[2023-03-15 04:45:50,560] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,562] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgccbe919e-e9f1-4c0e-9396-47a81b26a11e/dqc_reference
[2023-03-15 04:45:51,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,675] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,675] [INFO] Running command: cat /var/lib/cwl/stg2c287738-9557-47af-a7ae-560810f24cc3/OceanDNA-b32052.fa | prodigal -d OceanDNA-b32052/cds.fna -a OceanDNA-b32052/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:46:08,822] [INFO] Task succeeded: Prodigal
[2023-03-15 04:46:08,822] [INFO] Task started: HMMsearch
[2023-03-15 04:46:08,822] [INFO] Running command: hmmsearch --tblout OceanDNA-b32052/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccbe919e-e9f1-4c0e-9396-47a81b26a11e/dqc_reference/reference_markers.hmm OceanDNA-b32052/protein.faa > /dev/null
[2023-03-15 04:46:09,018] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:46:09,019] [INFO] Found 6/6 markers.
[2023-03-15 04:46:09,054] [INFO] Query marker FASTA was written to OceanDNA-b32052/markers.fasta
[2023-03-15 04:46:09,055] [INFO] Task started: Blastn
[2023-03-15 04:46:09,055] [INFO] Running command: blastn -query OceanDNA-b32052/markers.fasta -db /var/lib/cwl/stgccbe919e-e9f1-4c0e-9396-47a81b26a11e/dqc_reference/reference_markers.fasta -out OceanDNA-b32052/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:09,803] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:09,811] [INFO] Selected 24 target genomes.
[2023-03-15 04:46:09,811] [INFO] Target genome list was writen to OceanDNA-b32052/target_genomes.txt
[2023-03-15 04:46:09,826] [INFO] Task started: fastANI
[2023-03-15 04:46:09,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c287738-9557-47af-a7ae-560810f24cc3/OceanDNA-b32052.fa --refList OceanDNA-b32052/target_genomes.txt --output OceanDNA-b32052/fastani_result.tsv --threads 1
[2023-03-15 04:46:28,864] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:28,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccbe919e-e9f1-4c0e-9396-47a81b26a11e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:28,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccbe919e-e9f1-4c0e-9396-47a81b26a11e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:28,878] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:28,878] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:46:28,878] [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 fluviale	strain=CHR27	GCA_004122115.1	2506423	2506423	type	True	87.5415	642	902	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	80.0294	434	902	95	below_threshold
Sphingobium subterraneum	strain=DSM 102255	GCA_014199435.1	627688	627688	type	True	79.247	338	902	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	78.7474	327	902	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	78.6822	312	902	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	78.6478	314	902	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	78.643	289	902	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	78.5711	289	902	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	78.5204	308	902	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	78.3716	279	902	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	78.3084	317	902	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.3003	284	902	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	78.2819	286	902	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	78.2071	287	902	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	78.1985	283	902	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.1747	310	902	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	78.082	284	902	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.8054	237	902	95	below_threshold
Sphingobium bisphenolivorans	strain=YL23	GCA_000412635.1	1335760	1335760	type	True	77.8044	260	902	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.6409	219	902	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.5339	234	902	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.414	196	902	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.0702	190	902	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.932	185	902	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:46:28,879] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32052/tc_result.tsv
[2023-03-15 04:46:28,884] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:28,884] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:28,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccbe919e-e9f1-4c0e-9396-47a81b26a11e/dqc_reference/checkm_data
[2023-03-15 04:46:28,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:28,890] [INFO] Task started: CheckM
[2023-03-15 04:46:28,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32052/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32052/checkm_input OceanDNA-b32052/checkm_result
[2023-03-15 04:47:13,484] [INFO] Task succeeded: CheckM
[2023-03-15 04:47:13,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:47:13,555] [INFO] ===== Completeness check finished =====
[2023-03-15 04:47:13,555] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:47:13,555] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32052/markers.fasta)
[2023-03-15 04:47:13,556] [INFO] Task started: Blastn
[2023-03-15 04:47:13,556] [INFO] Running command: blastn -query OceanDNA-b32052/markers.fasta -db /var/lib/cwl/stgccbe919e-e9f1-4c0e-9396-47a81b26a11e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32052/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:47:14,985] [INFO] Task succeeded: Blastn
[2023-03-15 04:47:14,994] [INFO] Selected 20 target genomes.
[2023-03-15 04:47:14,994] [INFO] Target genome list was writen to OceanDNA-b32052/target_genomes_gtdb.txt
[2023-03-15 04:47:15,041] [INFO] Task started: fastANI
[2023-03-15 04:47:15,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c287738-9557-47af-a7ae-560810f24cc3/OceanDNA-b32052.fa --refList OceanDNA-b32052/target_genomes_gtdb.txt --output OceanDNA-b32052/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:47:29,615] [INFO] Task succeeded: fastANI
[2023-03-15 04:47:29,626] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:47:29,627] [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_004122115.1	s__Sphingobium fluviale	87.5552	641	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984895.1	s__Sphingobium sp017984895	83.1802	481	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.97	99.94	0.94	0.89	4	-
GCF_014196495.1	s__Sphingobium jiangsuense	80.0295	434	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199435.1	s__Sphingobium subterraneum	79.2535	337	902	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	78.76	346	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.90	99.90	0.86	0.86	2	-
GCA_000264945.2	s__Sphingobium indicum	78.7474	327	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_002355855.1	s__Sphingobium cloacae	78.6831	310	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001005725.1	s__Sphingobium chungbukense	78.6289	290	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_014196635.1	s__Sphingobium fontiphilum	78.6002	287	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	78.4854	309	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367345.1	s__Sphingobium xenophagum	78.3788	295	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.29	96.67	0.79	0.71	22	-
GCF_900013425.1	s__Sphingobium sp900013425	78.3498	283	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.97	0.99	0.99	6	-
GCF_009720145.1	s__Sphingobium sp009720145	78.3015	321	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152845.1	s__Sphingobium fuliginis	78.2683	287	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_000315525.1	s__Sphingobium yanoikuyae	78.1749	310	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCA_002457415.1	s__Sphingobium sp002457415	78.1523	277	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716975.1	s__Sphingomonas trueperi_A	77.6738	213	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.23	95.23	0.88	0.88	2	-
GCF_012650175.1	s__Sphingomonas sp012650175	77.4167	229	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953135.1	s__Sphingobium sp002953135	77.3691	224	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	77.2479	230	902	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:47:29,633] [INFO] GTDB search result was written to OceanDNA-b32052/result_gtdb.tsv
[2023-03-15 04:47:29,638] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:47:29,645] [INFO] DFAST_QC result json was written to OceanDNA-b32052/dqc_result.json
[2023-03-15 04:47:29,645] [INFO] DFAST_QC completed!
[2023-03-15 04:47:29,645] [INFO] Total running time: 0h1m39s