[2023-03-15 13:55:08,247] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:55:08,247] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:55:08,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9494a73-f98a-4ebf-8fa2-0c6e2d568b89/dqc_reference
[2023-03-15 13:55:09,381] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:55:09,382] [INFO] Task started: Prodigal
[2023-03-15 13:55:09,383] [INFO] Running command: cat /var/lib/cwl/stgfea22e5d-b314-4521-a04d-c88dedbef990/OceanDNA-b23356.fa | prodigal -d OceanDNA-b23356/cds.fna -a OceanDNA-b23356/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:55:19,900] [INFO] Task succeeded: Prodigal
[2023-03-15 13:55:19,900] [INFO] Task started: HMMsearch
[2023-03-15 13:55:19,900] [INFO] Running command: hmmsearch --tblout OceanDNA-b23356/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9494a73-f98a-4ebf-8fa2-0c6e2d568b89/dqc_reference/reference_markers.hmm OceanDNA-b23356/protein.faa > /dev/null
[2023-03-15 13:55:20,075] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:55:20,075] [INFO] Found 6/6 markers.
[2023-03-15 13:55:20,107] [INFO] Query marker FASTA was written to OceanDNA-b23356/markers.fasta
[2023-03-15 13:55:20,108] [INFO] Task started: Blastn
[2023-03-15 13:55:20,108] [INFO] Running command: blastn -query OceanDNA-b23356/markers.fasta -db /var/lib/cwl/stgd9494a73-f98a-4ebf-8fa2-0c6e2d568b89/dqc_reference/reference_markers.fasta -out OceanDNA-b23356/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:55:20,815] [INFO] Task succeeded: Blastn
[2023-03-15 13:55:20,816] [INFO] Selected 19 target genomes.
[2023-03-15 13:55:20,816] [INFO] Target genome list was writen to OceanDNA-b23356/target_genomes.txt
[2023-03-15 13:55:20,832] [INFO] Task started: fastANI
[2023-03-15 13:55:20,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgfea22e5d-b314-4521-a04d-c88dedbef990/OceanDNA-b23356.fa --refList OceanDNA-b23356/target_genomes.txt --output OceanDNA-b23356/fastani_result.tsv --threads 1
[2023-03-15 13:55:32,681] [INFO] Task succeeded: fastANI
[2023-03-15 13:55:32,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9494a73-f98a-4ebf-8fa2-0c6e2d568b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:55:32,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9494a73-f98a-4ebf-8fa2-0c6e2d568b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:55:32,694] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:55:32,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:55:32,694] [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	81.8822	426	587	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.6137	415	587	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.4378	437	587	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	81.2878	421	587	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	81.2796	404	587	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	81.1828	406	587	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.1803	444	587	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	81.1333	406	587	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.9402	418	587	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.8083	417	587	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.7247	380	587	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.6945	398	587	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	80.5386	389	587	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.4977	375	587	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.2343	400	587	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	80.0311	355	587	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.9863	230	587	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.6414	243	587	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.7531	115	587	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:55:32,696] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23356/tc_result.tsv
[2023-03-15 13:55:32,699] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:55:32,699] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:55:32,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9494a73-f98a-4ebf-8fa2-0c6e2d568b89/dqc_reference/checkm_data
[2023-03-15 13:55:32,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:55:32,705] [INFO] Task started: CheckM
[2023-03-15 13:55:32,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23356/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23356/checkm_input OceanDNA-b23356/checkm_result
[2023-03-15 13:56:02,589] [INFO] Task succeeded: CheckM
[2023-03-15 13:56:02,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.73%
Contamintation: 3.47%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 13:56:02,647] [INFO] ===== Completeness check finished =====
[2023-03-15 13:56:02,648] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:56:02,648] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23356/markers.fasta)
[2023-03-15 13:56:02,649] [INFO] Task started: Blastn
[2023-03-15 13:56:02,649] [INFO] Running command: blastn -query OceanDNA-b23356/markers.fasta -db /var/lib/cwl/stgd9494a73-f98a-4ebf-8fa2-0c6e2d568b89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23356/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:56:03,865] [INFO] Task succeeded: Blastn
[2023-03-15 13:56:03,866] [INFO] Selected 30 target genomes.
[2023-03-15 13:56:03,866] [INFO] Target genome list was writen to OceanDNA-b23356/target_genomes_gtdb.txt
[2023-03-15 13:56:03,925] [INFO] Task started: fastANI
[2023-03-15 13:56:03,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgfea22e5d-b314-4521-a04d-c88dedbef990/OceanDNA-b23356.fa --refList OceanDNA-b23356/target_genomes_gtdb.txt --output OceanDNA-b23356/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:56:21,812] [INFO] Task succeeded: fastANI
[2023-03-15 13:56:21,829] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:56:21,829] [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	82.9736	437	587	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	82.7068	467	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_002483305.1	s__Brevundimonas sp002483305	82.6901	422	587	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	82.528	455	587	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	82.2397	430	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820665.1	s__Brevundimonas sp018820665	81.9684	419	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCA_006515835.1	s__Brevundimonas sp006515835	81.9155	365	587	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	81.8827	426	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343425.1	s__Brevundimonas sp002343425	81.8074	407	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.78	0.93	0.93	2	-
GCF_011927945.1	s__Brevundimonas alba	81.6137	415	587	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	81.6004	418	587	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	81.5372	443	587	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	81.464	309	587	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	81.4378	437	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196125.1	s__Brevundimonas mediterranea	81.2702	404	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
GCF_000144605.1	s__Brevundimonas subvibrioides	81.2456	424	587	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	81.1858	424	587	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	81.1847	443	587	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	81.1831	406	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	81.0934	411	587	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	80.9134	392	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017487345.1	s__Brevundimonas sp017487345	80.8231	415	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003938605.1	s__Brevundimonas sp003938605	80.7855	398	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.78	96.68	0.85	0.83	3	-
GCF_004614235.1	s__Brevundimonas intermedia	80.7605	413	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836405.1	s__Brevundimonas sp014836405	80.7253	380	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547065.1	s__Brevundimonas sp006547065	80.6886	417	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387245.1	s__Brevundimonas sp002387245	80.5128	410	587	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	80.3181	342	587	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	80.0015	358	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724985.1	s__Phenylobacterium sp001724985	77.959	177	587	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:56:21,831] [INFO] GTDB search result was written to OceanDNA-b23356/result_gtdb.tsv
[2023-03-15 13:56:21,833] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:56:21,837] [INFO] DFAST_QC result json was written to OceanDNA-b23356/dqc_result.json
[2023-03-15 13:56:21,838] [INFO] DFAST_QC completed!
[2023-03-15 13:56:21,838] [INFO] Total running time: 0h1m14s