[2024-01-24 11:05:25,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ba17068-2d86-498f-93aa-220b381fe0aa/dqc_reference
[2024-01-24 11:05:26,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,815] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f0cb436-9770-4b47-b98c-73365ab29d4b/GCF_014199685.1_ASM1419968v1_genomic.fna.gz | prodigal -d GCF_014199685.1_ASM1419968v1_genomic.fna/cds.fna -a GCF_014199685.1_ASM1419968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:37,259] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:37,259] [INFO] Task started: HMMsearch
[2024-01-24 11:05:37,259] [INFO] Running command: hmmsearch --tblout GCF_014199685.1_ASM1419968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ba17068-2d86-498f-93aa-220b381fe0aa/dqc_reference/reference_markers.hmm GCF_014199685.1_ASM1419968v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:37,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:37,562] [INFO] Found 6/6 markers.
[2024-01-24 11:05:37,595] [INFO] Query marker FASTA was written to GCF_014199685.1_ASM1419968v1_genomic.fna/markers.fasta
[2024-01-24 11:05:37,596] [INFO] Task started: Blastn
[2024-01-24 11:05:37,596] [INFO] Running command: blastn -query GCF_014199685.1_ASM1419968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba17068-2d86-498f-93aa-220b381fe0aa/dqc_reference/reference_markers.fasta -out GCF_014199685.1_ASM1419968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:38,551] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:38,554] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:38,554] [INFO] Target genome list was writen to GCF_014199685.1_ASM1419968v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:38,566] [INFO] Task started: fastANI
[2024-01-24 11:05:38,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f0cb436-9770-4b47-b98c-73365ab29d4b/GCF_014199685.1_ASM1419968v1_genomic.fna.gz --refList GCF_014199685.1_ASM1419968v1_genomic.fna/target_genomes.txt --output GCF_014199685.1_ASM1419968v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:55,368] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:55,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ba17068-2d86-498f-93aa-220b381fe0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:55,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ba17068-2d86-498f-93aa-220b381fe0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:55,391] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:55,392] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:55,392] [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
Sphingosinicella soli	strain=DSM 17328	GCA_014199685.1	333708	333708	type	True	100.0	1207	1210	95	conclusive
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	86.0314	825	1210	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.0056	288	1210	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	77.8377	185	1210	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.7545	260	1210	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.7225	259	1210	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	77.7024	306	1210	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	77.6606	256	1210	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	77.6208	298	1210	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.5928	268	1210	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	77.5668	211	1210	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.5612	337	1210	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	77.4793	182	1210	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	77.4522	225	1210	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.3981	289	1210	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.3893	317	1210	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.3377	238	1210	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	77.315	278	1210	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	77.2955	163	1210	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	77.2807	265	1210	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	77.253	268	1210	95	below_threshold
Croceicoccus gelatinilyticus	strain=1NDH52	GCA_018398395.1	2835536	2835536	type	True	77.1625	175	1210	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	77.026	275	1210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:55,395] [INFO] DFAST Taxonomy check result was written to GCF_014199685.1_ASM1419968v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:55,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:55,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:55,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ba17068-2d86-498f-93aa-220b381fe0aa/dqc_reference/checkm_data
[2024-01-24 11:05:55,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:55,437] [INFO] Task started: CheckM
[2024-01-24 11:05:55,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199685.1_ASM1419968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199685.1_ASM1419968v1_genomic.fna/checkm_input GCF_014199685.1_ASM1419968v1_genomic.fna/checkm_result
[2024-01-24 11:06:29,625] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:29,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:29,647] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:29,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:29,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199685.1_ASM1419968v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:29,648] [INFO] Task started: Blastn
[2024-01-24 11:06:29,648] [INFO] Running command: blastn -query GCF_014199685.1_ASM1419968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ba17068-2d86-498f-93aa-220b381fe0aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199685.1_ASM1419968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:31,438] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:31,442] [INFO] Selected 12 target genomes.
[2024-01-24 11:06:31,442] [INFO] Target genome list was writen to GCF_014199685.1_ASM1419968v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:31,453] [INFO] Task started: fastANI
[2024-01-24 11:06:31,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f0cb436-9770-4b47-b98c-73365ab29d4b/GCF_014199685.1_ASM1419968v1_genomic.fna.gz --refList GCF_014199685.1_ASM1419968v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199685.1_ASM1419968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:40,581] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:40,596] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:40,596] [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_014199685.1	s__Sphingosinicella soli	100.0	1207	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013911755.1	s__Sphingosinicella sp013911755	87.075	814	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793845.1	s__Sphingosinicella sp016793845	86.7773	631	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634215.1	s__Sphingosinicella microcystinivorans	86.0091	827	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004681125.1	s__Polymorphobacter_A arshaanensis	78.0505	259	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550065.1	s__Sphingomonas caeni	77.9852	299	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	77.7351	256	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	77.6495	351	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	77.6219	264	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139225.1	s__Sphingomonas sp018139225	77.5599	238	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017304615.1	s__Sphingomonas sp017304615	77.4011	226	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591045.1	s__Sphingopyxis granuli	77.3501	289	1210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.56	96.77	0.81	0.78	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:40,599] [INFO] GTDB search result was written to GCF_014199685.1_ASM1419968v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:40,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:40,605] [INFO] DFAST_QC result json was written to GCF_014199685.1_ASM1419968v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:40,606] [INFO] DFAST_QC completed!
[2024-01-24 11:06:40,606] [INFO] Total running time: 0h1m15s