [INFO] Task succeeded: CheckM
[2023-03-18 22:25:28,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.38%
Contamintation: 1.28%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 22:25:28,742] [INFO] ===== Completeness check finished =====
[2023-03-18 22:25:28,742] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:25:28,742] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20682/markers.fasta)
[2023-03-18 22:25:28,743] [INFO] Task started: Blastn
[2023-03-18 22:25:28,743] [INFO] Running command: blastn -query OceanDNA-b20682/markers.fasta -db /var/lib/cwl/stgbc274a32-68b8-45bd-a08c-5731a3c0844e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20682/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:29,499] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:29,500] [INFO] Selected 21 target genomes.
[2023-03-18 22:25:29,500] [INFO] Target genome list was writen to OceanDNA-b20682/target_genomes_gtdb.txt
[2023-03-18 22:25:29,521] [INFO] Task started: fastANI
[2023-03-18 22:25:29,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg741bebd0-80f3-4722-a22a-8bb584eb2671/OceanDNA-b20682.fa --refList OceanDNA-b20682/target_genomes_gtdb.txt --output OceanDNA-b20682/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:25:35,342] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:35,345] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:25:35,346] [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_002591605.1	s__TMED161 sp002591605	89.4026	51	121	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	-
GCA_002731795.1	s__TMED161 sp002731795	88.0811	97	121	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED161;g__TMED161	95.0	98.59	98.59	0.77	0.77	2	-
GCA_002171125.1	s__TMED161 sp002171125	87.7433	75	121	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 22:25:35,346] [INFO] GTDB search result was written to OceanDNA-b20682/result_gtdb.tsv
[2023-03-18 22:25:35,346] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:25:35,346] [INFO] DFAST_QC result json was written to OceanDNA-b20682/dqc_result.json
[2023-03-18 22:25:35,346] [INFO] DFAST_QC completed!
[2023-03-18 22:25:35,346] [INFO] Total running time: 0h0m31s