[2023-03-17 23:49:10,021] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:49:10,022] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:49:10,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg507f2ac7-5221-4c59-87b1-a436bbbdd0f6/dqc_reference
[2023-03-17 23:49:11,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:49:11,114] [INFO] Task started: Prodigal
[2023-03-17 23:49:11,114] [INFO] Running command: cat /var/lib/cwl/stg7fd928ba-664d-4ecd-8795-0fafb4f9ed58/OceanDNA-b23461.fa | prodigal -d OceanDNA-b23461/cds.fna -a OceanDNA-b23461/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:49:32,093] [INFO] Task succeeded: Prodigal
[2023-03-17 23:49:32,093] [INFO] Task started: HMMsearch
[2023-03-17 23:49:32,093] [INFO] Running command: hmmsearch --tblout OceanDNA-b23461/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg507f2ac7-5221-4c59-87b1-a436bbbdd0f6/dqc_reference/reference_markers.hmm OceanDNA-b23461/protein.faa > /dev/null
[2023-03-17 23:49:32,309] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:49:32,310] [INFO] Found 6/6 markers.
[2023-03-17 23:49:32,365] [INFO] Query marker FASTA was written to OceanDNA-b23461/markers.fasta
[2023-03-17 23:49:32,366] [INFO] Task started: Blastn
[2023-03-17 23:49:32,366] [INFO] Running command: blastn -query OceanDNA-b23461/markers.fasta -db /var/lib/cwl/stg507f2ac7-5221-4c59-87b1-a436bbbdd0f6/dqc_reference/reference_markers.fasta -out OceanDNA-b23461/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:49:33,145] [INFO] Task succeeded: Blastn
[2023-03-17 23:49:33,154] [INFO] Selected 18 target genomes.
[2023-03-17 23:49:33,154] [INFO] Target genome list was writen to OceanDNA-b23461/target_genomes.txt
[2023-03-17 23:49:33,168] [INFO] Task started: fastANI
[2023-03-17 23:49:33,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fd928ba-664d-4ecd-8795-0fafb4f9ed58/OceanDNA-b23461.fa --refList OceanDNA-b23461/target_genomes.txt --output OceanDNA-b23461/fastani_result.tsv --threads 1
[2023-03-17 23:49:47,881] [INFO] Task succeeded: fastANI
[2023-03-17 23:49:47,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg507f2ac7-5221-4c59-87b1-a436bbbdd0f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:49:47,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg507f2ac7-5221-4c59-87b1-a436bbbdd0f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:49:47,893] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:49:47,893] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:49:47,893] [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 aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	80.8985	683	1172	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.6155	664	1172	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	80.5344	587	1172	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.952	617	1172	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	79.9349	592	1172	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.9255	555	1172	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.3564	528	1172	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	79.2262	531	1172	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	79.1607	484	1172	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	78.7427	555	1172	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	77.9758	318	1172	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	77.9458	320	1172	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	76.1315	121	1172	95	below_threshold
Phaeovibrio sulfidiphilus	strain=DSM 23193	GCA_014861485.1	1220600	1220600	type	True	75.9639	81	1172	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.9047	162	1172	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.897	187	1172	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.8356	190	1172	95	below_threshold
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	75.2033	69	1172	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:49:47,893] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23461/tc_result.tsv
[2023-03-17 23:49:47,893] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:49:47,893] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:49:47,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg507f2ac7-5221-4c59-87b1-a436bbbdd0f6/dqc_reference/checkm_data
[2023-03-17 23:49:47,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:49:47,899] [INFO] Task started: CheckM
[2023-03-17 23:49:47,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23461/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23461/checkm_input OceanDNA-b23461/checkm_result
[2023-03-17 23:50:40,455] [INFO] Task succeeded: CheckM
[2023-03-17 23:50:40,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:50:40,485] [INFO] ===== Completeness check finished =====
[2023-03-17 23:50:40,485] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:50:40,486] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23461/markers.fasta)
[2023-03-17 23:50:40,486] [INFO] Task started: Blastn
[2023-03-17 23:50:40,487] [INFO] Running command: blastn -query OceanDNA-b23461/markers.fasta -db /var/lib/cwl/stg507f2ac7-5221-4c59-87b1-a436bbbdd0f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23461/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:50:41,877] [INFO] Task succeeded: Blastn
[2023-03-17 23:50:41,882] [INFO] Selected 22 target genomes.
[2023-03-17 23:50:41,882] [INFO] Target genome list was writen to OceanDNA-b23461/target_genomes_gtdb.txt
[2023-03-17 23:50:41,917] [INFO] Task started: fastANI
[2023-03-17 23:50:41,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fd928ba-664d-4ecd-8795-0fafb4f9ed58/OceanDNA-b23461.fa --refList OceanDNA-b23461/target_genomes_gtdb.txt --output OceanDNA-b23461/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:50:59,404] [INFO] Task succeeded: fastANI
[2023-03-17 23:50:59,417] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:50:59,417] [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_002363865.1	s__Phenylobacterium sp002363865	87.6755	900	1172	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	85.6902	639	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	84.1357	837	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_018001015.1	s__Phenylobacterium sp018001015	80.7661	647	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCF_016772415.1	s__Phenylobacterium sp016772415	80.6204	665	1172	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	80.548	586	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429025.1	s__Phenylobacterium sp001429025	80.4983	616	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.02	99.02	0.94	0.94	2	-
GCA_018240795.1	s__Phenylobacterium sp018240795	80.1025	565	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822795.1	s__Phenylobacterium sp013822795	80.0963	585	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	80.0334	562	1172	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	79.9357	618	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCF_003254475.1	s__Phenylobacterium soli	79.9305	555	1172	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	79.6247	591	1172	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	79.4035	562	1172	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	79.3745	476	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241335.1	s__Palsa-881 sp018241335	79.3076	478	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281955.1	s__Caulobacter sp000281955	79.2943	537	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912465.1	s__Phenylobacterium sp903912465	78.832	305	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903933475.1	s__Phenylobacterium sp903933475	78.523	320	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.29	99.29	0.84	0.84	2	-
GCA_903851655.1	s__CAIMFV01 sp903851655	78.4375	347	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.52	99.51	0.87	0.86	3	-
GCF_000466985.1	s__Brevundimonas abyssalis	78.1237	331	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
GCA_903874895.1	s__CAIMFV01 sp903874895	77.7865	289	1172	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	98.54	98.54	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:50:59,419] [INFO] GTDB search result was written to OceanDNA-b23461/result_gtdb.tsv
[2023-03-17 23:50:59,421] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:50:59,423] [INFO] DFAST_QC result json was written to OceanDNA-b23461/dqc_result.json
[2023-03-17 23:50:59,423] [INFO] DFAST_QC completed!
[2023-03-17 23:50:59,423] [INFO] Total running time: 0h1m49s