[2023-03-15 07:29:11,757] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg87bed9f6-ec4c-4b4e-af4f-38836fd36083/dqc_reference
[2023-03-15 07:29:13,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,591] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,591] [INFO] Running command: cat /var/lib/cwl/stgd8b1741f-4302-452f-ab03-90d691370ebd/OceanDNA-b16103.fa | prodigal -d OceanDNA-b16103/cds.fna -a OceanDNA-b16103/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:52,209] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:52,210] [INFO] Task started: HMMsearch
[2023-03-15 07:29:52,210] [INFO] Running command: hmmsearch --tblout OceanDNA-b16103/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87bed9f6-ec4c-4b4e-af4f-38836fd36083/dqc_reference/reference_markers.hmm OceanDNA-b16103/protein.faa > /dev/null
[2023-03-15 07:29:52,548] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:52,548] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd8b1741f-4302-452f-ab03-90d691370ebd/OceanDNA-b16103.fa]
[2023-03-15 07:29:52,592] [INFO] Query marker FASTA was written to OceanDNA-b16103/markers.fasta
[2023-03-15 07:29:52,593] [INFO] Task started: Blastn
[2023-03-15 07:29:52,594] [INFO] Running command: blastn -query OceanDNA-b16103/markers.fasta -db /var/lib/cwl/stg87bed9f6-ec4c-4b4e-af4f-38836fd36083/dqc_reference/reference_markers.fasta -out OceanDNA-b16103/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:53,115] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:53,116] [INFO] Selected 23 target genomes.
[2023-03-15 07:29:53,116] [INFO] Target genome list was writen to OceanDNA-b16103/target_genomes.txt
[2023-03-15 07:29:53,130] [INFO] Task started: fastANI
[2023-03-15 07:29:53,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8b1741f-4302-452f-ab03-90d691370ebd/OceanDNA-b16103.fa --refList OceanDNA-b16103/target_genomes.txt --output OceanDNA-b16103/fastani_result.tsv --threads 1
[2023-03-15 07:30:17,887] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:17,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87bed9f6-ec4c-4b4e-af4f-38836fd36083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:30:17,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87bed9f6-ec4c-4b4e-af4f-38836fd36083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:30:17,897] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:30:17,897] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:30:17,897] [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
Mastigocoleus testarum	strain=BC008	GCA_001456025.1	996925	996925	type	True	76.7882	432	2518	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.4145	275	2518	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.3045	289	2518	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.2707	283	2518	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	76.2583	285	2518	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.1869	298	2518	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	76.1673	305	2518	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	76.1295	270	2518	95	below_threshold
Scytonema hofmannii	strain=PCC 7110	GCA_000346485.2	34078	34078	type	True	76.0507	284	2518	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	75.9975	235	2518	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	75.9269	239	2518	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	75.9158	93	2518	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_003991905.1	32056	32056	type	True	75.6618	244	2518	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_007830875.1	32056	32056	type	True	75.6506	242	2518	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.2653	69	2518	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.1373	50	2518	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:30:17,898] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16103/tc_result.tsv
[2023-03-15 07:30:17,898] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:30:17,898] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:30:17,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87bed9f6-ec4c-4b4e-af4f-38836fd36083/dqc_reference/checkm_data
[2023-03-15 07:30:17,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:30:17,908] [INFO] Task started: CheckM
[2023-03-15 07:30:17,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16103/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16103/checkm_input OceanDNA-b16103/checkm_result
[2023-03-15 07:31:48,553] [INFO] Task succeeded: CheckM
[2023-03-15 07:31:48,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:31:48,558] [INFO] ===== Completeness check finished =====
[2023-03-15 07:31:48,558] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:31:48,558] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16103/markers.fasta)
[2023-03-15 07:31:48,559] [INFO] Task started: Blastn
[2023-03-15 07:31:48,559] [INFO] Running command: blastn -query OceanDNA-b16103/markers.fasta -db /var/lib/cwl/stg87bed9f6-ec4c-4b4e-af4f-38836fd36083/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16103/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:31:49,286] [INFO] Task succeeded: Blastn
[2023-03-15 07:31:49,287] [INFO] Selected 11 target genomes.
[2023-03-15 07:31:49,287] [INFO] Target genome list was writen to OceanDNA-b16103/target_genomes_gtdb.txt
[2023-03-15 07:31:49,296] [INFO] Task started: fastANI
[2023-03-15 07:31:49,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8b1741f-4302-452f-ab03-90d691370ebd/OceanDNA-b16103.fa --refList OceanDNA-b16103/target_genomes_gtdb.txt --output OceanDNA-b16103/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:32:08,316] [INFO] Task succeeded: fastANI
[2023-03-15 07:32:08,323] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:32:08,323] [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_002361335.1	s__Rivularia sp002361335	83.8492	1535	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	99.89	99.88	0.93	0.93	3	-
GCA_012033205.1	s__Rivularia sp012033205	81.8363	1304	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	99.41	99.20	0.91	0.88	5	-
GCF_015207665.1	s__Rivularia radiosum	81.8306	1318	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272215.1	s__Rivularia sp015272215	81.7364	1222	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316665.1	s__Rivularia sp000316665	81.3989	1491	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368095.1	s__Rivularia parasitica	81.2704	1557	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192545.1	s__Rivularia sp019192545	80.9963	1482	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Rivularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317285.1	s__Chlorogloeopsis fritschii	76.29	280	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Chlorogloeopsis	95.0	99.29	97.93	0.97	0.93	4	-
GCF_002608075.1	s__Nostoc linckia	76.1631	310	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	99.35	97.13	0.95	0.84	14	-
GCA_017114985.1	s__Nostoc sp017114985	76.0483	269	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317435.1	s__Calothrix sp000317435	75.8879	230	2518	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:32:08,323] [INFO] GTDB search result was written to OceanDNA-b16103/result_gtdb.tsv
[2023-03-15 07:32:08,323] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:32:08,325] [INFO] DFAST_QC result json was written to OceanDNA-b16103/dqc_result.json
[2023-03-15 07:32:08,325] [INFO] DFAST_QC completed!
[2023-03-15 07:32:08,325] [INFO] Total running time: 0h2m57s