[2023-03-16 23:35:12,970] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,970] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg15857d12-3074-4ac8-96d0-b84d16cacdfa/dqc_reference
[2023-03-16 23:35:14,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stgd5b1d295-8cac-4afc-8f21-c952bc3cb30f/OceanDNA-b32076.fa | prodigal -d OceanDNA-b32076/cds.fna -a OceanDNA-b32076/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:41,341] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:41,342] [INFO] Task started: HMMsearch
[2023-03-16 23:35:41,342] [INFO] Running command: hmmsearch --tblout OceanDNA-b32076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15857d12-3074-4ac8-96d0-b84d16cacdfa/dqc_reference/reference_markers.hmm OceanDNA-b32076/protein.faa > /dev/null
[2023-03-16 23:35:41,544] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:41,544] [INFO] Found 6/6 markers.
[2023-03-16 23:35:41,568] [INFO] Query marker FASTA was written to OceanDNA-b32076/markers.fasta
[2023-03-16 23:35:41,568] [INFO] Task started: Blastn
[2023-03-16 23:35:41,568] [INFO] Running command: blastn -query OceanDNA-b32076/markers.fasta -db /var/lib/cwl/stg15857d12-3074-4ac8-96d0-b84d16cacdfa/dqc_reference/reference_markers.fasta -out OceanDNA-b32076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:42,306] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:42,307] [INFO] Selected 18 target genomes.
[2023-03-16 23:35:42,307] [INFO] Target genome list was writen to OceanDNA-b32076/target_genomes.txt
[2023-03-16 23:35:42,317] [INFO] Task started: fastANI
[2023-03-16 23:35:42,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b1d295-8cac-4afc-8f21-c952bc3cb30f/OceanDNA-b32076.fa --refList OceanDNA-b32076/target_genomes.txt --output OceanDNA-b32076/fastani_result.tsv --threads 1
[2023-03-16 23:35:59,007] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:59,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15857d12-3074-4ac8-96d0-b84d16cacdfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:59,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15857d12-3074-4ac8-96d0-b84d16cacdfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:59,019] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:59,019] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:35:59,019] [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
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	89.6235	908	1437	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	89.4414	999	1437	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	83.4348	812	1437	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.2721	821	1437	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	82.6521	735	1437	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.6114	696	1437	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.5677	687	1437	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	82.2414	668	1437	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	82.2055	773	1437	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	82.1875	649	1437	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	82.1171	705	1437	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	81.9424	697	1437	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	81.9351	633	1437	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	81.9036	737	1437	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.0665	323	1437	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.0097	292	1437	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.5605	298	1437	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.5022	317	1437	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:35:59,019] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32076/tc_result.tsv
[2023-03-16 23:35:59,019] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:59,019] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:59,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15857d12-3074-4ac8-96d0-b84d16cacdfa/dqc_reference/checkm_data
[2023-03-16 23:35:59,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:59,026] [INFO] Task started: CheckM
[2023-03-16 23:35:59,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32076/checkm_input OceanDNA-b32076/checkm_result
[2023-03-16 23:37:04,956] [INFO] Task succeeded: CheckM
[2023-03-16 23:37:04,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:37:04,959] [INFO] ===== Completeness check finished =====
[2023-03-16 23:37:04,959] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:37:04,959] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32076/markers.fasta)
[2023-03-16 23:37:04,960] [INFO] Task started: Blastn
[2023-03-16 23:37:04,960] [INFO] Running command: blastn -query OceanDNA-b32076/markers.fasta -db /var/lib/cwl/stg15857d12-3074-4ac8-96d0-b84d16cacdfa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:37:06,242] [INFO] Task succeeded: Blastn
[2023-03-16 23:37:06,242] [INFO] Selected 11 target genomes.
[2023-03-16 23:37:06,243] [INFO] Target genome list was writen to OceanDNA-b32076/target_genomes_gtdb.txt
[2023-03-16 23:37:06,417] [INFO] Task started: fastANI
[2023-03-16 23:37:06,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b1d295-8cac-4afc-8f21-c952bc3cb30f/OceanDNA-b32076.fa --refList OceanDNA-b32076/target_genomes_gtdb.txt --output OceanDNA-b32076/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:37:17,145] [INFO] Task succeeded: fastANI
[2023-03-16 23:37:17,152] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:37:17,152] [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_000153545.1	s__Sphingobium sp000153545	97.6251	1062	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.72	97.49	0.82	0.71	9	conclusive
GCF_001598335.1	s__Sphingobium abikonense	89.6235	908	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_000445105.1	s__Sphingobium lactosutens	89.4492	998	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	86.1213	773	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650725.1	s__Sphingobium sp001650725	85.2752	910	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_000315525.1	s__Sphingobium yanoikuyae	83.4223	814	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_008710155.1	s__Sphingobium limneticum	83.2827	820	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_009720145.1	s__Sphingobium sp009720145	83.2059	779	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556865.1	s__Sphingobium sp001556865	82.9743	716	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	82.9165	811	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967075.1	s__Sphingobium amiense	82.6131	695	1437	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 23:37:17,152] [INFO] GTDB search result was written to OceanDNA-b32076/result_gtdb.tsv
[2023-03-16 23:37:17,152] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:37:17,154] [INFO] DFAST_QC result json was written to OceanDNA-b32076/dqc_result.json
[2023-03-16 23:37:17,154] [INFO] DFAST_QC completed!
[2023-03-16 23:37:17,154] [INFO] Total running time: 0h2m4s