[2023-03-18 01:08:39,145] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,145] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,145] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb8289d0-c2cc-4b9c-bf9e-7eef00ebaf3a/dqc_reference
[2023-03-18 01:08:40,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,244] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,244] [INFO] Running command: cat /var/lib/cwl/stg70753e18-b10f-491d-b0b9-b12ffc546b0e/OceanDNA-b23364.fa | prodigal -d OceanDNA-b23364/cds.fna -a OceanDNA-b23364/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:08:58,254] [INFO] Task succeeded: Prodigal
[2023-03-18 01:08:58,255] [INFO] Task started: HMMsearch
[2023-03-18 01:08:58,255] [INFO] Running command: hmmsearch --tblout OceanDNA-b23364/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb8289d0-c2cc-4b9c-bf9e-7eef00ebaf3a/dqc_reference/reference_markers.hmm OceanDNA-b23364/protein.faa > /dev/null
[2023-03-18 01:08:58,457] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:08:58,457] [INFO] Found 6/6 markers.
[2023-03-18 01:08:58,479] [INFO] Query marker FASTA was written to OceanDNA-b23364/markers.fasta
[2023-03-18 01:08:58,480] [INFO] Task started: Blastn
[2023-03-18 01:08:58,480] [INFO] Running command: blastn -query OceanDNA-b23364/markers.fasta -db /var/lib/cwl/stgeb8289d0-c2cc-4b9c-bf9e-7eef00ebaf3a/dqc_reference/reference_markers.fasta -out OceanDNA-b23364/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:08:59,341] [INFO] Task succeeded: Blastn
[2023-03-18 01:08:59,343] [INFO] Selected 17 target genomes.
[2023-03-18 01:08:59,344] [INFO] Target genome list was writen to OceanDNA-b23364/target_genomes.txt
[2023-03-18 01:08:59,355] [INFO] Task started: fastANI
[2023-03-18 01:08:59,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg70753e18-b10f-491d-b0b9-b12ffc546b0e/OceanDNA-b23364.fa --refList OceanDNA-b23364/target_genomes.txt --output OceanDNA-b23364/fastani_result.tsv --threads 1
[2023-03-18 01:09:11,121] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:11,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb8289d0-c2cc-4b9c-bf9e-7eef00ebaf3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:11,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb8289d0-c2cc-4b9c-bf9e-7eef00ebaf3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:11,132] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:11,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:11,132] [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	81.9502	587	992	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.7356	609	992	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.6095	624	992	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.5229	590	992	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.4797	625	992	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	81.3669	607	992	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	81.2502	585	992	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.1976	578	992	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	81.1667	587	992	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	81.1459	589	992	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.76	540	992	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.736	563	992	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.7208	522	992	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.7075	539	992	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.3491	512	992	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.3534	383	992	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.3391	310	992	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:11,133] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23364/tc_result.tsv
[2023-03-18 01:09:11,133] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:11,133] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:11,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb8289d0-c2cc-4b9c-bf9e-7eef00ebaf3a/dqc_reference/checkm_data
[2023-03-18 01:09:11,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:11,140] [INFO] Task started: CheckM
[2023-03-18 01:09:11,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23364/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23364/checkm_input OceanDNA-b23364/checkm_result
[2023-03-18 01:09:57,983] [INFO] Task succeeded: CheckM
[2023-03-18 01:09:57,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:09:57,987] [INFO] ===== Completeness check finished =====
[2023-03-18 01:09:57,987] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:09:57,987] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23364/markers.fasta)
[2023-03-18 01:09:57,988] [INFO] Task started: Blastn
[2023-03-18 01:09:57,988] [INFO] Running command: blastn -query OceanDNA-b23364/markers.fasta -db /var/lib/cwl/stgeb8289d0-c2cc-4b9c-bf9e-7eef00ebaf3a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23364/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:59,665] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:59,667] [INFO] Selected 21 target genomes.
[2023-03-18 01:09:59,667] [INFO] Target genome list was writen to OceanDNA-b23364/target_genomes_gtdb.txt
[2023-03-18 01:09:59,685] [INFO] Task started: fastANI
[2023-03-18 01:09:59,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg70753e18-b10f-491d-b0b9-b12ffc546b0e/OceanDNA-b23364.fa --refList OceanDNA-b23364/target_genomes_gtdb.txt --output OceanDNA-b23364/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:13,491] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:13,503] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:10:13,503] [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_004296955.1	s__Brevundimonas sp004296955	82.9195	651	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_018826515.1	s__Brevundimonas sp018826515	82.9188	645	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_002483305.1	s__Brevundimonas sp002483305	82.9019	618	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427825.1	s__Brevundimonas sp001427825	82.714	626	992	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	82.1825	582	992	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	81.9556	588	992	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	81.9391	605	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006515835.1	s__Brevundimonas sp006515835	81.7864	517	992	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	81.7161	611	992	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	81.5589	597	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234495.1	s__Brevundimonas sp015234495	81.5298	383	992	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	81.5193	622	992	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	81.4951	594	992	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	81.3551	588	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116065.1	s__Brevundimonas viscosa	81.1974	584	992	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	81.1181	468	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292165.1	s__Brevundimonas sp002292165	81.0617	531	992	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	81.0589	576	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002386585.1	s__Brevundimonas sp002386585	80.7821	495	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.28	96.28	0.79	0.79	2	-
GCA_002280475.1	s__Brevundimonas subvibrioides_C	80.7334	526	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.76	99.76	0.91	0.91	2	-
GCF_014199945.1	s__Brevundimonas variabilis	80.3491	512	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:13,504] [INFO] GTDB search result was written to OceanDNA-b23364/result_gtdb.tsv
[2023-03-18 01:10:13,504] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:13,507] [INFO] DFAST_QC result json was written to OceanDNA-b23364/dqc_result.json
[2023-03-18 01:10:13,507] [INFO] DFAST_QC completed!
[2023-03-18 01:10:13,507] [INFO] Total running time: 0h1m34s