[2024-01-24 13:32:33,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:33,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:33,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f6591df-4a6b-410c-8b58-c26138880b12/dqc_reference
[2024-01-24 13:32:34,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:34,555] [INFO] Task started: Prodigal
[2024-01-24 13:32:34,556] [INFO] Running command: gunzip -c /var/lib/cwl/stgf27505e6-7173-422e-a4d9-2422271af72b/GCF_000445105.1_ASM44510v1_genomic.fna.gz | prodigal -d GCF_000445105.1_ASM44510v1_genomic.fna/cds.fna -a GCF_000445105.1_ASM44510v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:50,853] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:50,854] [INFO] Task started: HMMsearch
[2024-01-24 13:32:50,854] [INFO] Running command: hmmsearch --tblout GCF_000445105.1_ASM44510v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f6591df-4a6b-410c-8b58-c26138880b12/dqc_reference/reference_markers.hmm GCF_000445105.1_ASM44510v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:51,255] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:51,257] [INFO] Found 6/6 markers.
[2024-01-24 13:32:51,306] [INFO] Query marker FASTA was written to GCF_000445105.1_ASM44510v1_genomic.fna/markers.fasta
[2024-01-24 13:32:51,306] [INFO] Task started: Blastn
[2024-01-24 13:32:51,306] [INFO] Running command: blastn -query GCF_000445105.1_ASM44510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f6591df-4a6b-410c-8b58-c26138880b12/dqc_reference/reference_markers.fasta -out GCF_000445105.1_ASM44510v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:52,214] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:52,219] [INFO] Selected 20 target genomes.
[2024-01-24 13:32:52,219] [INFO] Target genome list was writen to GCF_000445105.1_ASM44510v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:52,227] [INFO] Task started: fastANI
[2024-01-24 13:32:52,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27505e6-7173-422e-a4d9-2422271af72b/GCF_000445105.1_ASM44510v1_genomic.fna.gz --refList GCF_000445105.1_ASM44510v1_genomic.fna/target_genomes.txt --output GCF_000445105.1_ASM44510v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:13,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:13,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f6591df-4a6b-410c-8b58-c26138880b12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:13,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f6591df-4a6b-410c-8b58-c26138880b12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:13,390] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:13,390] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:33:13,391] [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 lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	100.0	1707	1734	95	inconclusive
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	95.3946	978	1734	95	inconclusive
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	83.1987	800	1734	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	83.1429	846	1734	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	83.1397	754	1734	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.0464	836	1734	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	83.0081	723	1734	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	82.6958	699	1734	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	82.5916	741	1734	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	82.4929	695	1734	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	82.3227	824	1734	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	82.2337	722	1734	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	82.0721	617	1734	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	81.9576	668	1734	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	81.9495	671	1734	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2729	366	1734	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.0619	363	1734	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.7602	347	1734	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.6618	344	1734	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.4386	272	1734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:13,392] [INFO] DFAST Taxonomy check result was written to GCF_000445105.1_ASM44510v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:13,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:13,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:13,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f6591df-4a6b-410c-8b58-c26138880b12/dqc_reference/checkm_data
[2024-01-24 13:33:13,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:13,446] [INFO] Task started: CheckM
[2024-01-24 13:33:13,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000445105.1_ASM44510v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000445105.1_ASM44510v1_genomic.fna/checkm_input GCF_000445105.1_ASM44510v1_genomic.fna/checkm_result
[2024-01-24 13:34:01,839] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:01,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:01,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:01,867] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:01,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000445105.1_ASM44510v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:01,867] [INFO] Task started: Blastn
[2024-01-24 13:34:01,867] [INFO] Running command: blastn -query GCF_000445105.1_ASM44510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f6591df-4a6b-410c-8b58-c26138880b12/dqc_reference/reference_markers_gtdb.fasta -out GCF_000445105.1_ASM44510v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:03,256] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:03,259] [INFO] Selected 13 target genomes.
[2024-01-24 13:34:03,260] [INFO] Target genome list was writen to GCF_000445105.1_ASM44510v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:03,293] [INFO] Task started: fastANI
[2024-01-24 13:34:03,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27505e6-7173-422e-a4d9-2422271af72b/GCF_000445105.1_ASM44510v1_genomic.fna.gz --refList GCF_000445105.1_ASM44510v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000445105.1_ASM44510v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:17,069] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:17,087] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:17,087] [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_000445105.1	s__Sphingobium lactosutens	100.0	1706	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	conclusive
GCF_001598335.1	s__Sphingobium abikonense	95.3946	978	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_000153545.1	s__Sphingobium sp000153545	89.9401	978	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.72	97.49	0.82	0.71	9	-
GCA_002457415.1	s__Sphingobium sp002457415	86.2797	779	1734	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	84.1178	877	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_000508185.1	s__Sphingobium sp000508185	83.9599	830	1734	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	83.617	816	1734	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	83.2874	817	1734	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	83.1892	843	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_003967075.1	s__Sphingobium amiense	83.1128	753	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008710155.1	s__Sphingobium limneticum	83.011	840	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_900109095.1	s__Sphingobium sp900109095	82.6612	843	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911745.1	s__Sphingobium sp013911745	82.6063	570	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:17,089] [INFO] GTDB search result was written to GCF_000445105.1_ASM44510v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:17,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:17,094] [INFO] DFAST_QC result json was written to GCF_000445105.1_ASM44510v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:17,094] [INFO] DFAST_QC completed!
[2024-01-24 13:34:17,094] [INFO] Total running time: 0h1m44s