[2023-03-14 12:28:23,284] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:28:23,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:28:23,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgd85697e7-09dd-4b1b-ae0e-90242479988f/dqc_reference
[2023-03-14 12:28:25,335] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:28:25,336] [INFO] Task started: Prodigal
[2023-03-14 12:28:25,337] [INFO] Running command: cat /var/lib/cwl/stgdbc7ddb5-9502-48d7-9f32-e9113ce5cc1e/OceanDNA-b16126.fa | prodigal -d OceanDNA-b16126/cds.fna -a OceanDNA-b16126/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:28:44,756] [INFO] Task succeeded: Prodigal
[2023-03-14 12:28:44,756] [INFO] Task started: HMMsearch
[2023-03-14 12:28:44,756] [INFO] Running command: hmmsearch --tblout OceanDNA-b16126/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd85697e7-09dd-4b1b-ae0e-90242479988f/dqc_reference/reference_markers.hmm OceanDNA-b16126/protein.faa > /dev/null
[2023-03-14 12:28:44,991] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:28:44,992] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdbc7ddb5-9502-48d7-9f32-e9113ce5cc1e/OceanDNA-b16126.fa]
[2023-03-14 12:28:45,015] [INFO] Query marker FASTA was written to OceanDNA-b16126/markers.fasta
[2023-03-14 12:28:45,015] [INFO] Task started: Blastn
[2023-03-14 12:28:45,015] [INFO] Running command: blastn -query OceanDNA-b16126/markers.fasta -db /var/lib/cwl/stgd85697e7-09dd-4b1b-ae0e-90242479988f/dqc_reference/reference_markers.fasta -out OceanDNA-b16126/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:28:45,527] [INFO] Task succeeded: Blastn
[2023-03-14 12:28:45,528] [INFO] Selected 18 target genomes.
[2023-03-14 12:28:45,529] [INFO] Target genome list was writen to OceanDNA-b16126/target_genomes.txt
[2023-03-14 12:28:45,542] [INFO] Task started: fastANI
[2023-03-14 12:28:45,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc7ddb5-9502-48d7-9f32-e9113ce5cc1e/OceanDNA-b16126.fa --refList OceanDNA-b16126/target_genomes.txt --output OceanDNA-b16126/fastani_result.tsv --threads 1
[2023-03-14 12:28:56,629] [INFO] Task succeeded: fastANI
[2023-03-14 12:28:56,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd85697e7-09dd-4b1b-ae0e-90242479988f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:28:56,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd85697e7-09dd-4b1b-ae0e-90242479988f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:28:56,633] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:28:56,633] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:28:56,633] [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
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	76.9276	316	1250	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:28:56,633] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16126/tc_result.tsv
[2023-03-14 12:28:56,634] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:28:56,634] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:28:56,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd85697e7-09dd-4b1b-ae0e-90242479988f/dqc_reference/checkm_data
[2023-03-14 12:28:56,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:28:56,971] [INFO] Task started: CheckM
[2023-03-14 12:28:56,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16126/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16126/checkm_input OceanDNA-b16126/checkm_result
[2023-03-14 12:29:46,159] [INFO] Task succeeded: CheckM
[2023-03-14 12:29:46,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:29:46,162] [INFO] ===== Completeness check finished =====
[2023-03-14 12:29:46,163] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:29:46,163] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16126/markers.fasta)
[2023-03-14 12:29:46,164] [INFO] Task started: Blastn
[2023-03-14 12:29:46,164] [INFO] Running command: blastn -query OceanDNA-b16126/markers.fasta -db /var/lib/cwl/stgd85697e7-09dd-4b1b-ae0e-90242479988f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16126/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:29:46,863] [INFO] Task succeeded: Blastn
[2023-03-14 12:29:46,865] [INFO] Selected 16 target genomes.
[2023-03-14 12:29:46,865] [INFO] Target genome list was writen to OceanDNA-b16126/target_genomes_gtdb.txt
[2023-03-14 12:29:46,882] [INFO] Task started: fastANI
[2023-03-14 12:29:46,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc7ddb5-9502-48d7-9f32-e9113ce5cc1e/OceanDNA-b16126.fa --refList OceanDNA-b16126/target_genomes_gtdb.txt --output OceanDNA-b16126/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:30:01,721] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:01,726] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:30:01,727] [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_015207195.1	s__Pleurocapsa sp015207195	78.3134	502	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003995.1	s__Pleurocapsa sp003003995	77.279	323	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	76.9576	318	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCF_000332195.1	s__Pleurocapsa sp000332195	76.7347	332	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756305.1	s__Myxosarcina sp000756305	76.231	207	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Myxosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368355.1	s__Pleurocapsa sp002368355	76.2014	186	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659865.1	s__Hyella patelloides	75.7948	159	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	75.3552	101	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:30:01,727] [INFO] GTDB search result was written to OceanDNA-b16126/result_gtdb.tsv
[2023-03-14 12:30:01,727] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:30:01,728] [INFO] DFAST_QC result json was written to OceanDNA-b16126/dqc_result.json
[2023-03-14 12:30:01,728] [INFO] DFAST_QC completed!
[2023-03-14 12:30:01,728] [INFO] Total running time: 0h1m38s