[2023-03-16 04:54:07,041] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,041] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f99435a-986e-482a-ba72-fea33eeb0ba0/dqc_reference
[2023-03-16 04:54:08,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,380] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,380] [INFO] Running command: cat /var/lib/cwl/stg3adf8960-9be5-43db-98b5-4321f5b3fca8/OceanDNA-b23369.fa | prodigal -d OceanDNA-b23369/cds.fna -a OceanDNA-b23369/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:22,868] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:22,868] [INFO] Task started: HMMsearch
[2023-03-16 04:54:22,868] [INFO] Running command: hmmsearch --tblout OceanDNA-b23369/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f99435a-986e-482a-ba72-fea33eeb0ba0/dqc_reference/reference_markers.hmm OceanDNA-b23369/protein.faa > /dev/null
[2023-03-16 04:54:23,130] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:23,131] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3adf8960-9be5-43db-98b5-4321f5b3fca8/OceanDNA-b23369.fa]
[2023-03-16 04:54:23,147] [INFO] Query marker FASTA was written to OceanDNA-b23369/markers.fasta
[2023-03-16 04:54:23,148] [INFO] Task started: Blastn
[2023-03-16 04:54:23,148] [INFO] Running command: blastn -query OceanDNA-b23369/markers.fasta -db /var/lib/cwl/stg1f99435a-986e-482a-ba72-fea33eeb0ba0/dqc_reference/reference_markers.fasta -out OceanDNA-b23369/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:23,954] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:23,955] [INFO] Selected 18 target genomes.
[2023-03-16 04:54:23,956] [INFO] Target genome list was writen to OceanDNA-b23369/target_genomes.txt
[2023-03-16 04:54:23,970] [INFO] Task started: fastANI
[2023-03-16 04:54:23,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg3adf8960-9be5-43db-98b5-4321f5b3fca8/OceanDNA-b23369.fa --refList OceanDNA-b23369/target_genomes.txt --output OceanDNA-b23369/fastani_result.tsv --threads 1
[2023-03-16 04:54:35,966] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:35,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f99435a-986e-482a-ba72-fea33eeb0ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:35,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f99435a-986e-482a-ba72-fea33eeb0ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:35,979] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:35,979] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:54:35,979] [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	81.3129	500	787	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.2629	520	787	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.1898	533	787	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.0778	512	787	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	80.9667	523	787	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	80.8827	479	787	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	80.8293	513	787	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	80.803	485	787	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.6875	491	787	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.6369	508	787	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.4164	466	787	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.3937	443	787	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	80.3819	450	787	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.371	459	787	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.2366	462	787	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	79.7471	438	787	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.8434	262	787	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.6924	279	787	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:54:35,979] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23369/tc_result.tsv
[2023-03-16 04:54:35,979] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:35,979] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:35,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f99435a-986e-482a-ba72-fea33eeb0ba0/dqc_reference/checkm_data
[2023-03-16 04:54:35,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:36,012] [INFO] Task started: CheckM
[2023-03-16 04:54:36,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23369/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23369/checkm_input OceanDNA-b23369/checkm_result
[2023-03-16 04:55:13,920] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:13,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:13,923] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:13,923] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:13,923] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23369/markers.fasta)
[2023-03-16 04:55:13,924] [INFO] Task started: Blastn
[2023-03-16 04:55:13,924] [INFO] Running command: blastn -query OceanDNA-b23369/markers.fasta -db /var/lib/cwl/stg1f99435a-986e-482a-ba72-fea33eeb0ba0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23369/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:15,329] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:15,330] [INFO] Selected 21 target genomes.
[2023-03-16 04:55:15,330] [INFO] Target genome list was writen to OceanDNA-b23369/target_genomes_gtdb.txt
[2023-03-16 04:55:15,352] [INFO] Task started: fastANI
[2023-03-16 04:55:15,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg3adf8960-9be5-43db-98b5-4321f5b3fca8/OceanDNA-b23369.fa --refList OceanDNA-b23369/target_genomes_gtdb.txt --output OceanDNA-b23369/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:28,570] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:28,583] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:55:28,583] [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	82.3762	536	787	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	82.307	540	787	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	82.1536	504	787	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	82.1057	537	787	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	81.487	503	787	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	81.2497	521	787	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	81.1974	532	787	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	81.079	512	787	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	81.0481	523	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCF_000144605.1	s__Brevundimonas subvibrioides	80.966	523	787	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	80.914	455	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350205.1	s__Brevundimonas bullata	80.8612	481	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.07	95.78	0.81	0.78	3	-
GCF_014196125.1	s__Brevundimonas mediterranea	80.8176	514	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
GCF_014207965.1	s__Brevundimonas bullata_A	80.7944	509	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	80.7896	484	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479495.1	s__Brevundimonas sp002479495	80.789	494	787	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	80.6896	484	787	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	80.3939	443	787	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	80.3677	398	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683885.1	s__Brevundimonas sp004683885	80.1997	421	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014199945.1	s__Brevundimonas variabilis	79.7471	438	787	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:28,583] [INFO] GTDB search result was written to OceanDNA-b23369/result_gtdb.tsv
[2023-03-16 04:55:28,583] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:28,585] [INFO] DFAST_QC result json was written to OceanDNA-b23369/dqc_result.json
[2023-03-16 04:55:28,585] [INFO] DFAST_QC completed!
[2023-03-16 04:55:28,586] [INFO] Total running time: 0h1m22s