[2023-03-15 06:03:50,991] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:03:50,991] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:03:50,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg4739008e-11e2-445c-b2ec-e3c9bfd25056/dqc_reference
[2023-03-15 06:03:52,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:03:52,086] [INFO] Task started: Prodigal
[2023-03-15 06:03:52,086] [INFO] Running command: cat /var/lib/cwl/stgb49b041a-6fa0-4201-a1d4-1047d5920cb8/OceanDNA-b23367.fa | prodigal -d OceanDNA-b23367/cds.fna -a OceanDNA-b23367/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:04:06,010] [INFO] Task succeeded: Prodigal
[2023-03-15 06:04:06,011] [INFO] Task started: HMMsearch
[2023-03-15 06:04:06,011] [INFO] Running command: hmmsearch --tblout OceanDNA-b23367/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4739008e-11e2-445c-b2ec-e3c9bfd25056/dqc_reference/reference_markers.hmm OceanDNA-b23367/protein.faa > /dev/null
[2023-03-15 06:04:06,193] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:04:06,193] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb49b041a-6fa0-4201-a1d4-1047d5920cb8/OceanDNA-b23367.fa]
[2023-03-15 06:04:06,210] [INFO] Query marker FASTA was written to OceanDNA-b23367/markers.fasta
[2023-03-15 06:04:06,211] [INFO] Task started: Blastn
[2023-03-15 06:04:06,211] [INFO] Running command: blastn -query OceanDNA-b23367/markers.fasta -db /var/lib/cwl/stg4739008e-11e2-445c-b2ec-e3c9bfd25056/dqc_reference/reference_markers.fasta -out OceanDNA-b23367/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:04:06,773] [INFO] Task succeeded: Blastn
[2023-03-15 06:04:06,774] [INFO] Selected 15 target genomes.
[2023-03-15 06:04:06,774] [INFO] Target genome list was writen to OceanDNA-b23367/target_genomes.txt
[2023-03-15 06:04:06,784] [INFO] Task started: fastANI
[2023-03-15 06:04:06,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgb49b041a-6fa0-4201-a1d4-1047d5920cb8/OceanDNA-b23367.fa --refList OceanDNA-b23367/target_genomes.txt --output OceanDNA-b23367/fastani_result.tsv --threads 1
[2023-03-15 06:04:16,255] [INFO] Task succeeded: fastANI
[2023-03-15 06:04:16,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4739008e-11e2-445c-b2ec-e3c9bfd25056/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:04:16,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4739008e-11e2-445c-b2ec-e3c9bfd25056/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:04:16,265] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:04:16,265] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:04:16,265] [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
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.2555	471	783	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.8582	482	783	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	80.8338	471	783	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	80.4929	460	783	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	80.4664	460	783	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	80.4344	496	783	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.3345	443	783	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.1619	474	783	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	80.155	454	783	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.9624	423	783	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.7624	420	783	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	79.4467	406	783	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	79.3781	421	783	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.5779	234	783	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.3656	279	783	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:04:16,266] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23367/tc_result.tsv
[2023-03-15 06:04:16,266] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:04:16,266] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:04:16,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4739008e-11e2-445c-b2ec-e3c9bfd25056/dqc_reference/checkm_data
[2023-03-15 06:04:16,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:04:16,271] [INFO] Task started: CheckM
[2023-03-15 06:04:16,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23367/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23367/checkm_input OceanDNA-b23367/checkm_result
[2023-03-15 06:04:53,701] [INFO] Task succeeded: CheckM
[2023-03-15 06:04:53,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:04:53,740] [INFO] ===== Completeness check finished =====
[2023-03-15 06:04:53,740] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:04:53,740] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23367/markers.fasta)
[2023-03-15 06:04:53,742] [INFO] Task started: Blastn
[2023-03-15 06:04:53,742] [INFO] Running command: blastn -query OceanDNA-b23367/markers.fasta -db /var/lib/cwl/stg4739008e-11e2-445c-b2ec-e3c9bfd25056/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23367/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:04:54,654] [INFO] Task succeeded: Blastn
[2023-03-15 06:04:54,657] [INFO] Selected 14 target genomes.
[2023-03-15 06:04:54,657] [INFO] Target genome list was writen to OceanDNA-b23367/target_genomes_gtdb.txt
[2023-03-15 06:04:54,673] [INFO] Task started: fastANI
[2023-03-15 06:04:54,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgb49b041a-6fa0-4201-a1d4-1047d5920cb8/OceanDNA-b23367.fa --refList OceanDNA-b23367/target_genomes_gtdb.txt --output OceanDNA-b23367/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:05:03,422] [INFO] Task succeeded: fastANI
[2023-03-15 06:05:03,430] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:05:03,430] [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_018826515.1	s__Brevundimonas sp018826515	82.0185	520	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_004296955.1	s__Brevundimonas sp004296955	82.0179	532	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCF_001427825.1	s__Brevundimonas sp001427825	81.9768	495	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	81.2827	480	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202075.1	s__Brevundimonas basaltis	81.2419	472	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002865.1	s__Brevundimonas sp002002865	81.0934	460	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196335.1	s__Brevundimonas lenta	80.8811	480	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927945.1	s__Brevundimonas alba	80.8554	469	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280785.1	s__Brevundimonas subvibrioides_B	80.4845	481	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017487405.1	s__Brevundimonas sp017487405	80.4755	493	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000144605.1	s__Brevundimonas subvibrioides	80.4674	462	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795885.1	s__Brevundimonas sp017795885	80.3756	433	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912065.1	s__Brevundimonas sp013912065	80.2838	463	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826885.1	s__Brevundimonas sp018826885	80.1936	367	783	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:05:03,432] [INFO] GTDB search result was written to OceanDNA-b23367/result_gtdb.tsv
[2023-03-15 06:05:03,433] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:05:03,436] [INFO] DFAST_QC result json was written to OceanDNA-b23367/dqc_result.json
[2023-03-15 06:05:03,436] [INFO] DFAST_QC completed!
[2023-03-15 06:05:03,436] [INFO] Total running time: 0h1m12s