[2023-03-16 18:07:24,868] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:07:24,868] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:07:24,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg536a2b87-1efe-4485-8ad6-c68038f4d11b/dqc_reference
[2023-03-16 18:07:25,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:07:25,958] [INFO] Task started: Prodigal
[2023-03-16 18:07:25,958] [INFO] Running command: cat /var/lib/cwl/stg33dc5429-40bb-4d60-b5da-c5c26b5c460c/OceanDNA-b32054.fa | prodigal -d OceanDNA-b32054/cds.fna -a OceanDNA-b32054/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:07:43,800] [INFO] Task succeeded: Prodigal
[2023-03-16 18:07:43,801] [INFO] Task started: HMMsearch
[2023-03-16 18:07:43,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b32054/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg536a2b87-1efe-4485-8ad6-c68038f4d11b/dqc_reference/reference_markers.hmm OceanDNA-b32054/protein.faa > /dev/null
[2023-03-16 18:07:44,064] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:07:44,064] [INFO] Found 6/6 markers.
[2023-03-16 18:07:44,087] [INFO] Query marker FASTA was written to OceanDNA-b32054/markers.fasta
[2023-03-16 18:07:44,088] [INFO] Task started: Blastn
[2023-03-16 18:07:44,088] [INFO] Running command: blastn -query OceanDNA-b32054/markers.fasta -db /var/lib/cwl/stg536a2b87-1efe-4485-8ad6-c68038f4d11b/dqc_reference/reference_markers.fasta -out OceanDNA-b32054/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:07:44,890] [INFO] Task succeeded: Blastn
[2023-03-16 18:07:44,891] [INFO] Selected 22 target genomes.
[2023-03-16 18:07:44,891] [INFO] Target genome list was writen to OceanDNA-b32054/target_genomes.txt
[2023-03-16 18:07:44,923] [INFO] Task started: fastANI
[2023-03-16 18:07:44,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg33dc5429-40bb-4d60-b5da-c5c26b5c460c/OceanDNA-b32054.fa --refList OceanDNA-b32054/target_genomes.txt --output OceanDNA-b32054/fastani_result.tsv --threads 1
[2023-03-16 18:08:09,351] [INFO] Task succeeded: fastANI
[2023-03-16 18:08:09,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg536a2b87-1efe-4485-8ad6-c68038f4d11b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:08:09,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg536a2b87-1efe-4485-8ad6-c68038f4d11b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:08:09,372] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:08:09,372] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:08:09,372] [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 jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	81.3415	457	706	95	below_threshold
Sphingobium fluviale	strain=CHR27	GCA_004122115.1	2506423	2506423	type	True	80.557	368	706	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	79.6277	354	706	95	below_threshold
Sphingobium subterraneum	strain=DSM 102255	GCA_014199435.1	627688	627688	type	True	79.3831	358	706	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	79.3003	337	706	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	79.1254	332	706	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	79.1006	335	706	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	79.0183	332	706	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.9102	342	706	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	78.8795	298	706	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	78.8443	317	706	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	78.7677	345	706	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	78.6566	334	706	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	78.4103	324	706	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.3259	236	706	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.8436	245	706	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.8177	227	706	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.6728	214	706	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	77.6331	217	706	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	77.5141	206	706	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.4916	224	706	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.4561	212	706	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:08:09,372] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32054/tc_result.tsv
[2023-03-16 18:08:09,372] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:08:09,372] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:08:09,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg536a2b87-1efe-4485-8ad6-c68038f4d11b/dqc_reference/checkm_data
[2023-03-16 18:08:09,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:08:09,716] [INFO] Task started: CheckM
[2023-03-16 18:08:09,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32054/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32054/checkm_input OceanDNA-b32054/checkm_result
[2023-03-16 18:08:57,212] [INFO] Task succeeded: CheckM
[2023-03-16 18:08:57,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:08:57,214] [INFO] ===== Completeness check finished =====
[2023-03-16 18:08:57,214] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:08:57,214] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32054/markers.fasta)
[2023-03-16 18:08:57,216] [INFO] Task started: Blastn
[2023-03-16 18:08:57,216] [INFO] Running command: blastn -query OceanDNA-b32054/markers.fasta -db /var/lib/cwl/stg536a2b87-1efe-4485-8ad6-c68038f4d11b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32054/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:08:58,829] [INFO] Task succeeded: Blastn
[2023-03-16 18:08:58,830] [INFO] Selected 20 target genomes.
[2023-03-16 18:08:58,830] [INFO] Target genome list was writen to OceanDNA-b32054/target_genomes_gtdb.txt
[2023-03-16 18:08:58,851] [INFO] Task started: fastANI
[2023-03-16 18:08:58,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg33dc5429-40bb-4d60-b5da-c5c26b5c460c/OceanDNA-b32054.fa --refList OceanDNA-b32054/target_genomes_gtdb.txt --output OceanDNA-b32054/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:09:13,434] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:13,446] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:09:13,446] [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_014196495.1	s__Sphingobium jiangsuense	81.2997	459	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122115.1	s__Sphingobium fluviale	80.5476	369	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226685.1	s__Sphingobium sp006226685	79.9741	377	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.90	99.90	0.86	0.86	2	-
GCA_017984895.1	s__Sphingobium sp017984895	79.9406	336	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.97	99.94	0.94	0.89	4	-
GCF_014199435.1	s__Sphingobium subterraneum	79.3834	358	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196635.1	s__Sphingobium fontiphilum	79.1396	331	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	79.1283	333	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
GCF_002355855.1	s__Sphingobium cloacae	79.1217	351	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009720145.1	s__Sphingobium sp009720145	79.1175	356	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315525.1	s__Sphingobium yanoikuyae	78.8611	347	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_004152845.1	s__Sphingobium fuliginis	78.8587	328	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	78.7273	309	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_014203965.1	s__Sphingobium sp014203965	78.6857	327	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000588875.1	s__Sphingobium sp000588875	78.5428	324	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153545.1	s__Sphingobium sp000153545	78.4791	314	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.72	97.49	0.82	0.71	9	-
GCF_000445105.1	s__Sphingobium lactosutens	78.4034	324	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_006439055.1	s__Sphingomonas glacialis_A	77.6117	217	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	77.4624	233	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	77.3486	214	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421805.1	s__Sphingomonas sp001421805	77.2073	179	706	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.24	98.24	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-16 18:09:13,446] [INFO] GTDB search result was written to OceanDNA-b32054/result_gtdb.tsv
[2023-03-16 18:09:13,446] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:09:13,449] [INFO] DFAST_QC result json was written to OceanDNA-b32054/dqc_result.json
[2023-03-16 18:09:13,449] [INFO] DFAST_QC completed!
[2023-03-16 18:09:13,449] [INFO] Total running time: 0h1m49s