[2023-03-15 12:33:51,700] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,701] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,701] [INFO] DQC Reference Directory: /var/lib/cwl/stgc80bfa8e-9668-42bc-a205-88e3c824f4fe/dqc_reference
[2023-03-15 12:33:52,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,808] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,808] [INFO] Running command: cat /var/lib/cwl/stgfdd084f3-3c10-4da9-81a9-80b13f958d3a/OceanDNA-b16275.fa | prodigal -d OceanDNA-b16275/cds.fna -a OceanDNA-b16275/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:07,866] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:07,866] [INFO] Task started: HMMsearch
[2023-03-15 12:34:07,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b16275/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc80bfa8e-9668-42bc-a205-88e3c824f4fe/dqc_reference/reference_markers.hmm OceanDNA-b16275/protein.faa > /dev/null
[2023-03-15 12:34:08,025] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:08,025] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfdd084f3-3c10-4da9-81a9-80b13f958d3a/OceanDNA-b16275.fa]
[2023-03-15 12:34:08,040] [INFO] Query marker FASTA was written to OceanDNA-b16275/markers.fasta
[2023-03-15 12:34:08,040] [INFO] Task started: Blastn
[2023-03-15 12:34:08,040] [INFO] Running command: blastn -query OceanDNA-b16275/markers.fasta -db /var/lib/cwl/stgc80bfa8e-9668-42bc-a205-88e3c824f4fe/dqc_reference/reference_markers.fasta -out OceanDNA-b16275/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:08,566] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:08,568] [INFO] Selected 17 target genomes.
[2023-03-15 12:34:08,568] [INFO] Target genome list was writen to OceanDNA-b16275/target_genomes.txt
[2023-03-15 12:34:08,578] [INFO] Task started: fastANI
[2023-03-15 12:34:08,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd084f3-3c10-4da9-81a9-80b13f958d3a/OceanDNA-b16275.fa --refList OceanDNA-b16275/target_genomes.txt --output OceanDNA-b16275/fastani_result.tsv --threads 1
[2023-03-15 12:34:20,598] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:20,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc80bfa8e-9668-42bc-a205-88e3c824f4fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:20,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc80bfa8e-9668-42bc-a205-88e3c824f4fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:20,602] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:20,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:20,602] [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	76.7007	106	512	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:20,603] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16275/tc_result.tsv
[2023-03-15 12:34:20,605] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:20,605] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:20,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc80bfa8e-9668-42bc-a205-88e3c824f4fe/dqc_reference/checkm_data
[2023-03-15 12:34:20,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:20,611] [INFO] Task started: CheckM
[2023-03-15 12:34:20,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16275/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16275/checkm_input OceanDNA-b16275/checkm_result
[2023-03-15 12:35:02,813] [INFO] Task succeeded: CheckM
[2023-03-15 12:35:02,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 12:35:02,844] [INFO] ===== Completeness check finished =====
[2023-03-15 12:35:02,844] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:35:02,845] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16275/markers.fasta)
[2023-03-15 12:35:02,846] [INFO] Task started: Blastn
[2023-03-15 12:35:02,846] [INFO] Running command: blastn -query OceanDNA-b16275/markers.fasta -db /var/lib/cwl/stgc80bfa8e-9668-42bc-a205-88e3c824f4fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16275/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:35:03,601] [INFO] Task succeeded: Blastn
[2023-03-15 12:35:03,603] [INFO] Selected 21 target genomes.
[2023-03-15 12:35:03,604] [INFO] Target genome list was writen to OceanDNA-b16275/target_genomes_gtdb.txt
[2023-03-15 12:35:03,861] [INFO] Task started: fastANI
[2023-03-15 12:35:03,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd084f3-3c10-4da9-81a9-80b13f958d3a/OceanDNA-b16275.fa --refList OceanDNA-b16275/target_genomes_gtdb.txt --output OceanDNA-b16275/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:35:13,348] [INFO] Task succeeded: fastANI
[2023-03-15 12:35:13,359] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:35:13,359] [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_016882525.1	s__NIES-981 sp016882525	78.2124	206	512	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	-
GCA_018399015.1	s__NIES-981 sp018399015	78.1089	227	512	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	-
GCA_007135755.1	s__NIES-981 sp007135755	78.0112	199	512	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.54	99.54	0.92	0.92	2	-
GCF_001039265.1	s__NIES-981 sp001039265	77.9506	142	512	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	-
GCA_018400215.1	s__NIES-981 sp018400215	77.8553	123	512	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	99.01	99.01	0.86	0.86	2	-
GCF_000155635.1	s__NIES-981 sp000155635	77.8473	196	512	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	-
GCA_903862155.1	s__UBA5018 sp903862155	77.7662	134	512	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__UBA5018	95.0	99.05	99.00	0.85	0.80	5	-
GCF_900088535.1	s__NIES-981 sp900088535	77.7187	210	512	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	-
GCA_014654725.1	s__Vulcanococcus sp014654725	77.6062	139	512	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_016882545.1	s__Vulcanococcus sp016882545	77.5048	131	512	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_016882415.1	s__Vulcanococcus sp016882415	77.3937	87	512	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011885.1	s__Cyanobium_A usitatum	77.3377	142	512	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_903882285.1	s__Cyanobium sp903882285	77.2972	127	512	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_016882345.1	s__RGUW01 sp016882345	77.1096	91	512	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RGUW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279595.1	s__Synechococcus_C sp000153065	77.1046	115	512	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	76.8587	120	512	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_000737535.1	s__Synechococcus_E sp000737535	76.8542	62	512	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	-
GCA_003211535.1	s__Synechococcus_E sp003211535	76.7957	64	512	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	-
--------------------------------------------------------------------------------
[2023-03-15 12:35:13,360] [INFO] GTDB search result was written to OceanDNA-b16275/result_gtdb.tsv
[2023-03-15 12:35:13,363] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:35:13,366] [INFO] DFAST_QC result json was written to OceanDNA-b16275/dqc_result.json
[2023-03-15 12:35:13,366] [INFO] DFAST_QC completed!
[2023-03-15 12:35:13,366] [INFO] Total running time: 0h1m22s