[2024-01-24 14:54:56,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ff12713-4160-4e39-bc5a-06dd089d4756/dqc_reference
[2024-01-24 14:54:57,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,794] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg145a86c7-f1d1-484c-ad57-70e60a4c4a74/GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/cds.fna -a GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:07,650] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:07,651] [INFO] Task started: HMMsearch
[2024-01-24 14:55:07,651] [INFO] Running command: hmmsearch --tblout GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ff12713-4160-4e39-bc5a-06dd089d4756/dqc_reference/reference_markers.hmm GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:07,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:07,965] [INFO] Found 6/6 markers.
[2024-01-24 14:55:07,999] [INFO] Query marker FASTA was written to GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:55:07,999] [INFO] Task started: Blastn
[2024-01-24 14:55:07,999] [INFO] Running command: blastn -query GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ff12713-4160-4e39-bc5a-06dd089d4756/dqc_reference/reference_markers.fasta -out GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:09,038] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:09,042] [INFO] Selected 12 target genomes.
[2024-01-24 14:55:09,042] [INFO] Target genome list was writen to GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:55:09,048] [INFO] Task started: fastANI
[2024-01-24 14:55:09,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg145a86c7-f1d1-484c-ad57-70e60a4c4a74/GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna.gz --refList GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:19,955] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:19,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ff12713-4160-4e39-bc5a-06dd089d4756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:19,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ff12713-4160-4e39-bc5a-06dd089d4756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:19,971] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:19,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:19,971] [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 palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	100.0	1085	1086	95	conclusive
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	87.1417	850	1086	95	below_threshold
Sphingomonas hominis	strain=HHU CXW	GCA_013328205.1	2741495	2741495	type	True	86.7209	836	1086	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	81.4872	693	1086	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	81.3376	662	1086	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	81.3347	643	1086	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	81.3337	678	1086	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	81.3326	688	1086	95	below_threshold
Sphingomonas ginsenosidimutans	strain=KACC 14949	GCA_002374835.1	862134	862134	type	True	81.3087	650	1086	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	80.9667	620	1086	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	79.9539	557	1086	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	79.8399	563	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:19,976] [INFO] DFAST Taxonomy check result was written to GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:55:19,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:19,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:19,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ff12713-4160-4e39-bc5a-06dd089d4756/dqc_reference/checkm_data
[2024-01-24 14:55:19,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:20,025] [INFO] Task started: CheckM
[2024-01-24 14:55:20,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/checkm_input GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:55:51,865] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:51,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:51,889] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:51,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:51,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:55:51,891] [INFO] Task started: Blastn
[2024-01-24 14:55:51,891] [INFO] Running command: blastn -query GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ff12713-4160-4e39-bc5a-06dd089d4756/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:53,917] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:53,921] [INFO] Selected 12 target genomes.
[2024-01-24 14:55:53,921] [INFO] Target genome list was writen to GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:53,936] [INFO] Task started: fastANI
[2024-01-24 14:55:53,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg145a86c7-f1d1-484c-ad57-70e60a4c4a74/GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna.gz --refList GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:04,569] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:04,583] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:04,584] [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_900109565.1	s__Sphingomonas palmae	100.0	1085	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000382485.1	s__Sphingomonas sp000382485	88.7685	869	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328205.1	s__Sphingomonas hominis	86.734	836	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	81.7301	688	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	81.4574	682	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	81.3603	684	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_014199415.1	s__Sphingomonas endophytica	81.3517	641	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_012035195.1	s__Sphingomonas sp012035195	81.3471	661	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	81.2844	653	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_902506455.1	s__Sphingomonas sp902506455	80.9766	609	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010450875.1	s__Sphingomonas insulae	79.9836	554	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016820445.1	s__Sphingomonas sp016820445	79.8737	562	1086	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:04,585] [INFO] GTDB search result was written to GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:04,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:04,589] [INFO] DFAST_QC result json was written to GCF_900109565.1_IMG-taxon_2657245271_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:56:04,590] [INFO] DFAST_QC completed!
[2024-01-24 14:56:04,590] [INFO] Total running time: 0h1m8s