[2024-01-24 15:32:04,451] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:32:04,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:32:04,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg8544a411-4cb5-498f-b40f-858ff6f1a452/dqc_reference
[2024-01-24 15:32:05,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:32:05,676] [INFO] Task started: Prodigal
[2024-01-24 15:32:05,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg89436673-774e-4390-8392-40d8e3ef005f/GCF_017052355.1_ASM1705235v1_genomic.fna.gz | prodigal -d GCF_017052355.1_ASM1705235v1_genomic.fna/cds.fna -a GCF_017052355.1_ASM1705235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:32:16,932] [INFO] Task succeeded: Prodigal
[2024-01-24 15:32:16,932] [INFO] Task started: HMMsearch
[2024-01-24 15:32:16,932] [INFO] Running command: hmmsearch --tblout GCF_017052355.1_ASM1705235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8544a411-4cb5-498f-b40f-858ff6f1a452/dqc_reference/reference_markers.hmm GCF_017052355.1_ASM1705235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:32:17,183] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:32:17,185] [INFO] Found 6/6 markers.
[2024-01-24 15:32:17,221] [INFO] Query marker FASTA was written to GCF_017052355.1_ASM1705235v1_genomic.fna/markers.fasta
[2024-01-24 15:32:17,221] [INFO] Task started: Blastn
[2024-01-24 15:32:17,221] [INFO] Running command: blastn -query GCF_017052355.1_ASM1705235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8544a411-4cb5-498f-b40f-858ff6f1a452/dqc_reference/reference_markers.fasta -out GCF_017052355.1_ASM1705235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:32:18,250] [INFO] Task succeeded: Blastn
[2024-01-24 15:32:18,254] [INFO] Selected 14 target genomes.
[2024-01-24 15:32:18,254] [INFO] Target genome list was writen to GCF_017052355.1_ASM1705235v1_genomic.fna/target_genomes.txt
[2024-01-24 15:32:18,263] [INFO] Task started: fastANI
[2024-01-24 15:32:18,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg89436673-774e-4390-8392-40d8e3ef005f/GCF_017052355.1_ASM1705235v1_genomic.fna.gz --refList GCF_017052355.1_ASM1705235v1_genomic.fna/target_genomes.txt --output GCF_017052355.1_ASM1705235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:32:32,929] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:32,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8544a411-4cb5-498f-b40f-858ff6f1a452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:32:32,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8544a411-4cb5-498f-b40f-858ff6f1a452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:32:32,941] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:32:32,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:32:32,942] [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
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_017052355.1	413712	413712	type	True	100.0	1270	1273	95	conclusive
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	99.9895	1255	1273	95	conclusive
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	89.1537	982	1273	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	89.1529	1040	1273	95	below_threshold
Sphingomonas parapaucimobilis	strain=NBRC 15100	GCA_000787715.1	28213	28213	type	True	88.3772	898	1273	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	88.2371	948	1273	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	88.1783	959	1273	95	below_threshold
Sphingomonas sanguinis	strain=NBRC 13937	GCA_001591005.1	33051	33051	suspected-type	True	87.6375	905	1273	95	below_threshold
Sphingomonas zeae	strain=DSM 100049	GCA_014197135.1	1646122	1646122	type	True	87.5734	918	1273	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	80.1571	605	1273	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.014	642	1273	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.8661	608	1273	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.6092	552	1273	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.5443	586	1273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:32:32,944] [INFO] DFAST Taxonomy check result was written to GCF_017052355.1_ASM1705235v1_genomic.fna/tc_result.tsv
[2024-01-24 15:32:32,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:32:32,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:32:32,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8544a411-4cb5-498f-b40f-858ff6f1a452/dqc_reference/checkm_data
[2024-01-24 15:32:32,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:32:32,990] [INFO] Task started: CheckM
[2024-01-24 15:32:32,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017052355.1_ASM1705235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017052355.1_ASM1705235v1_genomic.fna/checkm_input GCF_017052355.1_ASM1705235v1_genomic.fna/checkm_result
[2024-01-24 15:33:08,700] [INFO] Task succeeded: CheckM
[2024-01-24 15:33:08,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:33:08,723] [INFO] ===== Completeness check finished =====
[2024-01-24 15:33:08,724] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:33:08,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017052355.1_ASM1705235v1_genomic.fna/markers.fasta)
[2024-01-24 15:33:08,725] [INFO] Task started: Blastn
[2024-01-24 15:33:08,725] [INFO] Running command: blastn -query GCF_017052355.1_ASM1705235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8544a411-4cb5-498f-b40f-858ff6f1a452/dqc_reference/reference_markers_gtdb.fasta -out GCF_017052355.1_ASM1705235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:33:10,768] [INFO] Task succeeded: Blastn
[2024-01-24 15:33:10,772] [INFO] Selected 9 target genomes.
[2024-01-24 15:33:10,773] [INFO] Target genome list was writen to GCF_017052355.1_ASM1705235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:33:10,800] [INFO] Task started: fastANI
[2024-01-24 15:33:10,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg89436673-774e-4390-8392-40d8e3ef005f/GCF_017052355.1_ASM1705235v1_genomic.fna.gz --refList GCF_017052355.1_ASM1705235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017052355.1_ASM1705235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:33:22,252] [INFO] Task succeeded: fastANI
[2024-01-24 15:33:22,264] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:33:22,264] [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_014196255.1	s__Sphingomonas pseudosanguinis	99.9895	1255	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000739895.2	s__Sphingomonas paucimobilis	89.158	981	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
GCF_000787715.1	s__Sphingomonas parapaucimobilis	88.397	896	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.90	97.90	0.87	0.87	2	-
GCF_014199595.1	s__Sphingomonas yabuuchiae	88.2033	951	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	88.1179	843	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	88.0525	872	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	87.6491	880	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_001591005.1	s__Sphingomonas sanguinis	87.6391	904	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.09	96.84	0.89	0.83	8	-
GCF_014197135.1	s__Sphingomonas zeae	87.5589	919	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:33:22,266] [INFO] GTDB search result was written to GCF_017052355.1_ASM1705235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:33:22,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:33:22,270] [INFO] DFAST_QC result json was written to GCF_017052355.1_ASM1705235v1_genomic.fna/dqc_result.json
[2024-01-24 15:33:22,270] [INFO] DFAST_QC completed!
[2024-01-24 15:33:22,270] [INFO] Total running time: 0h1m18s