[2023-06-17 01:07:32,603] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:07:32,605] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:07:32,605] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c067ed4-e1e0-46a1-a04a-8cf7fd3f8a03/dqc_reference
[2023-06-17 01:07:33,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:07:33,838] [INFO] Task started: Prodigal
[2023-06-17 01:07:33,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a9cda86-b5d0-48ba-a905-457a30654abb/GCA_003241685.1_ASM324168v1_genomic.fna.gz | prodigal -d GCA_003241685.1_ASM324168v1_genomic.fna/cds.fna -a GCA_003241685.1_ASM324168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:07:43,132] [INFO] Task succeeded: Prodigal
[2023-06-17 01:07:43,132] [INFO] Task started: HMMsearch
[2023-06-17 01:07:43,132] [INFO] Running command: hmmsearch --tblout GCA_003241685.1_ASM324168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c067ed4-e1e0-46a1-a04a-8cf7fd3f8a03/dqc_reference/reference_markers.hmm GCA_003241685.1_ASM324168v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:07:43,336] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:07:43,337] [INFO] Found 6/6 markers.
[2023-06-17 01:07:43,368] [INFO] Query marker FASTA was written to GCA_003241685.1_ASM324168v1_genomic.fna/markers.fasta
[2023-06-17 01:07:43,368] [INFO] Task started: Blastn
[2023-06-17 01:07:43,369] [INFO] Running command: blastn -query GCA_003241685.1_ASM324168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c067ed4-e1e0-46a1-a04a-8cf7fd3f8a03/dqc_reference/reference_markers.fasta -out GCA_003241685.1_ASM324168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:07:44,209] [INFO] Task succeeded: Blastn
[2023-06-17 01:07:44,213] [INFO] Selected 18 target genomes.
[2023-06-17 01:07:44,213] [INFO] Target genome list was writen to GCA_003241685.1_ASM324168v1_genomic.fna/target_genomes.txt
[2023-06-17 01:07:44,218] [INFO] Task started: fastANI
[2023-06-17 01:07:44,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9cda86-b5d0-48ba-a905-457a30654abb/GCA_003241685.1_ASM324168v1_genomic.fna.gz --refList GCA_003241685.1_ASM324168v1_genomic.fna/target_genomes.txt --output GCA_003241685.1_ASM324168v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:07:58,505] [INFO] Task succeeded: fastANI
[2023-06-17 01:07:58,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c067ed4-e1e0-46a1-a04a-8cf7fd3f8a03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:07:58,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c067ed4-e1e0-46a1-a04a-8cf7fd3f8a03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:07:58,520] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:07:58,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:07:58,520] [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
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.3498	729	1107	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.3456	797	1107	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	84.2924	753	1107	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	84.2725	746	1107	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	84.258	791	1107	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	84.2266	734	1107	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	84.1258	705	1107	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	84.0989	755	1107	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	84.0695	744	1107	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	84.0602	743	1107	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	83.8677	753	1107	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	83.8061	750	1107	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	83.6975	717	1107	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.4993	389	1107	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.3686	358	1107	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.9681	367	1107	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	77.5858	235	1107	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.4864	365	1107	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:07:58,522] [INFO] DFAST Taxonomy check result was written to GCA_003241685.1_ASM324168v1_genomic.fna/tc_result.tsv
[2023-06-17 01:07:58,523] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:07:58,523] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:07:58,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c067ed4-e1e0-46a1-a04a-8cf7fd3f8a03/dqc_reference/checkm_data
[2023-06-17 01:07:58,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:07:58,561] [INFO] Task started: CheckM
[2023-06-17 01:07:58,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003241685.1_ASM324168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003241685.1_ASM324168v1_genomic.fna/checkm_input GCA_003241685.1_ASM324168v1_genomic.fna/checkm_result
[2023-06-17 01:08:29,201] [INFO] Task succeeded: CheckM
[2023-06-17 01:08:29,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:08:29,219] [INFO] ===== Completeness check finished =====
[2023-06-17 01:08:29,219] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:08:29,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003241685.1_ASM324168v1_genomic.fna/markers.fasta)
[2023-06-17 01:08:29,220] [INFO] Task started: Blastn
[2023-06-17 01:08:29,220] [INFO] Running command: blastn -query GCA_003241685.1_ASM324168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c067ed4-e1e0-46a1-a04a-8cf7fd3f8a03/dqc_reference/reference_markers_gtdb.fasta -out GCA_003241685.1_ASM324168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:08:30,585] [INFO] Task succeeded: Blastn
[2023-06-17 01:08:30,590] [INFO] Selected 18 target genomes.
[2023-06-17 01:08:30,590] [INFO] Target genome list was writen to GCA_003241685.1_ASM324168v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:08:30,602] [INFO] Task started: fastANI
[2023-06-17 01:08:30,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9cda86-b5d0-48ba-a905-457a30654abb/GCA_003241685.1_ASM324168v1_genomic.fna.gz --refList GCA_003241685.1_ASM324168v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003241685.1_ASM324168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:08:46,948] [INFO] Task succeeded: fastANI
[2023-06-17 01:08:46,962] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:08:46,963] [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_003241685.1	s__Sphingopyxis macrogoltabida_A	100.0	1100	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013821905.1	s__Sphingopyxis sp013821905	84.6256	628	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018682675.1	s__Sphingopyxis soli	84.3637	727	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	84.3332	798	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002277025.1	s__Sphingopyxis sp002277025	84.29	770	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993885.1	s__Sphingopyxis lindanitolerans	84.2719	755	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598815.1	s__Sphingopyxis terrae	84.2663	746	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.70	95.58	0.84	0.76	19	-
GCF_001468395.1	s__Sphingopyxis sp001468395	84.2296	743	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCF_004795895.1	s__Sphingopyxis sp004795895	84.2125	809	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307295.1	s__Sphingopyxis macrogoltabida_B	84.1609	788	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591045.1	s__Sphingopyxis granuli	84.1331	704	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.56	96.77	0.81	0.78	6	-
GCA_002842935.1	s__Sphingopyxis sp002842935	84.0307	475	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	84.0169	774	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCA_017309275.1	s__Sphingopyxis sp017309275	83.9789	764	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984035.1	s__Sphingopyxis sp001984035	83.8605	780	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793775.1	s__Sphingopyxis sp016793775	83.8513	728	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199295.1	s__Sphingopyxis panaciterrulae	83.8088	750	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797775.2	s__Sphingopyxis sp001427085	83.7404	786	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.11	97.01	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-17 01:08:46,964] [INFO] GTDB search result was written to GCA_003241685.1_ASM324168v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:08:46,965] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:08:46,969] [INFO] DFAST_QC result json was written to GCA_003241685.1_ASM324168v1_genomic.fna/dqc_result.json
[2023-06-17 01:08:46,969] [INFO] DFAST_QC completed!
[2023-06-17 01:08:46,969] [INFO] Total running time: 0h1m14s