[2023-03-18 10:46:22,219] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,221] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg15dbc36d-bd63-4326-9299-6e56c69956bc/dqc_reference
[2023-03-18 10:46:23,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,312] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,312] [INFO] Running command: cat /var/lib/cwl/stge5233334-33d1-4ab7-b013-82605af2a643/OceanDNA-b23401.fa | prodigal -d OceanDNA-b23401/cds.fna -a OceanDNA-b23401/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:46:35,144] [INFO] Task succeeded: Prodigal
[2023-03-18 10:46:35,145] [INFO] Task started: HMMsearch
[2023-03-18 10:46:35,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b23401/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15dbc36d-bd63-4326-9299-6e56c69956bc/dqc_reference/reference_markers.hmm OceanDNA-b23401/protein.faa > /dev/null
[2023-03-18 10:46:35,324] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:46:35,325] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge5233334-33d1-4ab7-b013-82605af2a643/OceanDNA-b23401.fa]
[2023-03-18 10:46:35,373] [INFO] Query marker FASTA was written to OceanDNA-b23401/markers.fasta
[2023-03-18 10:46:35,374] [INFO] Task started: Blastn
[2023-03-18 10:46:35,374] [INFO] Running command: blastn -query OceanDNA-b23401/markers.fasta -db /var/lib/cwl/stg15dbc36d-bd63-4326-9299-6e56c69956bc/dqc_reference/reference_markers.fasta -out OceanDNA-b23401/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:36,058] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:36,190] [INFO] Selected 17 target genomes.
[2023-03-18 10:46:36,190] [INFO] Target genome list was writen to OceanDNA-b23401/target_genomes.txt
[2023-03-18 10:46:36,199] [INFO] Task started: fastANI
[2023-03-18 10:46:36,199] [INFO] Running command: fastANI --query /var/lib/cwl/stge5233334-33d1-4ab7-b013-82605af2a643/OceanDNA-b23401.fa --refList OceanDNA-b23401/target_genomes.txt --output OceanDNA-b23401/fastani_result.tsv --threads 1
[2023-03-18 10:46:46,438] [INFO] Task succeeded: fastANI
[2023-03-18 10:46:46,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15dbc36d-bd63-4326-9299-6e56c69956bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:46:46,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15dbc36d-bd63-4326-9299-6e56c69956bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:46:46,449] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:46:46,449] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:46:46,449] [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 albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	79.8828	399	653	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	79.7855	352	653	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	79.7698	353	653	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.5398	329	653	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	79.4902	333	653	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	79.3856	386	653	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	79.3418	371	653	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	79.3132	348	653	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	79.2335	380	653	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	79.0778	397	653	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	79.0486	349	653	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	79.0415	338	653	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	78.6688	333	653	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	78.4429	304	653	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	77.9857	267	653	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.0637	206	653	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	76.98	168	653	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:46:46,451] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23401/tc_result.tsv
[2023-03-18 10:46:46,458] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:46:46,459] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:46:46,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15dbc36d-bd63-4326-9299-6e56c69956bc/dqc_reference/checkm_data
[2023-03-18 10:46:46,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:46:46,552] [INFO] Task started: CheckM
[2023-03-18 10:46:46,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23401/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23401/checkm_input OceanDNA-b23401/checkm_result
[2023-03-18 10:47:19,267] [INFO] Task succeeded: CheckM
[2023-03-18 10:47:19,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.46%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 10:47:19,309] [INFO] ===== Completeness check finished =====
[2023-03-18 10:47:19,310] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:47:19,310] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23401/markers.fasta)
[2023-03-18 10:47:19,311] [INFO] Task started: Blastn
[2023-03-18 10:47:19,311] [INFO] Running command: blastn -query OceanDNA-b23401/markers.fasta -db /var/lib/cwl/stg15dbc36d-bd63-4326-9299-6e56c69956bc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23401/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:47:20,451] [INFO] Task succeeded: Blastn
[2023-03-18 10:47:20,457] [INFO] Selected 19 target genomes.
[2023-03-18 10:47:20,457] [INFO] Target genome list was writen to OceanDNA-b23401/target_genomes_gtdb.txt
[2023-03-18 10:47:20,475] [INFO] Task started: fastANI
[2023-03-18 10:47:20,475] [INFO] Running command: fastANI --query /var/lib/cwl/stge5233334-33d1-4ab7-b013-82605af2a643/OceanDNA-b23401.fa --refList OceanDNA-b23401/target_genomes_gtdb.txt --output OceanDNA-b23401/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:47:31,849] [INFO] Task succeeded: fastANI
[2023-03-18 10:47:31,859] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:47:31,859] [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_000466985.1	s__Brevundimonas abyssalis	98.2937	561	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	conclusive
GCA_013823285.1	s__Brevundimonas sp013823285	92.1407	528	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308115.1	s__Brevundimonas sp017308115	79.7783	356	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204035.1	s__Brevundimonas diminuta	79.7778	354	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.62	95.74	0.88	0.81	19	-
GCA_013912005.1	s__Brevundimonas sp013912005	79.7593	366	653	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	79.7369	341	653	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	79.6055	338	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCA_001794825.1	s__Brevundimonas sp001794825	79.4797	374	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421705.1	s__Brevundimonas naejangsanensis	79.453	336	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.43	97.43	0.89	0.89	2	-
GCF_001427825.1	s__Brevundimonas sp001427825	79.45	370	653	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	79.4151	354	653	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	79.3356	370	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCF_900116065.1	s__Brevundimonas viscosa	79.3205	374	653	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	79.2911	351	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	79.2553	367	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826515.1	s__Brevundimonas sp018826515	79.2252	392	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCF_011927945.1	s__Brevundimonas alba	79.0493	349	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270135.1	s__Brevundimonas sp012270135	78.7083	277	653	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463295.1	s__Brevundimonas sp016463295	78.4653	296	653	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 10:47:31,863] [INFO] GTDB search result was written to OceanDNA-b23401/result_gtdb.tsv
[2023-03-18 10:47:31,868] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:47:31,871] [INFO] DFAST_QC result json was written to OceanDNA-b23401/dqc_result.json
[2023-03-18 10:47:31,871] [INFO] DFAST_QC completed!
[2023-03-18 10:47:31,872] [INFO] Total running time: 0h1m10s