[2023-03-16 12:14:10,939] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:14:10,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:14:10,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d5bd9ef-5dc5-43c0-a39f-b8c37d2a40e2/dqc_reference
[2023-03-16 12:14:13,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:14:13,506] [INFO] Task started: Prodigal
[2023-03-16 12:14:13,506] [INFO] Running command: cat /var/lib/cwl/stgbb6e4689-2251-42aa-84b5-aa766e4774e4/OceanDNA-b32047.fa | prodigal -d OceanDNA-b32047/cds.fna -a OceanDNA-b32047/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:14:53,427] [INFO] Task succeeded: Prodigal
[2023-03-16 12:14:53,427] [INFO] Task started: HMMsearch
[2023-03-16 12:14:53,428] [INFO] Running command: hmmsearch --tblout OceanDNA-b32047/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d5bd9ef-5dc5-43c0-a39f-b8c37d2a40e2/dqc_reference/reference_markers.hmm OceanDNA-b32047/protein.faa > /dev/null
[2023-03-16 12:14:53,719] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:14:53,719] [INFO] Found 6/6 markers.
[2023-03-16 12:14:53,766] [INFO] Query marker FASTA was written to OceanDNA-b32047/markers.fasta
[2023-03-16 12:14:53,767] [INFO] Task started: Blastn
[2023-03-16 12:14:53,768] [INFO] Running command: blastn -query OceanDNA-b32047/markers.fasta -db /var/lib/cwl/stg4d5bd9ef-5dc5-43c0-a39f-b8c37d2a40e2/dqc_reference/reference_markers.fasta -out OceanDNA-b32047/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:14:54,737] [INFO] Task succeeded: Blastn
[2023-03-16 12:14:54,738] [INFO] Selected 18 target genomes.
[2023-03-16 12:14:54,738] [INFO] Target genome list was writen to OceanDNA-b32047/target_genomes.txt
[2023-03-16 12:14:54,750] [INFO] Task started: fastANI
[2023-03-16 12:14:54,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb6e4689-2251-42aa-84b5-aa766e4774e4/OceanDNA-b32047.fa --refList OceanDNA-b32047/target_genomes.txt --output OceanDNA-b32047/fastani_result.tsv --threads 1
[2023-03-16 12:15:10,955] [INFO] Task succeeded: fastANI
[2023-03-16 12:15:10,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d5bd9ef-5dc5-43c0-a39f-b8c37d2a40e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:15:10,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d5bd9ef-5dc5-43c0-a39f-b8c37d2a40e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:15:10,968] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:15:10,968] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:15:10,968] [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 limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.4874	917	1679	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	83.4198	939	1679	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	83.3083	834	1679	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	83.0271	935	1679	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	82.7583	880	1679	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.4438	732	1679	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.4068	715	1679	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	82.3974	805	1679	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	82.3963	732	1679	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	82.1974	801	1679	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	81.8974	660	1679	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	81.895	744	1679	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	81.8206	689	1679	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	81.6798	716	1679	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.856	331	1679	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.786	300	1679	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.6207	314	1679	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.3131	295	1679	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:15:10,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32047/tc_result.tsv
[2023-03-16 12:15:10,968] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:15:10,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:15:10,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d5bd9ef-5dc5-43c0-a39f-b8c37d2a40e2/dqc_reference/checkm_data
[2023-03-16 12:15:10,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:15:10,976] [INFO] Task started: CheckM
[2023-03-16 12:15:10,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32047/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32047/checkm_input OceanDNA-b32047/checkm_result
[2023-03-16 12:16:49,135] [INFO] Task succeeded: CheckM
[2023-03-16 12:16:49,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:16:49,138] [INFO] ===== Completeness check finished =====
[2023-03-16 12:16:49,138] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:16:49,138] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32047/markers.fasta)
[2023-03-16 12:16:49,140] [INFO] Task started: Blastn
[2023-03-16 12:16:49,140] [INFO] Running command: blastn -query OceanDNA-b32047/markers.fasta -db /var/lib/cwl/stg4d5bd9ef-5dc5-43c0-a39f-b8c37d2a40e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32047/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:16:50,727] [INFO] Task succeeded: Blastn
[2023-03-16 12:16:50,728] [INFO] Selected 20 target genomes.
[2023-03-16 12:16:50,728] [INFO] Target genome list was writen to OceanDNA-b32047/target_genomes_gtdb.txt
[2023-03-16 12:16:51,205] [INFO] Task started: fastANI
[2023-03-16 12:16:51,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb6e4689-2251-42aa-84b5-aa766e4774e4/OceanDNA-b32047.fa --refList OceanDNA-b32047/target_genomes_gtdb.txt --output OceanDNA-b32047/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:17:11,262] [INFO] Task succeeded: fastANI
[2023-03-16 12:17:11,273] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:17:11,273] [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_900111125.1	s__Sphingobium sp900111125	83.9978	926	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203965.1	s__Sphingobium sp014203965	83.916	873	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109095.1	s__Sphingobium sp900109095	83.882	923	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720145.1	s__Sphingobium sp009720145	83.6628	831	1679	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	83.6174	857	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710155.1	s__Sphingobium limneticum	83.4805	918	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_014197035.1	s__Sphingobium scionense	83.3953	941	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152865.1	s__Sphingobium cupriresistens	83.319	833	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCF_001421665.1	s__Sphingobium sp001421665	83.3052	862	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822485.1	s__Sphingobium sp013822485	83.1249	660	1679	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	83.0202	936	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_001650725.1	s__Sphingobium sp001650725	82.9784	854	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_900013425.1	s__Sphingobium sp900013425	82.8436	858	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.97	0.99	0.99	6	-
GCF_000281715.1	s__Sphingobium sp000281715	82.6909	811	1679	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	82.4625	730	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003591655.1	s__Sphingobium sp003591655	82.4029	804	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508185.1	s__Sphingobium sp000508185	82.3765	809	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008692605.1	s__Sphingobium estronivorans	82.0663	669	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598335.1	s__Sphingobium abikonense	81.9178	742	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	81.8067	690	1679	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-16 12:17:11,274] [INFO] GTDB search result was written to OceanDNA-b32047/result_gtdb.tsv
[2023-03-16 12:17:11,274] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:17:11,276] [INFO] DFAST_QC result json was written to OceanDNA-b32047/dqc_result.json
[2023-03-16 12:17:11,276] [INFO] DFAST_QC completed!
[2023-03-16 12:17:11,276] [INFO] Total running time: 0h3m0s