[2023-03-17 03:11:36,289] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,289] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,289] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b023050-3f3a-45e7-9445-b473e8842896/dqc_reference
[2023-03-17 03:11:37,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,555] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,555] [INFO] Running command: cat /var/lib/cwl/stga41a23f6-c977-4823-a238-d6cc88180a23/OceanDNA-b23394.fa | prodigal -d OceanDNA-b23394/cds.fna -a OceanDNA-b23394/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:11:49,698] [INFO] Task succeeded: Prodigal
[2023-03-17 03:11:49,699] [INFO] Task started: HMMsearch
[2023-03-17 03:11:49,699] [INFO] Running command: hmmsearch --tblout OceanDNA-b23394/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b023050-3f3a-45e7-9445-b473e8842896/dqc_reference/reference_markers.hmm OceanDNA-b23394/protein.faa > /dev/null
[2023-03-17 03:11:49,910] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:11:49,911] [INFO] Found 6/6 markers.
[2023-03-17 03:11:49,932] [INFO] Query marker FASTA was written to OceanDNA-b23394/markers.fasta
[2023-03-17 03:11:49,932] [INFO] Task started: Blastn
[2023-03-17 03:11:49,932] [INFO] Running command: blastn -query OceanDNA-b23394/markers.fasta -db /var/lib/cwl/stg8b023050-3f3a-45e7-9445-b473e8842896/dqc_reference/reference_markers.fasta -out OceanDNA-b23394/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:11:50,723] [INFO] Task succeeded: Blastn
[2023-03-17 03:11:50,724] [INFO] Selected 17 target genomes.
[2023-03-17 03:11:50,724] [INFO] Target genome list was writen to OceanDNA-b23394/target_genomes.txt
[2023-03-17 03:11:50,743] [INFO] Task started: fastANI
[2023-03-17 03:11:50,743] [INFO] Running command: fastANI --query /var/lib/cwl/stga41a23f6-c977-4823-a238-d6cc88180a23/OceanDNA-b23394.fa --refList OceanDNA-b23394/target_genomes.txt --output OceanDNA-b23394/fastani_result.tsv --threads 1
[2023-03-17 03:12:01,236] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:01,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b023050-3f3a-45e7-9445-b473e8842896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:12:01,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b023050-3f3a-45e7-9445-b473e8842896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:12:01,248] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:12:01,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:12:01,248] [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 subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	83.1942	425	644	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.5204	407	644	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	81.5191	382	644	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.8705	370	644	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	80.8504	361	644	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	80.7423	346	644	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	80.3965	339	644	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	80.3958	317	644	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	80.3726	349	644	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	80.3442	325	644	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.3383	325	644	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.1798	359	644	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.1431	320	644	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.9946	319	644	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.832	329	644	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.5203	165	644	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.019	190	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:12:01,248] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23394/tc_result.tsv
[2023-03-17 03:12:01,248] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:12:01,248] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:12:01,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b023050-3f3a-45e7-9445-b473e8842896/dqc_reference/checkm_data
[2023-03-17 03:12:01,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:12:01,271] [INFO] Task started: CheckM
[2023-03-17 03:12:01,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23394/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23394/checkm_input OceanDNA-b23394/checkm_result
[2023-03-17 03:12:35,105] [INFO] Task succeeded: CheckM
[2023-03-17 03:12:35,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:12:35,107] [INFO] ===== Completeness check finished =====
[2023-03-17 03:12:35,108] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:12:35,108] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23394/markers.fasta)
[2023-03-17 03:12:35,109] [INFO] Task started: Blastn
[2023-03-17 03:12:35,109] [INFO] Running command: blastn -query OceanDNA-b23394/markers.fasta -db /var/lib/cwl/stg8b023050-3f3a-45e7-9445-b473e8842896/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23394/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:12:36,442] [INFO] Task succeeded: Blastn
[2023-03-17 03:12:36,443] [INFO] Selected 10 target genomes.
[2023-03-17 03:12:36,443] [INFO] Target genome list was writen to OceanDNA-b23394/target_genomes_gtdb.txt
[2023-03-17 03:12:36,569] [INFO] Task started: fastANI
[2023-03-17 03:12:36,569] [INFO] Running command: fastANI --query /var/lib/cwl/stga41a23f6-c977-4823-a238-d6cc88180a23/OceanDNA-b23394.fa --refList OceanDNA-b23394/target_genomes_gtdb.txt --output OceanDNA-b23394/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:12:43,120] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:43,127] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:12:43,127] [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_018820205.1	s__Brevundimonas sp018820205	99.6584	556	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.87	99.87	0.87	0.87	2	conclusive
GCA_002280785.1	s__Brevundimonas subvibrioides_B	84.3897	445	644	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	83.2116	425	644	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	83.1886	425	644	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	82.8296	408	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280475.1	s__Brevundimonas subvibrioides_C	82.3148	409	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.76	99.76	0.91	0.91	2	-
GCF_017487405.1	s__Brevundimonas sp017487405	81.5027	409	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463485.1	s__Brevundimonas sp016463485	81.2905	357	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248925.1	s__Brevundimonas sp003248925	80.4928	326	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199945.1	s__Brevundimonas variabilis	80.1254	321	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:12:43,127] [INFO] GTDB search result was written to OceanDNA-b23394/result_gtdb.tsv
[2023-03-17 03:12:43,127] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:12:43,129] [INFO] DFAST_QC result json was written to OceanDNA-b23394/dqc_result.json
[2023-03-17 03:12:43,129] [INFO] DFAST_QC completed!
[2023-03-17 03:12:43,129] [INFO] Total running time: 0h1m7s