[2023-03-19 05:04:10,730] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:04:10,731] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:04:10,731] [INFO] DQC Reference Directory: /var/lib/cwl/stga8bdf918-7737-4825-8a5f-42d6f2224dd6/dqc_reference
[2023-03-19 05:04:11,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:04:11,997] [INFO] Task started: Prodigal
[2023-03-19 05:04:11,997] [INFO] Running command: cat /var/lib/cwl/stgff5219e7-4463-4259-bf8a-18e14118891e/OceanDNA-b16037.fa | prodigal -d OceanDNA-b16037/cds.fna -a OceanDNA-b16037/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:04:42,296] [INFO] Task succeeded: Prodigal
[2023-03-19 05:04:42,296] [INFO] Task started: HMMsearch
[2023-03-19 05:04:42,297] [INFO] Running command: hmmsearch --tblout OceanDNA-b16037/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8bdf918-7737-4825-8a5f-42d6f2224dd6/dqc_reference/reference_markers.hmm OceanDNA-b16037/protein.faa > /dev/null
[2023-03-19 05:04:42,574] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:04:42,575] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgff5219e7-4463-4259-bf8a-18e14118891e/OceanDNA-b16037.fa]
[2023-03-19 05:04:42,608] [INFO] Query marker FASTA was written to OceanDNA-b16037/markers.fasta
[2023-03-19 05:04:42,608] [INFO] Task started: Blastn
[2023-03-19 05:04:42,608] [INFO] Running command: blastn -query OceanDNA-b16037/markers.fasta -db /var/lib/cwl/stga8bdf918-7737-4825-8a5f-42d6f2224dd6/dqc_reference/reference_markers.fasta -out OceanDNA-b16037/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:04:43,109] [INFO] Task succeeded: Blastn
[2023-03-19 05:04:43,109] [INFO] Selected 20 target genomes.
[2023-03-19 05:04:43,110] [INFO] Target genome list was writen to OceanDNA-b16037/target_genomes.txt
[2023-03-19 05:04:43,120] [INFO] Task started: fastANI
[2023-03-19 05:04:43,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5219e7-4463-4259-bf8a-18e14118891e/OceanDNA-b16037.fa --refList OceanDNA-b16037/target_genomes.txt --output OceanDNA-b16037/fastani_result.tsv --threads 1
[2023-03-19 05:04:58,316] [INFO] Task succeeded: fastANI
[2023-03-19 05:04:58,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8bdf918-7737-4825-8a5f-42d6f2224dd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:04:58,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8bdf918-7737-4825-8a5f-42d6f2224dd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:04:58,323] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:04:58,323] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:04:58,323] [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
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.6518	105	1959	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	75.6342	67	1959	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	75.4498	68	1959	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.2619	52	1959	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.16	64	1959	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	75.1591	64	1959	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.1487	68	1959	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	74.9934	53	1959	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:04:58,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16037/tc_result.tsv
[2023-03-19 05:04:58,323] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:04:58,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:04:58,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8bdf918-7737-4825-8a5f-42d6f2224dd6/dqc_reference/checkm_data
[2023-03-19 05:04:58,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:04:58,525] [INFO] Task started: CheckM
[2023-03-19 05:04:58,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16037/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16037/checkm_input OceanDNA-b16037/checkm_result
[2023-03-19 05:06:10,700] [INFO] Task succeeded: CheckM
[2023-03-19 05:06:10,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:06:10,704] [INFO] ===== Completeness check finished =====
[2023-03-19 05:06:10,704] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:06:10,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16037/markers.fasta)
[2023-03-19 05:06:10,704] [INFO] Task started: Blastn
[2023-03-19 05:06:10,704] [INFO] Running command: blastn -query OceanDNA-b16037/markers.fasta -db /var/lib/cwl/stga8bdf918-7737-4825-8a5f-42d6f2224dd6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16037/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:06:11,379] [INFO] Task succeeded: Blastn
[2023-03-19 05:06:11,380] [INFO] Selected 29 target genomes.
[2023-03-19 05:06:11,380] [INFO] Target genome list was writen to OceanDNA-b16037/target_genomes_gtdb.txt
[2023-03-19 05:06:11,478] [INFO] Task started: fastANI
[2023-03-19 05:06:11,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5219e7-4463-4259-bf8a-18e14118891e/OceanDNA-b16037.fa --refList OceanDNA-b16037/target_genomes_gtdb.txt --output OceanDNA-b16037/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:06:37,334] [INFO] Task succeeded: fastANI
[2023-03-19 05:06:37,344] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:06:37,344] [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_010672865.1	s__SIO1D9 sp010672865	75.9781	81	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__SIO1D9;g__SIO1D9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692635.1	s__SIO2C1 sp010692635	75.8224	102	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__SIO2C1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672925.1	s__SIO2C1 sp010672925	75.8001	124	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__SIO2C1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207585.1	s__LEGE-06147 sp015207585	75.7948	72	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__LEGE-06147	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332195.1	s__Pleurocapsa sp000332195	75.7584	77	1959	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	75.6872	58	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Myxosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	75.6401	106	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000167195.1	s__Crocosphaera watsonii	75.6342	67	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	99.01	98.50	0.92	0.88	4	-
GCA_003448685.1	s__Rippkaea sp003448685	75.6051	69	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000252485.1	s__Prochloron didemni	75.5821	60	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Prochloraceae;g__Prochloron	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021805.1	s__Rippkaea orientalis	75.4646	67	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	98.84	98.84	0.95	0.95	2	-
GCF_003013815.1	s__Crocosphaera sp003013815	75.3897	66	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390955.1	s__Planktothricoides sp011390955	75.3587	60	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277295.1	s__Dolichospermum sp001277295	75.2811	59	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	96.95	95.52	0.83	0.75	11	-
GCF_002368315.1	s__Fischerella sp002368315	75.2522	70	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154725.1	s__Aulosira sp002154725	75.0777	69	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	98.17	98.17	0.91	0.91	2	-
GCF_000332155.1	s__Kamptonema formosum	74.9933	55	1959	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Kamptonema	95.0	99.87	99.87	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-19 05:06:37,344] [INFO] GTDB search result was written to OceanDNA-b16037/result_gtdb.tsv
[2023-03-19 05:06:37,344] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:06:37,346] [INFO] DFAST_QC result json was written to OceanDNA-b16037/dqc_result.json
[2023-03-19 05:06:37,346] [INFO] DFAST_QC completed!
[2023-03-19 05:06:37,346] [INFO] Total running time: 0h2m27s