[2023-03-16 19:13:52,397] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:13:52,398] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:13:52,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg40f328c2-3ab4-429b-9d6f-25693d09866b/dqc_reference
[2023-03-16 19:13:55,295] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:13:55,302] [INFO] Task started: Prodigal
[2023-03-16 19:13:55,302] [INFO] Running command: cat /var/lib/cwl/stg77c59b18-70c4-4ba9-ba0b-74972a440ac0/OceanDNA-b16107.fa | prodigal -d OceanDNA-b16107/cds.fna -a OceanDNA-b16107/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:14:18,563] [INFO] Task succeeded: Prodigal
[2023-03-16 19:14:18,563] [INFO] Task started: HMMsearch
[2023-03-16 19:14:18,563] [INFO] Running command: hmmsearch --tblout OceanDNA-b16107/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40f328c2-3ab4-429b-9d6f-25693d09866b/dqc_reference/reference_markers.hmm OceanDNA-b16107/protein.faa > /dev/null
[2023-03-16 19:14:19,071] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:14:19,072] [INFO] Found 6/6 markers.
[2023-03-16 19:14:19,097] [INFO] Query marker FASTA was written to OceanDNA-b16107/markers.fasta
[2023-03-16 19:14:19,101] [INFO] Task started: Blastn
[2023-03-16 19:14:19,101] [INFO] Running command: blastn -query OceanDNA-b16107/markers.fasta -db /var/lib/cwl/stg40f328c2-3ab4-429b-9d6f-25693d09866b/dqc_reference/reference_markers.fasta -out OceanDNA-b16107/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:14:20,531] [INFO] Task succeeded: Blastn
[2023-03-16 19:14:20,532] [INFO] Selected 15 target genomes.
[2023-03-16 19:14:20,532] [INFO] Target genome list was writen to OceanDNA-b16107/target_genomes.txt
[2023-03-16 19:14:20,542] [INFO] Task started: fastANI
[2023-03-16 19:14:20,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c59b18-70c4-4ba9-ba0b-74972a440ac0/OceanDNA-b16107.fa --refList OceanDNA-b16107/target_genomes.txt --output OceanDNA-b16107/fastani_result.tsv --threads 1
[2023-03-16 19:14:44,485] [INFO] Task succeeded: fastANI
[2023-03-16 19:14:44,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40f328c2-3ab4-429b-9d6f-25693d09866b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:14:44,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40f328c2-3ab4-429b-9d6f-25693d09866b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:14:44,494] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:14:44,495] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:14:44,495] [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
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	79.8587	702	1275	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	79.7795	708	1275	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	76.9395	337	1275	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	76.9082	263	1275	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.9041	345	1275	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	76.379	200	1275	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.3421	208	1275	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.33	196	1275	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.3128	204	1275	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.2256	219	1275	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.2179	169	1275	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	76.2084	154	1275	95	below_threshold
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	75.944	157	1275	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:14:44,495] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16107/tc_result.tsv
[2023-03-16 19:14:44,495] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:14:44,495] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:14:44,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40f328c2-3ab4-429b-9d6f-25693d09866b/dqc_reference/checkm_data
[2023-03-16 19:14:44,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:14:44,603] [INFO] Task started: CheckM
[2023-03-16 19:14:44,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16107/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16107/checkm_input OceanDNA-b16107/checkm_result
[2023-03-16 19:15:48,218] [INFO] Task succeeded: CheckM
[2023-03-16 19:15:48,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:15:48,222] [INFO] ===== Completeness check finished =====
[2023-03-16 19:15:48,222] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:15:48,222] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16107/markers.fasta)
[2023-03-16 19:15:48,223] [INFO] Task started: Blastn
[2023-03-16 19:15:48,223] [INFO] Running command: blastn -query OceanDNA-b16107/markers.fasta -db /var/lib/cwl/stg40f328c2-3ab4-429b-9d6f-25693d09866b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16107/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:15:49,143] [INFO] Task succeeded: Blastn
[2023-03-16 19:15:49,144] [INFO] Selected 11 target genomes.
[2023-03-16 19:15:49,145] [INFO] Target genome list was writen to OceanDNA-b16107/target_genomes_gtdb.txt
[2023-03-16 19:15:49,182] [INFO] Task started: fastANI
[2023-03-16 19:15:49,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c59b18-70c4-4ba9-ba0b-74972a440ac0/OceanDNA-b16107.fa --refList OceanDNA-b16107/target_genomes_gtdb.txt --output OceanDNA-b16107/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:16:10,736] [INFO] Task succeeded: fastANI
[2023-03-16 19:16:10,743] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:16:10,743] [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_014698755.1	s__Dolichospermum flosaquae	98.3003	1135	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	98.82	97.73	0.93	0.87	17	conclusive
GCF_012516395.1	s__Dolichospermum sp000312705	87.2458	1010	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	96.37	95.92	0.82	0.80	18	-
GCF_001277295.1	s__Dolichospermum sp001277295	86.8976	1032	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	96.95	95.52	0.83	0.75	11	-
GCF_014697585.1	s__Dolichospermum sp014697585	86.8104	934	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426925.1	s__Dolichospermum circinale	86.7249	967	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	95.89	95.31	0.82	0.78	3	-
GCF_002368115.1	s__Dolichospermum compactum	86.4497	1005	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207875.1	s__Dolichospermum sp015207875	86.3293	983	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848645.1	s__Dolichospermum sp903848645	86.2424	938	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712035.1	s__Dolichospermum sp009712035	86.2338	951	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711935.1	s__Dolichospermum sp009711935	86.1855	964	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017355425.1	s__Dolichospermum sp017355425	86.0302	1058	1275	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	100.00	100.00	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2023-03-16 19:16:10,744] [INFO] GTDB search result was written to OceanDNA-b16107/result_gtdb.tsv
[2023-03-16 19:16:10,747] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:16:10,749] [INFO] DFAST_QC result json was written to OceanDNA-b16107/dqc_result.json
[2023-03-16 19:16:10,749] [INFO] DFAST_QC completed!
[2023-03-16 19:16:10,749] [INFO] Total running time: 0h2m18s