[2024-01-24 14:32:30,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:30,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:30,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8e31ec2-be6d-44e6-8847-8ef067877192/dqc_reference
[2024-01-24 14:32:31,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:31,560] [INFO] Task started: Prodigal
[2024-01-24 14:32:31,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgada07d8e-2889-44c5-b1e5-a6ceb5b9ebd4/GCF_017591665.1_ASM1759166v1_genomic.fna.gz | prodigal -d GCF_017591665.1_ASM1759166v1_genomic.fna/cds.fna -a GCF_017591665.1_ASM1759166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:48,768] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:48,768] [INFO] Task started: HMMsearch
[2024-01-24 14:32:48,768] [INFO] Running command: hmmsearch --tblout GCF_017591665.1_ASM1759166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8e31ec2-be6d-44e6-8847-8ef067877192/dqc_reference/reference_markers.hmm GCF_017591665.1_ASM1759166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:49,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:49,197] [INFO] Found 6/6 markers.
[2024-01-24 14:32:49,269] [INFO] Query marker FASTA was written to GCF_017591665.1_ASM1759166v1_genomic.fna/markers.fasta
[2024-01-24 14:32:49,270] [INFO] Task started: Blastn
[2024-01-24 14:32:49,270] [INFO] Running command: blastn -query GCF_017591665.1_ASM1759166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e31ec2-be6d-44e6-8847-8ef067877192/dqc_reference/reference_markers.fasta -out GCF_017591665.1_ASM1759166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:49,879] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:49,883] [INFO] Selected 15 target genomes.
[2024-01-24 14:32:49,883] [INFO] Target genome list was writen to GCF_017591665.1_ASM1759166v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:49,892] [INFO] Task started: fastANI
[2024-01-24 14:32:49,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgada07d8e-2889-44c5-b1e5-a6ceb5b9ebd4/GCF_017591665.1_ASM1759166v1_genomic.fna.gz --refList GCF_017591665.1_ASM1759166v1_genomic.fna/target_genomes.txt --output GCF_017591665.1_ASM1759166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:33:12,316] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:12,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8e31ec2-be6d-44e6-8847-8ef067877192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:33:12,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8e31ec2-be6d-44e6-8847-8ef067877192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:33:12,332] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:33:12,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:33:12,333] [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
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	100.0	2758	2773	95	conclusive
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.4029	653	2773	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.3474	483	2773	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	77.336	546	2773	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.1521	382	2773	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	77.0342	419	2773	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	77.0131	547	2773	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	77.0026	548	2773	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.9954	552	2773	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	76.6677	342	2773	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	76.6619	338	2773	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.2345	81	2773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:33:12,335] [INFO] DFAST Taxonomy check result was written to GCF_017591665.1_ASM1759166v1_genomic.fna/tc_result.tsv
[2024-01-24 14:33:12,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:33:12,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:33:12,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8e31ec2-be6d-44e6-8847-8ef067877192/dqc_reference/checkm_data
[2024-01-24 14:33:12,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:33:12,432] [INFO] Task started: CheckM
[2024-01-24 14:33:12,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017591665.1_ASM1759166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017591665.1_ASM1759166v1_genomic.fna/checkm_input GCF_017591665.1_ASM1759166v1_genomic.fna/checkm_result
[2024-01-24 14:34:06,478] [INFO] Task succeeded: CheckM
[2024-01-24 14:34:06,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:34:06,550] [INFO] ===== Completeness check finished =====
[2024-01-24 14:34:06,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:34:06,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017591665.1_ASM1759166v1_genomic.fna/markers.fasta)
[2024-01-24 14:34:06,551] [INFO] Task started: Blastn
[2024-01-24 14:34:06,551] [INFO] Running command: blastn -query GCF_017591665.1_ASM1759166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e31ec2-be6d-44e6-8847-8ef067877192/dqc_reference/reference_markers_gtdb.fasta -out GCF_017591665.1_ASM1759166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:34:07,370] [INFO] Task succeeded: Blastn
[2024-01-24 14:34:07,375] [INFO] Selected 15 target genomes.
[2024-01-24 14:34:07,375] [INFO] Target genome list was writen to GCF_017591665.1_ASM1759166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:34:07,410] [INFO] Task started: fastANI
[2024-01-24 14:34:07,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgada07d8e-2889-44c5-b1e5-a6ceb5b9ebd4/GCF_017591665.1_ASM1759166v1_genomic.fna.gz --refList GCF_017591665.1_ASM1759166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017591665.1_ASM1759166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:33,839] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:33,855] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:33,855] [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_017591665.1	s__Aetokthonos hydrillicola	100.0	2758	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aetokthonos	95.0	99.67	99.67	0.88	0.88	2	conclusive
GCA_903903925.1	s__Stigonema sp903903925	79.4254	1066	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Stigonema	95.0	99.92	99.92	0.97	0.97	3	-
GCA_016903675.1	s__Stigonema ocellatum	79.1118	1117	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Stigonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315565.1	s__Mastigocladopsis repens	77.5462	587	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Mastigocladopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368435.1	s__Tolypothrix_B sp002368435	77.502	679	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828075.3	s__Tolypothrix_B campylonemoides	77.4967	648	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368235.1	s__Tolypothrix_B sp002368235	77.4379	702	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Tolypothrix_B	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000828085.3	s__Brasilonema tolypothrichoides	77.4089	564	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017982655.1	s__Brasilonema sp017982655	77.3431	566	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697355.1	s__Nostoc calcicola	77.2875	521	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000517105.1	s__Fischerella sp000517105	77.2672	496	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	97.28	97.28	0.93	0.93	2	-
GCF_012912105.1	s__Brasilonema sp012912105	77.2499	571	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001712795.1	s__Nostoc sp001712795	77.1993	508	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031965.1	s__Brasilonema sp012031965	77.1183	580	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Brasilonema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056295.1	s__Atlanticothrix silvestris	76.8931	466	2773	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Atlanticothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:33,857] [INFO] GTDB search result was written to GCF_017591665.1_ASM1759166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:33,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:33,866] [INFO] DFAST_QC result json was written to GCF_017591665.1_ASM1759166v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:33,866] [INFO] DFAST_QC completed!
[2024-01-24 14:34:33,867] [INFO] Total running time: 0h2m4s