[2023-03-18 04:04:53,908] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,908] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b261901-2c3e-47f1-9437-859684c23a15/dqc_reference
[2023-03-18 04:04:55,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stg788731f9-29d5-4c30-82ce-aff1618ff94f/OceanDNA-b23379.fa | prodigal -d OceanDNA-b23379/cds.fna -a OceanDNA-b23379/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:08,450] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:08,450] [INFO] Task started: HMMsearch
[2023-03-18 04:05:08,450] [INFO] Running command: hmmsearch --tblout OceanDNA-b23379/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b261901-2c3e-47f1-9437-859684c23a15/dqc_reference/reference_markers.hmm OceanDNA-b23379/protein.faa > /dev/null
[2023-03-18 04:05:08,666] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:08,666] [INFO] Found 6/6 markers.
[2023-03-18 04:05:08,686] [INFO] Query marker FASTA was written to OceanDNA-b23379/markers.fasta
[2023-03-18 04:05:08,686] [INFO] Task started: Blastn
[2023-03-18 04:05:08,686] [INFO] Running command: blastn -query OceanDNA-b23379/markers.fasta -db /var/lib/cwl/stg6b261901-2c3e-47f1-9437-859684c23a15/dqc_reference/reference_markers.fasta -out OceanDNA-b23379/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:09,431] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:09,431] [INFO] Selected 13 target genomes.
[2023-03-18 04:05:09,432] [INFO] Target genome list was writen to OceanDNA-b23379/target_genomes.txt
[2023-03-18 04:05:09,440] [INFO] Task started: fastANI
[2023-03-18 04:05:09,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg788731f9-29d5-4c30-82ce-aff1618ff94f/OceanDNA-b23379.fa --refList OceanDNA-b23379/target_genomes.txt --output OceanDNA-b23379/fastani_result.tsv --threads 1
[2023-03-18 04:05:18,215] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:18,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b261901-2c3e-47f1-9437-859684c23a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:18,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b261901-2c3e-47f1-9437-859684c23a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:18,223] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:05:18,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:05:18,224] [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	84.5158	530	766	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	83.9252	542	766	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	83.562	565	766	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	83.1384	550	766	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.2266	485	766	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.8657	443	766	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	80.8372	475	766	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	80.6298	475	766	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.2997	428	766	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	77.853	308	766	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	77.7767	338	766	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.6948	262	766	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.5772	125	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:05:18,224] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23379/tc_result.tsv
[2023-03-18 04:05:18,224] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:18,224] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:18,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b261901-2c3e-47f1-9437-859684c23a15/dqc_reference/checkm_data
[2023-03-18 04:05:18,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:18,232] [INFO] Task started: CheckM
[2023-03-18 04:05:18,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23379/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23379/checkm_input OceanDNA-b23379/checkm_result
[2023-03-18 04:05:54,242] [INFO] Task succeeded: CheckM
[2023-03-18 04:05:54,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.56%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:05:54,253] [INFO] ===== Completeness check finished =====
[2023-03-18 04:05:54,253] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:05:54,253] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23379/markers.fasta)
[2023-03-18 04:05:54,253] [INFO] Task started: Blastn
[2023-03-18 04:05:54,253] [INFO] Running command: blastn -query OceanDNA-b23379/markers.fasta -db /var/lib/cwl/stg6b261901-2c3e-47f1-9437-859684c23a15/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23379/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:55,525] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:55,526] [INFO] Selected 11 target genomes.
[2023-03-18 04:05:55,526] [INFO] Target genome list was writen to OceanDNA-b23379/target_genomes_gtdb.txt
[2023-03-18 04:05:55,726] [INFO] Task started: fastANI
[2023-03-18 04:05:55,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg788731f9-29d5-4c30-82ce-aff1618ff94f/OceanDNA-b23379.fa --refList OceanDNA-b23379/target_genomes_gtdb.txt --output OceanDNA-b23379/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:06:02,364] [INFO] Task succeeded: fastANI
[2023-03-18 04:06:02,371] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:06:02,371] [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	88.0681	616	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.85	99.80	0.97	0.95	6	-
GCA_002483305.1	s__Brevundimonas sp002483305	87.7024	560	766	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	87.5351	589	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCA_002343425.1	s__Brevundimonas sp002343425	86.6855	562	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.78	0.93	0.93	2	-
GCA_006515835.1	s__Brevundimonas sp006515835	86.2005	478	766	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	85.922	580	766	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	85.1525	513	766	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
GCA_016183935.1	s__Brevundimonas sp016183935	84.621	539	766	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	84.5106	530	766	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	83.8103	364	766	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	83.3207	525	766	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 04:06:02,382] [INFO] GTDB search result was written to OceanDNA-b23379/result_gtdb.tsv
[2023-03-18 04:06:02,404] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:06:02,413] [INFO] DFAST_QC result json was written to OceanDNA-b23379/dqc_result.json
[2023-03-18 04:06:02,413] [INFO] DFAST_QC completed!
[2023-03-18 04:06:02,413] [INFO] Total running time: 0h1m9s