[2023-03-18 23:50:29,205] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:50:29,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:50:29,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg6464a0fb-6da1-4edd-ab40-0042423d4020/dqc_reference
[2023-03-18 23:50:30,479] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:50:30,480] [INFO] Task started: Prodigal
[2023-03-18 23:50:30,480] [INFO] Running command: cat /var/lib/cwl/stg47195627-88d6-42b7-8147-89005656a897/OceanDNA-b23396.fa | prodigal -d OceanDNA-b23396/cds.fna -a OceanDNA-b23396/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:50:42,326] [INFO] Task succeeded: Prodigal
[2023-03-18 23:50:42,326] [INFO] Task started: HMMsearch
[2023-03-18 23:50:42,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b23396/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6464a0fb-6da1-4edd-ab40-0042423d4020/dqc_reference/reference_markers.hmm OceanDNA-b23396/protein.faa > /dev/null
[2023-03-18 23:50:42,492] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:50:42,493] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg47195627-88d6-42b7-8147-89005656a897/OceanDNA-b23396.fa]
[2023-03-18 23:50:42,532] [INFO] Query marker FASTA was written to OceanDNA-b23396/markers.fasta
[2023-03-18 23:50:42,534] [INFO] Task started: Blastn
[2023-03-18 23:50:42,534] [INFO] Running command: blastn -query OceanDNA-b23396/markers.fasta -db /var/lib/cwl/stg6464a0fb-6da1-4edd-ab40-0042423d4020/dqc_reference/reference_markers.fasta -out OceanDNA-b23396/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:50:43,099] [INFO] Task succeeded: Blastn
[2023-03-18 23:50:43,099] [INFO] Selected 17 target genomes.
[2023-03-18 23:50:43,100] [INFO] Target genome list was writen to OceanDNA-b23396/target_genomes.txt
[2023-03-18 23:50:43,112] [INFO] Task started: fastANI
[2023-03-18 23:50:43,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg47195627-88d6-42b7-8147-89005656a897/OceanDNA-b23396.fa --refList OceanDNA-b23396/target_genomes.txt --output OceanDNA-b23396/fastani_result.tsv --threads 1
[2023-03-18 23:50:53,749] [INFO] Task succeeded: fastANI
[2023-03-18 23:50:53,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6464a0fb-6da1-4edd-ab40-0042423d4020/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:50:53,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6464a0fb-6da1-4edd-ab40-0042423d4020/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:50:53,759] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:50:53,759] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:50:53,760] [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 lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	83.9898	509	699	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	82.417	458	699	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.5291	422	699	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.4605	441	699	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	80.9903	432	699	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	80.7164	420	699	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.7127	413	699	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	80.649	417	699	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.477	374	699	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.4716	381	699	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	80.4655	415	699	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	80.4605	429	699	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.4447	405	699	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.323	427	699	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.4465	354	699	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.9237	227	699	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	77.0767	292	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:50:53,760] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23396/tc_result.tsv
[2023-03-18 23:50:53,760] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:50:53,760] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:50:53,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6464a0fb-6da1-4edd-ab40-0042423d4020/dqc_reference/checkm_data
[2023-03-18 23:50:53,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:50:53,765] [INFO] Task started: CheckM
[2023-03-18 23:50:53,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23396/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23396/checkm_input OceanDNA-b23396/checkm_result
[2023-03-18 23:51:26,108] [INFO] Task succeeded: CheckM
[2023-03-18 23:51:26,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:51:26,155] [INFO] ===== Completeness check finished =====
[2023-03-18 23:51:26,155] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:51:26,155] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23396/markers.fasta)
[2023-03-18 23:51:26,156] [INFO] Task started: Blastn
[2023-03-18 23:51:26,156] [INFO] Running command: blastn -query OceanDNA-b23396/markers.fasta -db /var/lib/cwl/stg6464a0fb-6da1-4edd-ab40-0042423d4020/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23396/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:51:26,998] [INFO] Task succeeded: Blastn
[2023-03-18 23:51:27,006] [INFO] Selected 19 target genomes.
[2023-03-18 23:51:27,006] [INFO] Target genome list was writen to OceanDNA-b23396/target_genomes_gtdb.txt
[2023-03-18 23:51:27,016] [INFO] Task started: fastANI
[2023-03-18 23:51:27,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg47195627-88d6-42b7-8147-89005656a897/OceanDNA-b23396.fa --refList OceanDNA-b23396/target_genomes_gtdb.txt --output OceanDNA-b23396/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:51:38,224] [INFO] Task succeeded: fastANI
[2023-03-18 23:51:38,235] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:51:38,235] [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_006547065.1	s__Brevundimonas sp006547065	87.6973	566	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742215.1	s__Brevundimonas sp016742215	84.0489	336	699	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	83.9577	511	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425945.1	s__Brevundimonas sp001425945	83.3168	510	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912005.1	s__Brevundimonas sp013912005	82.8834	465	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296955.1	s__Brevundimonas sp004296955	82.5536	457	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_016183935.1	s__Brevundimonas sp016183935	82.4875	445	699	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	82.4417	456	699	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	82.3307	471	699	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	81.0877	390	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064825.1	s__Brevundimonas mediterranea_A	80.854	438	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCF_900163625.1	s__Brevundimonas diminuta_A	80.828	395	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820275.1	s__Brevundimonas sp018820275	80.7593	397	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCF_000204035.1	s__Brevundimonas diminuta	80.707	413	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.62	95.74	0.88	0.81	19	-
GCA_003248965.1	s__Brevundimonas sp003248965	80.6647	408	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.48	95.48	0.80	0.80	2	-
GCA_002386585.1	s__Brevundimonas sp002386585	80.6382	353	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.28	96.28	0.79	0.79	2	-
GCA_002434505.1	s__Brevundimonas sp002434505	80.6251	444	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.71	99.71	0.98	0.98	2	-
GCF_014836405.1	s__Brevundimonas sp014836405	80.5195	371	699	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614235.1	s__Brevundimonas intermedia	80.4633	440	699	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 23:51:38,236] [INFO] GTDB search result was written to OceanDNA-b23396/result_gtdb.tsv
[2023-03-18 23:51:38,236] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:51:38,238] [INFO] DFAST_QC result json was written to OceanDNA-b23396/dqc_result.json
[2023-03-18 23:51:38,238] [INFO] DFAST_QC completed!
[2023-03-18 23:51:38,238] [INFO] Total running time: 0h1m9s