[2023-03-18 23:56:04,493] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:56:04,493] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:56:04,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgda21c066-0286-4a4d-aac8-3813446e8207/dqc_reference
[2023-03-18 23:56:05,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:56:05,621] [INFO] Task started: Prodigal
[2023-03-18 23:56:05,621] [INFO] Running command: cat /var/lib/cwl/stg7d2504f7-66b5-4df9-9862-38d868e2555f/OceanDNA-b24884.fa | prodigal -d OceanDNA-b24884/cds.fna -a OceanDNA-b24884/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:56:24,138] [INFO] Task succeeded: Prodigal
[2023-03-18 23:56:24,139] [INFO] Task started: HMMsearch
[2023-03-18 23:56:24,139] [INFO] Running command: hmmsearch --tblout OceanDNA-b24884/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda21c066-0286-4a4d-aac8-3813446e8207/dqc_reference/reference_markers.hmm OceanDNA-b24884/protein.faa > /dev/null
[2023-03-18 23:56:24,334] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:56:24,335] [INFO] Found 6/6 markers.
[2023-03-18 23:56:24,357] [INFO] Query marker FASTA was written to OceanDNA-b24884/markers.fasta
[2023-03-18 23:56:24,358] [INFO] Task started: Blastn
[2023-03-18 23:56:24,358] [INFO] Running command: blastn -query OceanDNA-b24884/markers.fasta -db /var/lib/cwl/stgda21c066-0286-4a4d-aac8-3813446e8207/dqc_reference/reference_markers.fasta -out OceanDNA-b24884/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:56:25,247] [INFO] Task succeeded: Blastn
[2023-03-18 23:56:25,248] [INFO] Selected 21 target genomes.
[2023-03-18 23:56:25,248] [INFO] Target genome list was writen to OceanDNA-b24884/target_genomes.txt
[2023-03-18 23:56:25,262] [INFO] Task started: fastANI
[2023-03-18 23:56:25,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2504f7-66b5-4df9-9862-38d868e2555f/OceanDNA-b24884.fa --refList OceanDNA-b24884/target_genomes.txt --output OceanDNA-b24884/fastani_result.tsv --threads 1
[2023-03-18 23:56:40,441] [INFO] Task succeeded: fastANI
[2023-03-18 23:56:40,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda21c066-0286-4a4d-aac8-3813446e8207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:56:40,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda21c066-0286-4a4d-aac8-3813446e8207/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:56:40,454] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:56:40,454] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:56:40,454] [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
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	90.4864	892	1006	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	78.9095	451	1006	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	78.479	395	1006	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.6421	315	1006	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	77.2507	215	1006	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	77.2484	213	1006	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	77.2055	220	1006	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	76.8412	116	1006	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.7188	145	1006	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	76.7101	110	1006	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.6657	111	1006	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	76.645	114	1006	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.6432	135	1006	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	76.6321	123	1006	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.4979	98	1006	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.4817	123	1006	95	below_threshold
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	76.4813	104	1006	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	76.4619	105	1006	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.3956	106	1006	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	76.3069	124	1006	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.2048	103	1006	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:56:40,455] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24884/tc_result.tsv
[2023-03-18 23:56:40,455] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:56:40,455] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:56:40,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda21c066-0286-4a4d-aac8-3813446e8207/dqc_reference/checkm_data
[2023-03-18 23:56:40,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:56:40,461] [INFO] Task started: CheckM
[2023-03-18 23:56:40,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24884/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24884/checkm_input OceanDNA-b24884/checkm_result
[2023-03-18 23:57:27,486] [INFO] Task succeeded: CheckM
[2023-03-18 23:57:27,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:57:27,489] [INFO] ===== Completeness check finished =====
[2023-03-18 23:57:27,489] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:57:27,489] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24884/markers.fasta)
[2023-03-18 23:57:27,491] [INFO] Task started: Blastn
[2023-03-18 23:57:27,491] [INFO] Running command: blastn -query OceanDNA-b24884/markers.fasta -db /var/lib/cwl/stgda21c066-0286-4a4d-aac8-3813446e8207/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24884/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:57:29,238] [INFO] Task succeeded: Blastn
[2023-03-18 23:57:29,239] [INFO] Selected 12 target genomes.
[2023-03-18 23:57:29,240] [INFO] Target genome list was writen to OceanDNA-b24884/target_genomes_gtdb.txt
[2023-03-18 23:57:29,251] [INFO] Task started: fastANI
[2023-03-18 23:57:29,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2504f7-66b5-4df9-9862-38d868e2555f/OceanDNA-b24884.fa --refList OceanDNA-b24884/target_genomes_gtdb.txt --output OceanDNA-b24884/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:57:37,661] [INFO] Task succeeded: fastANI
[2023-03-18 23:57:37,668] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:57:37,668] [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_002684405.1	s__Parvibaculum sp002684405	99.9419	929	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011762095.1	s__Parvibaculum indicum	90.4864	892	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	79.1576	459	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_002842875.1	s__Parvibaculum sp002842875	79.0623	415	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	78.8997	452	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	78.8728	433	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_002694985.1	s__Parvibaculum sp002694985	78.8487	419	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_014359855.1	s__Parvibaculum sp014359855	78.7607	272	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	78.6616	390	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001402875.1	s__Blastochloris viridis	76.4821	104	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008802405.1	s__Aureimonas_A leprariae	76.4465	100	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	76.3069	124	1006	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:57:37,669] [INFO] GTDB search result was written to OceanDNA-b24884/result_gtdb.tsv
[2023-03-18 23:57:37,669] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:57:37,671] [INFO] DFAST_QC result json was written to OceanDNA-b24884/dqc_result.json
[2023-03-18 23:57:37,671] [INFO] DFAST_QC completed!
[2023-03-18 23:57:37,671] [INFO] Total running time: 0h1m33s