[2024-01-25 20:04:20,671] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:20,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:20,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b5d7fd1-bc81-4ac2-a58d-6b056d891d4d/dqc_reference
[2024-01-25 20:04:21,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:21,837] [INFO] Task started: Prodigal
[2024-01-25 20:04:21,837] [INFO] Running command: gunzip -c /var/lib/cwl/stga18fdda3-3434-436d-ba0c-59956ecdde73/GCF_015475875.1_ASM1547587v1_genomic.fna.gz | prodigal -d GCF_015475875.1_ASM1547587v1_genomic.fna/cds.fna -a GCF_015475875.1_ASM1547587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:30,489] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:30,489] [INFO] Task started: HMMsearch
[2024-01-25 20:04:30,489] [INFO] Running command: hmmsearch --tblout GCF_015475875.1_ASM1547587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b5d7fd1-bc81-4ac2-a58d-6b056d891d4d/dqc_reference/reference_markers.hmm GCF_015475875.1_ASM1547587v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:30,702] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:30,703] [INFO] Found 6/6 markers.
[2024-01-25 20:04:30,731] [INFO] Query marker FASTA was written to GCF_015475875.1_ASM1547587v1_genomic.fna/markers.fasta
[2024-01-25 20:04:30,731] [INFO] Task started: Blastn
[2024-01-25 20:04:30,731] [INFO] Running command: blastn -query GCF_015475875.1_ASM1547587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5d7fd1-bc81-4ac2-a58d-6b056d891d4d/dqc_reference/reference_markers.fasta -out GCF_015475875.1_ASM1547587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:31,620] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:31,622] [INFO] Selected 18 target genomes.
[2024-01-25 20:04:31,623] [INFO] Target genome list was writen to GCF_015475875.1_ASM1547587v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:31,643] [INFO] Task started: fastANI
[2024-01-25 20:04:31,643] [INFO] Running command: fastANI --query /var/lib/cwl/stga18fdda3-3434-436d-ba0c-59956ecdde73/GCF_015475875.1_ASM1547587v1_genomic.fna.gz --refList GCF_015475875.1_ASM1547587v1_genomic.fna/target_genomes.txt --output GCF_015475875.1_ASM1547587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:46,827] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:46,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b5d7fd1-bc81-4ac2-a58d-6b056d891d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:46,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b5d7fd1-bc81-4ac2-a58d-6b056d891d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:46,838] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:46,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:46,839] [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 solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	100.0	1094	1098	95	conclusive
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	86.9255	821	1098	95	below_threshold
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	86.27	853	1098	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	86.175	862	1098	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	84.7255	763	1098	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	84.4376	818	1098	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	84.3179	827	1098	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.1694	803	1098	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	83.8837	712	1098	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	83.3287	740	1098	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	83.0943	730	1098	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.041	731	1098	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	82.7825	756	1098	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.3716	343	1098	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.0884	355	1098	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.9767	324	1098	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	77.8981	337	1098	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.8644	337	1098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:46,840] [INFO] DFAST Taxonomy check result was written to GCF_015475875.1_ASM1547587v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:46,840] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:46,840] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:46,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b5d7fd1-bc81-4ac2-a58d-6b056d891d4d/dqc_reference/checkm_data
[2024-01-25 20:04:46,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:46,878] [INFO] Task started: CheckM
[2024-01-25 20:04:46,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015475875.1_ASM1547587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015475875.1_ASM1547587v1_genomic.fna/checkm_input GCF_015475875.1_ASM1547587v1_genomic.fna/checkm_result
[2024-01-25 20:05:14,650] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:14,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:14,680] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:14,680] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:14,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015475875.1_ASM1547587v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:14,681] [INFO] Task started: Blastn
[2024-01-25 20:05:14,681] [INFO] Running command: blastn -query GCF_015475875.1_ASM1547587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5d7fd1-bc81-4ac2-a58d-6b056d891d4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_015475875.1_ASM1547587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:16,431] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:16,434] [INFO] Selected 20 target genomes.
[2024-01-25 20:05:16,434] [INFO] Target genome list was writen to GCF_015475875.1_ASM1547587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:16,448] [INFO] Task started: fastANI
[2024-01-25 20:05:16,449] [INFO] Running command: fastANI --query /var/lib/cwl/stga18fdda3-3434-436d-ba0c-59956ecdde73/GCF_015475875.1_ASM1547587v1_genomic.fna.gz --refList GCF_015475875.1_ASM1547587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015475875.1_ASM1547587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:34,787] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:34,799] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:34,800] [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_015475875.1	s__Sphingopyxis solisilvae	100.0	1094	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	conclusive
GCF_012274265.1	s__Sphingopyxis microcysteis	86.9338	821	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.26	96.26	0.86	0.86	2	-
GCF_005503695.1	s__Sphingopyxis sp003609815	86.8216	819	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.15	97.15	0.90	0.90	2	-
GCA_002454115.1	s__Sphingopyxis sp002454115	86.6455	811	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCA_018823905.1	s__Sphingopyxis sp018823905	86.634	770	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.80	99.78	0.95	0.94	3	-
GCF_002205675.1	s__Sphingopyxis bauzanensis	86.2945	851	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_005502465.1	s__Sphingopyxis sp005502465	86.2786	828	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463225.1	s__Sphingopyxis sp016463225	86.0534	784	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704835.1	s__Sphingopyxis sp016704835	85.3834	790	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609835.1	s__Sphingopyxis sp003609835	84.9181	800	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756375.1	s__Sphingopyxis sp000756375	84.8402	817	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	84.7704	797	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013985.1	s__Sphingopyxis alaskensis	84.7419	762	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503215.1	s__Sphingopyxis sp005503215	84.7289	833	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCF_014595975.1	s__Sphingopyxis sp014595975	84.482	739	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756385.1	s__Sphingopyxis sp000756385	84.4666	814	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821905.1	s__Sphingopyxis sp013821905	84.4498	629	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000803645.1	s__Sphingopyxis fribergensis	84.339	825	1098	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	83.938	787	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	83.7811	716	1098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:34,801] [INFO] GTDB search result was written to GCF_015475875.1_ASM1547587v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:34,801] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:34,805] [INFO] DFAST_QC result json was written to GCF_015475875.1_ASM1547587v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:34,805] [INFO] DFAST_QC completed!
[2024-01-25 20:05:34,805] [INFO] Total running time: 0h1m14s