[2023-03-18 20:40:39,434] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg21e9f6b5-d345-4f4f-8f46-dbaf547ea6da/dqc_reference
[2023-03-18 20:40:41,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,208] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,208] [INFO] Running command: cat /var/lib/cwl/stg6d2b913c-244b-4192-af50-c70bbcc8511a/OceanDNA-b32474.fa | prodigal -d OceanDNA-b32474/cds.fna -a OceanDNA-b32474/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:46,917] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:46,917] [INFO] Task started: HMMsearch
[2023-03-18 20:40:46,917] [INFO] Running command: hmmsearch --tblout OceanDNA-b32474/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21e9f6b5-d345-4f4f-8f46-dbaf547ea6da/dqc_reference/reference_markers.hmm OceanDNA-b32474/protein.faa > /dev/null
[2023-03-18 20:40:47,119] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:47,120] [INFO] Found 6/6 markers.
[2023-03-18 20:40:47,131] [INFO] Query marker FASTA was written to OceanDNA-b32474/markers.fasta
[2023-03-18 20:40:47,131] [INFO] Task started: Blastn
[2023-03-18 20:40:47,131] [INFO] Running command: blastn -query OceanDNA-b32474/markers.fasta -db /var/lib/cwl/stg21e9f6b5-d345-4f4f-8f46-dbaf547ea6da/dqc_reference/reference_markers.fasta -out OceanDNA-b32474/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:47,649] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:47,650] [INFO] Selected 12 target genomes.
[2023-03-18 20:40:47,650] [INFO] Target genome list was writen to OceanDNA-b32474/target_genomes.txt
[2023-03-18 20:40:47,656] [INFO] Task started: fastANI
[2023-03-18 20:40:47,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d2b913c-244b-4192-af50-c70bbcc8511a/OceanDNA-b32474.fa --refList OceanDNA-b32474/target_genomes.txt --output OceanDNA-b32474/fastani_result.tsv --threads 1
[2023-03-18 20:40:51,575] [INFO] Task succeeded: fastANI
[2023-03-18 20:40:51,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21e9f6b5-d345-4f4f-8f46-dbaf547ea6da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:40:51,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21e9f6b5-d345-4f4f-8f46-dbaf547ea6da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:40:51,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:40:51,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:40:51,576] [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 20:40:51,576] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32474/tc_result.tsv
[2023-03-18 20:40:51,576] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:40:51,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:40:51,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21e9f6b5-d345-4f4f-8f46-dbaf547ea6da/dqc_reference/checkm_data
[2023-03-18 20:40:51,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:40:51,633] [INFO] Task started: CheckM
[2023-03-18 20:40:51,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32474/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32474/checkm_input OceanDNA-b32474/checkm_result
[2023-03-18 20:41:13,733] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:13,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 1.28%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 20:41:13,736] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:13,736] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:13,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32474/markers.fasta)
[2023-03-18 20:41:13,736] [INFO] Task started: Blastn
[2023-03-18 20:41:13,736] [INFO] Running command: blastn -query OceanDNA-b32474/markers.fasta -db /var/lib/cwl/stg21e9f6b5-d345-4f4f-8f46-dbaf547ea6da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32474/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:14,456] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:14,456] [INFO] Selected 17 target genomes.
[2023-03-18 20:41:14,457] [INFO] Target genome list was writen to OceanDNA-b32474/target_genomes_gtdb.txt
[2023-03-18 20:41:14,545] [INFO] Task started: fastANI
[2023-03-18 20:41:14,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d2b913c-244b-4192-af50-c70bbcc8511a/OceanDNA-b32474.fa --refList OceanDNA-b32474/target_genomes_gtdb.txt --output OceanDNA-b32474/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:18,635] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:18,641] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:41:18,641] [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_002715505.1	s__GCA-2715505 sp002715505	99.8094	384	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2715505	95.0	99.85	99.85	0.95	0.95	2	conclusive
GCA_002732015.1	s__GCA-2732015 sp002732015	78.0179	181	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171495.2	s__GCA-2732015 sp002171495	77.7473	142	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557845.1	s__GCA-2732015 sp902557845	77.6106	157	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571315.1	s__TMED62 sp902571315	76.5774	53	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615805.1	s__TMED62 sp902615805	76.2779	51	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720125.1	s__GCA-2720125 sp002720125	76.084	60	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2720125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170595.1	s__TMED62 sp002170595	75.9726	75	394	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	99.91	99.91	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:18,641] [INFO] GTDB search result was written to OceanDNA-b32474/result_gtdb.tsv
[2023-03-18 20:41:18,641] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:18,642] [INFO] DFAST_QC result json was written to OceanDNA-b32474/dqc_result.json
[2023-03-18 20:41:18,642] [INFO] DFAST_QC completed!
[2023-03-18 20:41:18,642] [INFO] Total running time: 0h0m39s