[2023-03-17 22:46:02,579] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:46:02,579] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:46:02,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg61efc5c0-95d5-4840-a09a-fbf2535abd45/dqc_reference
[2023-03-17 22:46:03,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:46:03,677] [INFO] Task started: Prodigal
[2023-03-17 22:46:03,677] [INFO] Running command: cat /var/lib/cwl/stg19ec3863-8027-4d02-b2d3-3f7b9b33d6fa/OceanDNA-b23458.fa | prodigal -d OceanDNA-b23458/cds.fna -a OceanDNA-b23458/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:46:19,444] [INFO] Task succeeded: Prodigal
[2023-03-17 22:46:19,444] [INFO] Task started: HMMsearch
[2023-03-17 22:46:19,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b23458/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61efc5c0-95d5-4840-a09a-fbf2535abd45/dqc_reference/reference_markers.hmm OceanDNA-b23458/protein.faa > /dev/null
[2023-03-17 22:46:19,640] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:46:19,641] [INFO] Found 6/6 markers.
[2023-03-17 22:46:19,663] [INFO] Query marker FASTA was written to OceanDNA-b23458/markers.fasta
[2023-03-17 22:46:19,663] [INFO] Task started: Blastn
[2023-03-17 22:46:19,663] [INFO] Running command: blastn -query OceanDNA-b23458/markers.fasta -db /var/lib/cwl/stg61efc5c0-95d5-4840-a09a-fbf2535abd45/dqc_reference/reference_markers.fasta -out OceanDNA-b23458/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:46:20,562] [INFO] Task succeeded: Blastn
[2023-03-17 22:46:20,563] [INFO] Selected 15 target genomes.
[2023-03-17 22:46:20,563] [INFO] Target genome list was writen to OceanDNA-b23458/target_genomes.txt
[2023-03-17 22:46:20,569] [INFO] Task started: fastANI
[2023-03-17 22:46:20,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ec3863-8027-4d02-b2d3-3f7b9b33d6fa/OceanDNA-b23458.fa --refList OceanDNA-b23458/target_genomes.txt --output OceanDNA-b23458/fastani_result.tsv --threads 1
[2023-03-17 22:46:32,189] [INFO] Task succeeded: fastANI
[2023-03-17 22:46:32,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61efc5c0-95d5-4840-a09a-fbf2535abd45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:46:32,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61efc5c0-95d5-4840-a09a-fbf2535abd45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:46:32,198] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:46:32,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:46:32,199] [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
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.3093	537	900	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	81.2376	584	900	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	81.2335	593	900	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	81.1285	565	900	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.9421	519	900	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	80.5779	558	900	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	80.248	494	900	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	79.7735	444	900	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	79.5867	532	900	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.572	523	900	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.551	492	900	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.6301	343	900	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.3645	289	900	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	77.8961	314	900	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	77.1887	136	900	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:46:32,199] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23458/tc_result.tsv
[2023-03-17 22:46:32,199] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:46:32,199] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:46:32,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61efc5c0-95d5-4840-a09a-fbf2535abd45/dqc_reference/checkm_data
[2023-03-17 22:46:32,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:46:32,204] [INFO] Task started: CheckM
[2023-03-17 22:46:32,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23458/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23458/checkm_input OceanDNA-b23458/checkm_result
[2023-03-17 22:47:14,621] [INFO] Task succeeded: CheckM
[2023-03-17 22:47:14,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:47:14,624] [INFO] ===== Completeness check finished =====
[2023-03-17 22:47:14,624] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:47:14,624] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23458/markers.fasta)
[2023-03-17 22:47:14,625] [INFO] Task started: Blastn
[2023-03-17 22:47:14,625] [INFO] Running command: blastn -query OceanDNA-b23458/markers.fasta -db /var/lib/cwl/stg61efc5c0-95d5-4840-a09a-fbf2535abd45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23458/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:47:16,456] [INFO] Task succeeded: Blastn
[2023-03-17 22:47:16,457] [INFO] Selected 18 target genomes.
[2023-03-17 22:47:16,457] [INFO] Target genome list was writen to OceanDNA-b23458/target_genomes_gtdb.txt
[2023-03-17 22:47:16,472] [INFO] Task started: fastANI
[2023-03-17 22:47:16,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ec3863-8027-4d02-b2d3-3f7b9b33d6fa/OceanDNA-b23458.fa --refList OceanDNA-b23458/target_genomes_gtdb.txt --output OceanDNA-b23458/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:47:30,793] [INFO] Task succeeded: fastANI
[2023-03-17 22:47:30,803] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:47:30,804] [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_013911965.1	s__Phenylobacterium sp013911965	89.8082	792	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_002363865.1	s__Phenylobacterium sp002363865	83.8686	672	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCA_002441055.1	s__Phenylobacterium sp002441055	82.6161	519	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724985.1	s__Phenylobacterium sp001724985	81.5212	411	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	81.3725	532	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	81.2803	580	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCF_016772415.1	s__Phenylobacterium sp016772415	81.141	565	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254475.1	s__Phenylobacterium soli	80.9208	521	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240795.1	s__Phenylobacterium sp018240795	80.8336	518	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425305.1	s__Phenylobacterium sp001425305	80.7224	553	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_004799515.1	s__Phenylobacterium sp004799515	80.6779	497	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799545.1	s__Phenylobacterium sp004799545	80.4551	493	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297125.1	s__Phenylobacterium sp004297125	80.095	552	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	80.0903	514	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793285.1	s__Phenylobacterium sp016793285	79.8327	475	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	79.7626	441	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799395.1	s__Phenylobacterium sp004799395	79.688	456	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722335.1	s__Caulobacter flavus	79.6409	526	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-17 22:47:30,804] [INFO] GTDB search result was written to OceanDNA-b23458/result_gtdb.tsv
[2023-03-17 22:47:30,804] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:47:30,806] [INFO] DFAST_QC result json was written to OceanDNA-b23458/dqc_result.json
[2023-03-17 22:47:30,806] [INFO] DFAST_QC completed!
[2023-03-17 22:47:30,806] [INFO] Total running time: 0h1m28s