[2023-03-17 03:11:36,344] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,344] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,344] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9654b07-47d8-42d9-a879-b7179cdb2533/dqc_reference
[2023-03-17 03:11:37,578] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,578] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,578] [INFO] Running command: cat /var/lib/cwl/stga1085f2a-0b22-4636-a4d3-a521c0a5d198/OceanDNA-b32144.fa | prodigal -d OceanDNA-b32144/cds.fna -a OceanDNA-b32144/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:11:58,475] [INFO] Task succeeded: Prodigal
[2023-03-17 03:11:58,475] [INFO] Task started: HMMsearch
[2023-03-17 03:11:58,475] [INFO] Running command: hmmsearch --tblout OceanDNA-b32144/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9654b07-47d8-42d9-a879-b7179cdb2533/dqc_reference/reference_markers.hmm OceanDNA-b32144/protein.faa > /dev/null
[2023-03-17 03:11:58,752] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:11:58,752] [INFO] Found 6/6 markers.
[2023-03-17 03:11:58,779] [INFO] Query marker FASTA was written to OceanDNA-b32144/markers.fasta
[2023-03-17 03:11:58,780] [INFO] Task started: Blastn
[2023-03-17 03:11:58,780] [INFO] Running command: blastn -query OceanDNA-b32144/markers.fasta -db /var/lib/cwl/stgf9654b07-47d8-42d9-a879-b7179cdb2533/dqc_reference/reference_markers.fasta -out OceanDNA-b32144/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:11:59,503] [INFO] Task succeeded: Blastn
[2023-03-17 03:11:59,504] [INFO] Selected 26 target genomes.
[2023-03-17 03:11:59,504] [INFO] Target genome list was writen to OceanDNA-b32144/target_genomes.txt
[2023-03-17 03:11:59,560] [INFO] Task started: fastANI
[2023-03-17 03:11:59,561] [INFO] Running command: fastANI --query /var/lib/cwl/stga1085f2a-0b22-4636-a4d3-a521c0a5d198/OceanDNA-b32144.fa --refList OceanDNA-b32144/target_genomes.txt --output OceanDNA-b32144/fastani_result.tsv --threads 1
[2023-03-17 03:12:19,633] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:19,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9654b07-47d8-42d9-a879-b7179cdb2533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:12:19,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9654b07-47d8-42d9-a879-b7179cdb2533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:12:19,648] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:12:19,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:12:19,648] [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
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	91.4219	913	1072	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	83.7479	747	1072	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.0751	501	1072	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.0028	491	1072	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	78.9382	519	1072	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	78.9233	548	1072	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	78.905	383	1072	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	78.8725	473	1072	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	78.8509	483	1072	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	78.8201	455	1072	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	78.7729	463	1072	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	78.7665	502	1072	95	below_threshold
Stakelama pacifica	strain=CGMCC 1.7294	GCA_014645395.1	517720	517720	type	True	78.7496	432	1072	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	78.6052	437	1072	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	78.5099	472	1072	95	below_threshold
Sphingomonas parapaucimobilis	strain=NBRC 15100	GCA_000787715.1	28213	28213	type	True	78.248	327	1072	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	78.2156	482	1072	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.167	388	1072	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.1428	424	1072	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.1328	416	1072	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.0006	380	1072	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.9779	335	1072	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	77.9634	336	1072	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.329	304	1072	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	76.9555	203	1072	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	76.8495	194	1072	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:12:19,648] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32144/tc_result.tsv
[2023-03-17 03:12:19,649] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:12:19,649] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:12:19,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9654b07-47d8-42d9-a879-b7179cdb2533/dqc_reference/checkm_data
[2023-03-17 03:12:19,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:12:19,826] [INFO] Task started: CheckM
[2023-03-17 03:12:19,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32144/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32144/checkm_input OceanDNA-b32144/checkm_result
[2023-03-17 03:13:09,745] [INFO] Task succeeded: CheckM
[2023-03-17 03:13:09,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.34%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:13:09,748] [INFO] ===== Completeness check finished =====
[2023-03-17 03:13:09,749] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:13:09,749] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32144/markers.fasta)
[2023-03-17 03:13:09,750] [INFO] Task started: Blastn
[2023-03-17 03:13:09,750] [INFO] Running command: blastn -query OceanDNA-b32144/markers.fasta -db /var/lib/cwl/stgf9654b07-47d8-42d9-a879-b7179cdb2533/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32144/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:13:10,876] [INFO] Task succeeded: Blastn
[2023-03-17 03:13:10,877] [INFO] Selected 17 target genomes.
[2023-03-17 03:13:10,877] [INFO] Target genome list was writen to OceanDNA-b32144/target_genomes_gtdb.txt
[2023-03-17 03:13:11,064] [INFO] Task started: fastANI
[2023-03-17 03:13:11,064] [INFO] Running command: fastANI --query /var/lib/cwl/stga1085f2a-0b22-4636-a4d3-a521c0a5d198/OceanDNA-b32144.fa --refList OceanDNA-b32144/target_genomes_gtdb.txt --output OceanDNA-b32144/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:13:23,831] [INFO] Task succeeded: fastANI
[2023-03-17 03:13:23,841] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:13:23,841] [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_002707985.1	s__Sphingomonas sp002707985	99.7555	999	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003171655.1	s__Sphingomonas portus	91.4033	914	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	83.723	749	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	79.4877	537	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826325.1	s__Sphingomonas sp902826325	79.1621	364	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.74	97.74	0.84	0.84	2	-
GCF_007833215.1	s__Sphingomonas sp007833215	78.9979	491	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	78.9285	505	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	78.9212	521	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002127225.1	s__Sphingomonas sp002127225	78.7771	506	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	78.7415	470	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	78.7304	480	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	78.6818	426	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_900114095.1	s__Sphingomonas sp900114095	78.677	471	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	78.6696	478	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	78.4358	414	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	78.2331	477	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281485.1	s__Sphingomonas sp002281485	78.2309	345	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:13:23,841] [INFO] GTDB search result was written to OceanDNA-b32144/result_gtdb.tsv
[2023-03-17 03:13:23,842] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:13:23,844] [INFO] DFAST_QC result json was written to OceanDNA-b32144/dqc_result.json
[2023-03-17 03:13:23,844] [INFO] DFAST_QC completed!
[2023-03-17 03:13:23,844] [INFO] Total running time: 0h1m48s