[2023-03-17 05:59:11,049] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:59:11,049] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:59:11,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbcd7e16-897e-4009-8100-a6f973a9628a/dqc_reference
[2023-03-17 05:59:12,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:59:12,175] [INFO] Task started: Prodigal
[2023-03-17 05:59:12,176] [INFO] Running command: cat /var/lib/cwl/stg5e76f4c8-701d-4118-a08c-a2580e1e4892/OceanDNA-b16511.fa | prodigal -d OceanDNA-b16511/cds.fna -a OceanDNA-b16511/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:59:23,215] [INFO] Task succeeded: Prodigal
[2023-03-17 05:59:23,215] [INFO] Task started: HMMsearch
[2023-03-17 05:59:23,215] [INFO] Running command: hmmsearch --tblout OceanDNA-b16511/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbcd7e16-897e-4009-8100-a6f973a9628a/dqc_reference/reference_markers.hmm OceanDNA-b16511/protein.faa > /dev/null
[2023-03-17 05:59:23,355] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:59:23,356] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5e76f4c8-701d-4118-a08c-a2580e1e4892/OceanDNA-b16511.fa]
[2023-03-17 05:59:23,368] [INFO] Query marker FASTA was written to OceanDNA-b16511/markers.fasta
[2023-03-17 05:59:23,368] [INFO] Task started: Blastn
[2023-03-17 05:59:23,368] [INFO] Running command: blastn -query OceanDNA-b16511/markers.fasta -db /var/lib/cwl/stgfbcd7e16-897e-4009-8100-a6f973a9628a/dqc_reference/reference_markers.fasta -out OceanDNA-b16511/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:59:23,811] [INFO] Task succeeded: Blastn
[2023-03-17 05:59:23,812] [INFO] Selected 14 target genomes.
[2023-03-17 05:59:23,812] [INFO] Target genome list was writen to OceanDNA-b16511/target_genomes.txt
[2023-03-17 05:59:23,818] [INFO] Task started: fastANI
[2023-03-17 05:59:23,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e76f4c8-701d-4118-a08c-a2580e1e4892/OceanDNA-b16511.fa --refList OceanDNA-b16511/target_genomes.txt --output OceanDNA-b16511/fastani_result.tsv --threads 1
[2023-03-17 05:59:31,911] [INFO] Task succeeded: fastANI
[2023-03-17 05:59:31,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbcd7e16-897e-4009-8100-a6f973a9628a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:59:31,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbcd7e16-897e-4009-8100-a6f973a9628a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:59:31,914] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:59:31,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:59:31,914] [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	77.8204	125	338	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:59:31,915] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16511/tc_result.tsv
[2023-03-17 05:59:31,915] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:59:31,915] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:59:31,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbcd7e16-897e-4009-8100-a6f973a9628a/dqc_reference/checkm_data
[2023-03-17 05:59:31,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:59:31,919] [INFO] Task started: CheckM
[2023-03-17 05:59:31,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16511/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16511/checkm_input OceanDNA-b16511/checkm_result
[2023-03-17 06:00:04,865] [INFO] Task succeeded: CheckM
[2023-03-17 06:00:04,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:00:04,868] [INFO] ===== Completeness check finished =====
[2023-03-17 06:00:04,868] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:00:04,868] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16511/markers.fasta)
[2023-03-17 06:00:04,868] [INFO] Task started: Blastn
[2023-03-17 06:00:04,868] [INFO] Running command: blastn -query OceanDNA-b16511/markers.fasta -db /var/lib/cwl/stgfbcd7e16-897e-4009-8100-a6f973a9628a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16511/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:00:05,317] [INFO] Task succeeded: Blastn
[2023-03-17 06:00:05,318] [INFO] Selected 14 target genomes.
[2023-03-17 06:00:05,319] [INFO] Target genome list was writen to OceanDNA-b16511/target_genomes_gtdb.txt
[2023-03-17 06:00:05,353] [INFO] Task started: fastANI
[2023-03-17 06:00:05,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e76f4c8-701d-4118-a08c-a2580e1e4892/OceanDNA-b16511.fa --refList OceanDNA-b16511/target_genomes_gtdb.txt --output OceanDNA-b16511/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:00:11,682] [INFO] Task succeeded: fastANI
[2023-03-17 06:00:11,690] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:00:11,690] [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_014217855.1	s__Synechococcus_C sp004332415	98.2152	325	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.38	96.99	0.88	0.86	3	conclusive
GCF_014279595.1	s__Synechococcus_C sp000153065	80.5347	231	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.83	99.83	0.99	0.99	2	-
GCF_004209775.1	s__Synechococcus_C sp004209775	80.5089	241	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000153825.1	s__Synechococcus_C sp000153825	78.7812	160	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153285.1	s__Synechococcus_C sp000153285	78.3587	128	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000063505.1	s__Synechococcus_C sp000063505	78.1985	149	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.52	97.52	0.89	0.89	2	-
GCF_014279815.1	s__Synechococcus_C sp014279815	77.7698	137	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882525.1	s__NIES-981 sp016882525	77.6652	122	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252675.1	s__Cyanobium sp002252675	77.5859	124	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCA_013911515.1	s__Synechococcus_E sp013911515	77.5361	108	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003925.1	s__Cyanobium minutissimum	77.4746	124	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	95.57	95.57	0.88	0.88	2	-
GCF_019038465.1	s__Cyanobium sp019038465	77.3576	122	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279755.1	s__Synechococcus_E sp014279755	77.3277	120	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698445.1	s__Cyanobium elabens	77.2409	116	338	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:00:11,691] [INFO] GTDB search result was written to OceanDNA-b16511/result_gtdb.tsv
[2023-03-17 06:00:11,691] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:00:11,692] [INFO] DFAST_QC result json was written to OceanDNA-b16511/dqc_result.json
[2023-03-17 06:00:11,692] [INFO] DFAST_QC completed!
[2023-03-17 06:00:11,692] [INFO] Total running time: 0h1m1s