[2023-03-15 11:10:12,412] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:10:12,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:10:12,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg543d73cc-2852-4871-b594-416f8ea3ba55/dqc_reference
[2023-03-15 11:10:13,511] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:10:13,511] [INFO] Task started: Prodigal
[2023-03-15 11:10:13,511] [INFO] Running command: cat /var/lib/cwl/stg250c5036-cbab-4f98-bdad-f84ae45d5748/OceanDNA-b16265.fa | prodigal -d OceanDNA-b16265/cds.fna -a OceanDNA-b16265/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:10:24,932] [INFO] Task succeeded: Prodigal
[2023-03-15 11:10:24,932] [INFO] Task started: HMMsearch
[2023-03-15 11:10:24,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b16265/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg543d73cc-2852-4871-b594-416f8ea3ba55/dqc_reference/reference_markers.hmm OceanDNA-b16265/protein.faa > /dev/null
[2023-03-15 11:10:25,105] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:10:25,105] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg250c5036-cbab-4f98-bdad-f84ae45d5748/OceanDNA-b16265.fa]
[2023-03-15 11:10:25,242] [INFO] Query marker FASTA was written to OceanDNA-b16265/markers.fasta
[2023-03-15 11:10:25,244] [INFO] Task started: Blastn
[2023-03-15 11:10:25,244] [INFO] Running command: blastn -query OceanDNA-b16265/markers.fasta -db /var/lib/cwl/stg543d73cc-2852-4871-b594-416f8ea3ba55/dqc_reference/reference_markers.fasta -out OceanDNA-b16265/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:25,810] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:25,847] [INFO] Selected 28 target genomes.
[2023-03-15 11:10:25,847] [INFO] Target genome list was writen to OceanDNA-b16265/target_genomes.txt
[2023-03-15 11:10:25,861] [INFO] Task started: fastANI
[2023-03-15 11:10:25,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg250c5036-cbab-4f98-bdad-f84ae45d5748/OceanDNA-b16265.fa --refList OceanDNA-b16265/target_genomes.txt --output OceanDNA-b16265/fastani_result.tsv --threads 1
[2023-03-15 11:10:44,149] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:44,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg543d73cc-2852-4871-b594-416f8ea3ba55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:10:44,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg543d73cc-2852-4871-b594-416f8ea3ba55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:10:44,153] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:10:44,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:10:44,153] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.4928	99	341	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	76.826	52	341	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:10:44,166] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16265/tc_result.tsv
[2023-03-15 11:10:44,201] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:10:44,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:10:44,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg543d73cc-2852-4871-b594-416f8ea3ba55/dqc_reference/checkm_data
[2023-03-15 11:10:44,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:10:44,208] [INFO] Task started: CheckM
[2023-03-15 11:10:44,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16265/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16265/checkm_input OceanDNA-b16265/checkm_result
[2023-03-15 11:11:17,165] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:17,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 1.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:17,321] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:17,321] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:17,321] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16265/markers.fasta)
[2023-03-15 11:11:17,323] [INFO] Task started: Blastn
[2023-03-15 11:11:17,323] [INFO] Running command: blastn -query OceanDNA-b16265/markers.fasta -db /var/lib/cwl/stg543d73cc-2852-4871-b594-416f8ea3ba55/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16265/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:18,170] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:18,171] [INFO] Selected 10 target genomes.
[2023-03-15 11:11:18,171] [INFO] Target genome list was writen to OceanDNA-b16265/target_genomes_gtdb.txt
[2023-03-15 11:11:18,182] [INFO] Task started: fastANI
[2023-03-15 11:11:18,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg250c5036-cbab-4f98-bdad-f84ae45d5748/OceanDNA-b16265.fa --refList OceanDNA-b16265/target_genomes_gtdb.txt --output OceanDNA-b16265/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:22,640] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:22,646] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:11:22,646] [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_003011885.1	s__Cyanobium_A usitatum	93.3184	322	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252665.1	s__Cyanobium_A sp002252665	83.5885	308	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882385.1	s__Cyanobium_A sp016882385	83.4453	246	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697415.1	s__Cyanobium_A sp014697415	82.9714	288	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015840335.1	s__Cyanobium_A sp015840335	82.9275	285	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205255.1	s__Cyanobium_A sp013205255	82.594	175	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252705.1	s__Vulcanococcus limneticus	80.33	238	341	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_014191535.1	s__Vulcanococcus sp014191535	80.2837	149	341	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_903882285.1	s__Cyanobium sp903882285	79.6811	192	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.61	99.61	0.88	0.88	2	-
GCA_003249115.1	s__QBMD01 sp003249115	78.4289	163	341	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:22,647] [INFO] GTDB search result was written to OceanDNA-b16265/result_gtdb.tsv
[2023-03-15 11:11:22,647] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:22,648] [INFO] DFAST_QC result json was written to OceanDNA-b16265/dqc_result.json
[2023-03-15 11:11:22,648] [INFO] DFAST_QC completed!
[2023-03-15 11:11:22,648] [INFO] Total running time: 0h1m10s