[2023-03-15 11:24:11,482] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,483] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ad09364-7969-492c-a4cb-54e4f65f027b/dqc_reference
[2023-03-15 11:24:12,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,649] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,649] [INFO] Running command: cat /var/lib/cwl/stgb416faac-fd50-4ba9-a7cd-23c4d91abb78/OceanDNA-b16707.fa | prodigal -d OceanDNA-b16707/cds.fna -a OceanDNA-b16707/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:26,549] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:26,550] [INFO] Task started: HMMsearch
[2023-03-15 11:24:26,550] [INFO] Running command: hmmsearch --tblout OceanDNA-b16707/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ad09364-7969-492c-a4cb-54e4f65f027b/dqc_reference/reference_markers.hmm OceanDNA-b16707/protein.faa > /dev/null
[2023-03-15 11:24:26,701] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:26,701] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb416faac-fd50-4ba9-a7cd-23c4d91abb78/OceanDNA-b16707.fa]
[2023-03-15 11:24:26,715] [INFO] Query marker FASTA was written to OceanDNA-b16707/markers.fasta
[2023-03-15 11:24:26,715] [INFO] Task started: Blastn
[2023-03-15 11:24:26,715] [INFO] Running command: blastn -query OceanDNA-b16707/markers.fasta -db /var/lib/cwl/stg9ad09364-7969-492c-a4cb-54e4f65f027b/dqc_reference/reference_markers.fasta -out OceanDNA-b16707/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:27,236] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:27,237] [INFO] Selected 13 target genomes.
[2023-03-15 11:24:27,237] [INFO] Target genome list was writen to OceanDNA-b16707/target_genomes.txt
[2023-03-15 11:24:27,244] [INFO] Task started: fastANI
[2023-03-15 11:24:27,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgb416faac-fd50-4ba9-a7cd-23c4d91abb78/OceanDNA-b16707.fa --refList OceanDNA-b16707/target_genomes.txt --output OceanDNA-b16707/fastani_result.tsv --threads 1
[2023-03-15 11:24:34,293] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:34,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ad09364-7969-492c-a4cb-54e4f65f027b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:34,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ad09364-7969-492c-a4cb-54e4f65f027b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:34,296] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:24:34,296] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:24:34,296] [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
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	80.7482	308	537	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:24:34,296] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16707/tc_result.tsv
[2023-03-15 11:24:34,296] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:34,296] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:34,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ad09364-7969-492c-a4cb-54e4f65f027b/dqc_reference/checkm_data
[2023-03-15 11:24:34,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:34,496] [INFO] Task started: CheckM
[2023-03-15 11:24:34,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16707/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16707/checkm_input OceanDNA-b16707/checkm_result
[2023-03-15 11:25:07,313] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:07,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:07,378] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:07,378] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:07,379] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16707/markers.fasta)
[2023-03-15 11:25:07,380] [INFO] Task started: Blastn
[2023-03-15 11:25:07,380] [INFO] Running command: blastn -query OceanDNA-b16707/markers.fasta -db /var/lib/cwl/stg9ad09364-7969-492c-a4cb-54e4f65f027b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16707/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:08,193] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:08,194] [INFO] Selected 15 target genomes.
[2023-03-15 11:25:08,194] [INFO] Target genome list was writen to OceanDNA-b16707/target_genomes_gtdb.txt
[2023-03-15 11:25:08,210] [INFO] Task started: fastANI
[2023-03-15 11:25:08,210] [INFO] Running command: fastANI --query /var/lib/cwl/stgb416faac-fd50-4ba9-a7cd-23c4d91abb78/OceanDNA-b16707.fa --refList OceanDNA-b16707/target_genomes_gtdb.txt --output OceanDNA-b16707/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:25:13,525] [INFO] Task succeeded: fastANI
[2023-03-15 11:25:13,530] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:25:13,530] [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_009914645.1	s__Synechococcus_D sp009914645	93.3256	263	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	98.11	98.11	0.86	0.86	2	-
GCF_003011125.1	s__Synechococcus_D lacustris	80.7602	307	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	95.83	95.10	0.90	0.78	20	-
GCA_903943975.1	s__Synechococcus_D lacustris_A	77.7834	115	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D	95.0	99.87	99.37	0.98	0.92	31	-
GCA_002168155.1	s__RCC307 sp002168155	76.5457	55	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104765.1	s__Vulcanococcus sp019104765	76.231	50	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934745.1	s__Cyanobium sp903934745	76.2307	54	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	98.56	98.31	0.81	0.80	4	-
GCA_002470305.1	s__RCC307 sp002470305	76.1432	54	537	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307	95.0	98.70	97.75	0.84	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-15 11:25:13,530] [INFO] GTDB search result was written to OceanDNA-b16707/result_gtdb.tsv
[2023-03-15 11:25:13,530] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:25:13,531] [INFO] DFAST_QC result json was written to OceanDNA-b16707/dqc_result.json
[2023-03-15 11:25:13,531] [INFO] DFAST_QC completed!
[2023-03-15 11:25:13,531] [INFO] Total running time: 0h1m2s