[2023-03-16 09:43:37,170] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,170] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,170] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa6bd944-4cf8-4fd2-ae73-3398fa02cbfb/dqc_reference
[2023-03-16 09:43:39,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,249] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,249] [INFO] Running command: cat /var/lib/cwl/stga0c6c466-ba6c-4a0e-ba70-8b4769988fd3/OceanDNA-b17036.fa | prodigal -d OceanDNA-b17036/cds.fna -a OceanDNA-b17036/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:43:52,067] [INFO] Task succeeded: Prodigal
[2023-03-16 09:43:52,067] [INFO] Task started: HMMsearch
[2023-03-16 09:43:52,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b17036/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa6bd944-4cf8-4fd2-ae73-3398fa02cbfb/dqc_reference/reference_markers.hmm OceanDNA-b17036/protein.faa > /dev/null
[2023-03-16 09:43:52,254] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:43:52,254] [INFO] Found 6/6 markers.
[2023-03-16 09:43:52,274] [INFO] Query marker FASTA was written to OceanDNA-b17036/markers.fasta
[2023-03-16 09:43:52,276] [INFO] Task started: Blastn
[2023-03-16 09:43:52,276] [INFO] Running command: blastn -query OceanDNA-b17036/markers.fasta -db /var/lib/cwl/stgaa6bd944-4cf8-4fd2-ae73-3398fa02cbfb/dqc_reference/reference_markers.fasta -out OceanDNA-b17036/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:43:52,880] [INFO] Task succeeded: Blastn
[2023-03-16 09:43:52,881] [INFO] Selected 18 target genomes.
[2023-03-16 09:43:52,881] [INFO] Target genome list was writen to OceanDNA-b17036/target_genomes.txt
[2023-03-16 09:43:53,102] [INFO] Task started: fastANI
[2023-03-16 09:43:53,102] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c6c466-ba6c-4a0e-ba70-8b4769988fd3/OceanDNA-b17036.fa --refList OceanDNA-b17036/target_genomes.txt --output OceanDNA-b17036/fastani_result.tsv --threads 1
[2023-03-16 09:44:04,183] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:04,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa6bd944-4cf8-4fd2-ae73-3398fa02cbfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:44:04,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa6bd944-4cf8-4fd2-ae73-3398fa02cbfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:44:04,186] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:44:04,187] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:44:04,187] [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
Truepera radiovictrix	strain=DSM 17093	GCA_000092425.1	332249	332249	type	True	77.1489	209	733	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:44:04,187] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17036/tc_result.tsv
[2023-03-16 09:44:04,187] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:44:04,187] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:44:04,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa6bd944-4cf8-4fd2-ae73-3398fa02cbfb/dqc_reference/checkm_data
[2023-03-16 09:44:04,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:44:04,192] [INFO] Task started: CheckM
[2023-03-16 09:44:04,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17036/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17036/checkm_input OceanDNA-b17036/checkm_result
[2023-03-16 09:44:39,581] [INFO] Task succeeded: CheckM
[2023-03-16 09:44:39,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:44:39,632] [INFO] ===== Completeness check finished =====
[2023-03-16 09:44:39,632] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:44:39,632] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17036/markers.fasta)
[2023-03-16 09:44:39,633] [INFO] Task started: Blastn
[2023-03-16 09:44:39,634] [INFO] Running command: blastn -query OceanDNA-b17036/markers.fasta -db /var/lib/cwl/stgaa6bd944-4cf8-4fd2-ae73-3398fa02cbfb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17036/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:40,671] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:40,684] [INFO] Selected 16 target genomes.
[2023-03-16 09:44:40,684] [INFO] Target genome list was writen to OceanDNA-b17036/target_genomes_gtdb.txt
[2023-03-16 09:44:40,822] [INFO] Task started: fastANI
[2023-03-16 09:44:40,822] [INFO] Running command: fastANI --query /var/lib/cwl/stga0c6c466-ba6c-4a0e-ba70-8b4769988fd3/OceanDNA-b17036.fa --refList OceanDNA-b17036/target_genomes_gtdb.txt --output OceanDNA-b17036/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:44:49,580] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:49,583] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:44:49,584] [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_902806425.1	s__Truepera sp902806425	79.0637	382	733	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__Truepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092425.1	s__Truepera radiovictrix	77.1613	208	733	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__Truepera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390455.1	s__JAABTL01 sp011390455	75.4594	51	733	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Trueperaceae;g__JAABTL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:44:49,586] [INFO] GTDB search result was written to OceanDNA-b17036/result_gtdb.tsv
[2023-03-16 09:44:49,589] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:44:49,592] [INFO] DFAST_QC result json was written to OceanDNA-b17036/dqc_result.json
[2023-03-16 09:44:49,592] [INFO] DFAST_QC completed!
[2023-03-16 09:44:49,592] [INFO] Total running time: 0h1m12s