[2023-03-17 11:57:19,287] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,287] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg4792cc96-d3ca-4b7e-83b5-11b3e7cf31db/dqc_reference
[2023-03-17 11:57:20,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,891] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,891] [INFO] Running command: cat /var/lib/cwl/stg95ae5c58-0d40-45b4-80b8-82196142ad26/OceanDNA-b16104.fa | prodigal -d OceanDNA-b16104/cds.fna -a OceanDNA-b16104/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:34,457] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:34,458] [INFO] Task started: HMMsearch
[2023-03-17 11:57:34,458] [INFO] Running command: hmmsearch --tblout OceanDNA-b16104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4792cc96-d3ca-4b7e-83b5-11b3e7cf31db/dqc_reference/reference_markers.hmm OceanDNA-b16104/protein.faa > /dev/null
[2023-03-17 11:57:34,726] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:34,727] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg95ae5c58-0d40-45b4-80b8-82196142ad26/OceanDNA-b16104.fa]
[2023-03-17 11:57:34,761] [INFO] Query marker FASTA was written to OceanDNA-b16104/markers.fasta
[2023-03-17 11:57:34,761] [INFO] Task started: Blastn
[2023-03-17 11:57:34,761] [INFO] Running command: blastn -query OceanDNA-b16104/markers.fasta -db /var/lib/cwl/stg4792cc96-d3ca-4b7e-83b5-11b3e7cf31db/dqc_reference/reference_markers.fasta -out OceanDNA-b16104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:35,274] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:35,274] [INFO] Selected 15 target genomes.
[2023-03-17 11:57:35,275] [INFO] Target genome list was writen to OceanDNA-b16104/target_genomes.txt
[2023-03-17 11:57:35,283] [INFO] Task started: fastANI
[2023-03-17 11:57:35,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg95ae5c58-0d40-45b4-80b8-82196142ad26/OceanDNA-b16104.fa --refList OceanDNA-b16104/target_genomes.txt --output OceanDNA-b16104/fastani_result.tsv --threads 1
[2023-03-17 11:57:47,226] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:47,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4792cc96-d3ca-4b7e-83b5-11b3e7cf31db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:47,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4792cc96-d3ca-4b7e-83b5-11b3e7cf31db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:47,231] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:47,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:57:47,231] [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
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	76.4148	79	483	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.2071	50	483	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.2071	50	483	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:57:47,231] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16104/tc_result.tsv
[2023-03-17 11:57:47,231] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:47,231] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:47,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4792cc96-d3ca-4b7e-83b5-11b3e7cf31db/dqc_reference/checkm_data
[2023-03-17 11:57:47,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:47,239] [INFO] Task started: CheckM
[2023-03-17 11:57:47,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16104/checkm_input OceanDNA-b16104/checkm_result
[2023-03-17 11:58:25,595] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:25,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.21%
Contamintation: 2.60%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:25,599] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:25,599] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:25,599] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16104/markers.fasta)
[2023-03-17 11:58:25,599] [INFO] Task started: Blastn
[2023-03-17 11:58:25,599] [INFO] Running command: blastn -query OceanDNA-b16104/markers.fasta -db /var/lib/cwl/stg4792cc96-d3ca-4b7e-83b5-11b3e7cf31db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:26,376] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:26,377] [INFO] Selected 14 target genomes.
[2023-03-17 11:58:26,377] [INFO] Target genome list was writen to OceanDNA-b16104/target_genomes_gtdb.txt
[2023-03-17 11:58:26,426] [INFO] Task started: fastANI
[2023-03-17 11:58:26,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg95ae5c58-0d40-45b4-80b8-82196142ad26/OceanDNA-b16104.fa --refList OceanDNA-b16104/target_genomes_gtdb.txt --output OceanDNA-b16104/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:42,545] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:42,551] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:58:42,552] [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
GCF_002368095.1	s__Rivularia parasitica	83.47	407	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316665.1	s__Rivularia sp000316665	82.0553	385	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192545.1	s__Rivularia sp019192545	82.0151	367	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361335.1	s__Rivularia sp002361335	80.7169	323	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	99.89	99.88	0.93	0.93	3	-
GCA_015272215.1	s__Rivularia sp015272215	80.6001	269	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207665.1	s__Rivularia radiosum	80.3424	306	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033205.1	s__Rivularia sp012033205	80.2103	289	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	99.41	99.20	0.91	0.88	5	-
GCF_002367995.1	s__Aulosira brevissima	75.9253	64	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368195.1	s__Aulosira sp002368195	75.7216	58	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696435.1	s__Aulosira anomala_A	75.6999	62	483	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	96.98	95.47	0.86	0.79	4	-
--------------------------------------------------------------------------------
[2023-03-17 11:58:42,552] [INFO] GTDB search result was written to OceanDNA-b16104/result_gtdb.tsv
[2023-03-17 11:58:42,552] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:42,553] [INFO] DFAST_QC result json was written to OceanDNA-b16104/dqc_result.json
[2023-03-17 11:58:42,553] [INFO] DFAST_QC completed!
[2023-03-17 11:58:42,553] [INFO] Total running time: 0h1m23s