[2023-03-17 10:08:39,088] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,089] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ac92a4b-01b7-4660-badb-fffce3d59d48/dqc_reference
[2023-03-17 10:08:40,197] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,198] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,198] [INFO] Running command: cat /var/lib/cwl/stg89385c64-c9a6-4372-ba93-2e4431216565/OceanDNA-b23343.fa | prodigal -d OceanDNA-b23343/cds.fna -a OceanDNA-b23343/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:08:47,009] [INFO] Task succeeded: Prodigal
[2023-03-17 10:08:47,009] [INFO] Task started: HMMsearch
[2023-03-17 10:08:47,009] [INFO] Running command: hmmsearch --tblout OceanDNA-b23343/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ac92a4b-01b7-4660-badb-fffce3d59d48/dqc_reference/reference_markers.hmm OceanDNA-b23343/protein.faa > /dev/null
[2023-03-17 10:08:47,175] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:08:47,176] [INFO] Found 6/6 markers.
[2023-03-17 10:08:47,191] [INFO] Query marker FASTA was written to OceanDNA-b23343/markers.fasta
[2023-03-17 10:08:47,191] [INFO] Task started: Blastn
[2023-03-17 10:08:47,191] [INFO] Running command: blastn -query OceanDNA-b23343/markers.fasta -db /var/lib/cwl/stg5ac92a4b-01b7-4660-badb-fffce3d59d48/dqc_reference/reference_markers.fasta -out OceanDNA-b23343/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:08:48,013] [INFO] Task succeeded: Blastn
[2023-03-17 10:08:48,014] [INFO] Selected 18 target genomes.
[2023-03-17 10:08:48,015] [INFO] Target genome list was writen to OceanDNA-b23343/target_genomes.txt
[2023-03-17 10:08:48,041] [INFO] Task started: fastANI
[2023-03-17 10:08:48,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg89385c64-c9a6-4372-ba93-2e4431216565/OceanDNA-b23343.fa --refList OceanDNA-b23343/target_genomes.txt --output OceanDNA-b23343/fastani_result.tsv --threads 1
[2023-03-17 10:08:57,625] [INFO] Task succeeded: fastANI
[2023-03-17 10:08:57,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ac92a4b-01b7-4660-badb-fffce3d59d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:08:57,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ac92a4b-01b7-4660-badb-fffce3d59d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:08:57,635] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:08:57,635] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:08:57,635] [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 halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	91.0257	267	291	95	below_threshold
Brevundimonas halotolerans	strain=DSM 24448	GCA_014199165.1	69670	69670	type	True	91.0032	267	291	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	80.3518	201	291	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	80.2562	188	291	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	80.2543	186	291	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.2204	175	291	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.119	185	291	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	80.0795	167	291	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	80.0033	189	291	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	79.9914	195	291	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	79.9863	179	291	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	79.9808	195	291	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	79.9496	171	291	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	79.8621	186	291	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	79.8425	197	291	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	79.5815	194	291	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:08:57,636] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23343/tc_result.tsv
[2023-03-17 10:08:57,636] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:08:57,636] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:08:57,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ac92a4b-01b7-4660-badb-fffce3d59d48/dqc_reference/checkm_data
[2023-03-17 10:08:57,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:08:57,640] [INFO] Task started: CheckM
[2023-03-17 10:08:57,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23343/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23343/checkm_input OceanDNA-b23343/checkm_result
[2023-03-17 10:09:20,256] [INFO] Task succeeded: CheckM
[2023-03-17 10:09:20,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:09:20,271] [INFO] ===== Completeness check finished =====
[2023-03-17 10:09:20,271] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:09:20,271] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23343/markers.fasta)
[2023-03-17 10:09:20,272] [INFO] Task started: Blastn
[2023-03-17 10:09:20,272] [INFO] Running command: blastn -query OceanDNA-b23343/markers.fasta -db /var/lib/cwl/stg5ac92a4b-01b7-4660-badb-fffce3d59d48/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23343/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:21,732] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:21,733] [INFO] Selected 15 target genomes.
[2023-03-17 10:09:21,733] [INFO] Target genome list was writen to OceanDNA-b23343/target_genomes_gtdb.txt
[2023-03-17 10:09:21,767] [INFO] Task started: fastANI
[2023-03-17 10:09:21,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg89385c64-c9a6-4372-ba93-2e4431216565/OceanDNA-b23343.fa --refList OceanDNA-b23343/target_genomes_gtdb.txt --output OceanDNA-b23343/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:09:29,376] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:29,385] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:09:29,386] [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_003730275.1	s__Brevundimonas halotolerans	91.0257	267	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.75	97.09	0.92	0.85	7	-
GCA_018826885.1	s__Brevundimonas sp018826885	90.4058	251	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742135.1	s__Brevundimonas sp016742135	88.8202	268	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744255.1	s__Brevundimonas sp017744255	85.9799	263	291	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	80.5968	194	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	80.5752	199	291	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	80.5134	210	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCA_013912005.1	s__Brevundimonas sp013912005	80.4653	183	291	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	80.2588	176	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210735.1	s__Brevundimonas sp004210735	80.1812	185	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000318405.1	s__Brevundimonas diminuta_B	80.0887	186	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.76	96.50	0.85	0.82	10	-
GCA_012270135.1	s__Brevundimonas sp012270135	79.8771	152	291	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	79.8771	176	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017795885.1	s__Brevundimonas sp017795885	79.8322	175	291	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	79.7548	167	291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:09:29,386] [INFO] GTDB search result was written to OceanDNA-b23343/result_gtdb.tsv
[2023-03-17 10:09:29,386] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:09:29,388] [INFO] DFAST_QC result json was written to OceanDNA-b23343/dqc_result.json
[2023-03-17 10:09:29,388] [INFO] DFAST_QC completed!
[2023-03-17 10:09:29,388] [INFO] Total running time: 0h0m50s