[2024-01-24 12:44:19,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:19,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:19,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd5a8d3c-f51a-4079-b2eb-43a09ec986ee/dqc_reference
[2024-01-24 12:44:20,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:20,773] [INFO] Task started: Prodigal
[2024-01-24 12:44:20,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg5baf4c66-7461-4f68-88ab-d593e9ba4b18/GCF_019429535.1_ASM1942953v1_genomic.fna.gz | prodigal -d GCF_019429535.1_ASM1942953v1_genomic.fna/cds.fna -a GCF_019429535.1_ASM1942953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:30,625] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:30,625] [INFO] Task started: HMMsearch
[2024-01-24 12:44:30,625] [INFO] Running command: hmmsearch --tblout GCF_019429535.1_ASM1942953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd5a8d3c-f51a-4079-b2eb-43a09ec986ee/dqc_reference/reference_markers.hmm GCF_019429535.1_ASM1942953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:30,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:30,871] [INFO] Found 6/6 markers.
[2024-01-24 12:44:30,903] [INFO] Query marker FASTA was written to GCF_019429535.1_ASM1942953v1_genomic.fna/markers.fasta
[2024-01-24 12:44:30,904] [INFO] Task started: Blastn
[2024-01-24 12:44:30,904] [INFO] Running command: blastn -query GCF_019429535.1_ASM1942953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd5a8d3c-f51a-4079-b2eb-43a09ec986ee/dqc_reference/reference_markers.fasta -out GCF_019429535.1_ASM1942953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:31,805] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:31,809] [INFO] Selected 14 target genomes.
[2024-01-24 12:44:31,809] [INFO] Target genome list was writen to GCF_019429535.1_ASM1942953v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:31,849] [INFO] Task started: fastANI
[2024-01-24 12:44:31,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg5baf4c66-7461-4f68-88ab-d593e9ba4b18/GCF_019429535.1_ASM1942953v1_genomic.fna.gz --refList GCF_019429535.1_ASM1942953v1_genomic.fna/target_genomes.txt --output GCF_019429535.1_ASM1942953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:42,326] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:42,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd5a8d3c-f51a-4079-b2eb-43a09ec986ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:42,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd5a8d3c-f51a-4079-b2eb-43a09ec986ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:42,341] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:42,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:42,342] [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 citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	100.0	1162	1163	95	conclusive
Sphingomonas hominis	strain=HHU CXW	GCA_013328205.1	2741495	2741495	type	True	87.4281	846	1163	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	87.0209	865	1163	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	81.6782	649	1163	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	81.6734	575	1163	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	81.5795	703	1163	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	81.5161	695	1163	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	81.4554	674	1163	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	81.4252	678	1163	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	78.7934	495	1163	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	75.5949	107	1163	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004343305.1	634155	634155	type	True	75.5139	72	1163	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004798975.1	634155	634155	type	True	75.5134	70	1163	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_003732435.1	634155	634155	type	True	75.4141	68	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:42,343] [INFO] DFAST Taxonomy check result was written to GCF_019429535.1_ASM1942953v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:42,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:42,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:42,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd5a8d3c-f51a-4079-b2eb-43a09ec986ee/dqc_reference/checkm_data
[2024-01-24 12:44:42,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:42,384] [INFO] Task started: CheckM
[2024-01-24 12:44:42,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019429535.1_ASM1942953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019429535.1_ASM1942953v1_genomic.fna/checkm_input GCF_019429535.1_ASM1942953v1_genomic.fna/checkm_result
[2024-01-24 12:45:14,619] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:14,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:14,648] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:14,649] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:14,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019429535.1_ASM1942953v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:14,649] [INFO] Task started: Blastn
[2024-01-24 12:45:14,650] [INFO] Running command: blastn -query GCF_019429535.1_ASM1942953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd5a8d3c-f51a-4079-b2eb-43a09ec986ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_019429535.1_ASM1942953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:16,139] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:16,144] [INFO] Selected 16 target genomes.
[2024-01-24 12:45:16,144] [INFO] Target genome list was writen to GCF_019429535.1_ASM1942953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:16,195] [INFO] Task started: fastANI
[2024-01-24 12:45:16,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg5baf4c66-7461-4f68-88ab-d593e9ba4b18/GCF_019429535.1_ASM1942953v1_genomic.fna.gz --refList GCF_019429535.1_ASM1942953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019429535.1_ASM1942953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:29,986] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:30,003] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:45:30,003] [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_013328205.1	s__Sphingomonas hominis	87.4281	846	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109565.1	s__Sphingomonas palmae	87.0063	866	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382485.1	s__Sphingomonas sp000382485	86.3324	841	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199415.1	s__Sphingomonas endophytica	81.6835	648	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.00	98.00	0.92	0.92	2	-
GCF_004345855.1	s__Sphingomonas sp004345855	81.5855	695	1163	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	81.5495	710	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	81.4653	673	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243195.1	s__Sphingomonas taxi_B	81.2635	607	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476895.1	s__Sphingomonas endophytica_A	81.2431	609	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506455.1	s__Sphingomonas sp902506455	81.2167	616	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820445.1	s__Sphingomonas sp016820445	80.1506	588	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
GCF_003050705.1	s__Sphingomonas aurantiaca	79.8961	618	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.29	95.02	0.87	0.86	4	-
GCF_001421415.1	s__Sphingomonas sp001421415	79.6565	555	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	78.9672	445	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_016743815.1	s__Sphingomonas sp016743815	78.7703	468	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	77.8623	388	1163	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:30,005] [INFO] GTDB search result was written to GCF_019429535.1_ASM1942953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:30,005] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:30,013] [INFO] DFAST_QC result json was written to GCF_019429535.1_ASM1942953v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:30,013] [INFO] DFAST_QC completed!
[2024-01-24 12:45:30,013] [INFO] Total running time: 0h1m10s