[2024-01-24 13:42:57,376] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,378] [INFO] DQC Reference Directory: /var/lib/cwl/stga05ce9af-1746-43b1-9538-2e1d857eb7d5/dqc_reference
[2024-01-24 13:42:58,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,642] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgd59599a7-3bb1-4865-9efe-36cc6e6a1aac/GCF_024496245.1_ASM2449624v1_genomic.fna.gz | prodigal -d GCF_024496245.1_ASM2449624v1_genomic.fna/cds.fna -a GCF_024496245.1_ASM2449624v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:08,953] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:08,953] [INFO] Task started: HMMsearch
[2024-01-24 13:43:08,954] [INFO] Running command: hmmsearch --tblout GCF_024496245.1_ASM2449624v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga05ce9af-1746-43b1-9538-2e1d857eb7d5/dqc_reference/reference_markers.hmm GCF_024496245.1_ASM2449624v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:09,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:09,221] [INFO] Found 6/6 markers.
[2024-01-24 13:43:09,252] [INFO] Query marker FASTA was written to GCF_024496245.1_ASM2449624v1_genomic.fna/markers.fasta
[2024-01-24 13:43:09,253] [INFO] Task started: Blastn
[2024-01-24 13:43:09,253] [INFO] Running command: blastn -query GCF_024496245.1_ASM2449624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga05ce9af-1746-43b1-9538-2e1d857eb7d5/dqc_reference/reference_markers.fasta -out GCF_024496245.1_ASM2449624v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:10,211] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:10,215] [INFO] Selected 22 target genomes.
[2024-01-24 13:43:10,216] [INFO] Target genome list was writen to GCF_024496245.1_ASM2449624v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:10,225] [INFO] Task started: fastANI
[2024-01-24 13:43:10,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgd59599a7-3bb1-4865-9efe-36cc6e6a1aac/GCF_024496245.1_ASM2449624v1_genomic.fna.gz --refList GCF_024496245.1_ASM2449624v1_genomic.fna/target_genomes.txt --output GCF_024496245.1_ASM2449624v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:29,092] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:29,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga05ce9af-1746-43b1-9538-2e1d857eb7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:29,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga05ce9af-1746-43b1-9538-2e1d857eb7d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:29,109] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:43:29,109] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:43:29,109] [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 baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	81.7971	631	1143	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	81.0849	604	1143	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	80.7359	630	1143	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	80.6605	639	1143	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	80.323	622	1143	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.9659	595	1143	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	79.9468	546	1143	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	79.931	576	1143	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	79.7975	565	1143	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.7334	556	1143	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.6794	560	1143	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.5626	545	1143	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	79.5562	530	1143	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.5519	540	1143	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	79.5363	585	1143	95	below_threshold
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	79.4866	513	1143	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.3575	539	1143	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.235	506	1143	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.17	568	1143	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	79.0949	525	1143	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	78.018	274	1143	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.5852	362	1143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:29,111] [INFO] DFAST Taxonomy check result was written to GCF_024496245.1_ASM2449624v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:29,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:29,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:29,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga05ce9af-1746-43b1-9538-2e1d857eb7d5/dqc_reference/checkm_data
[2024-01-24 13:43:29,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:29,158] [INFO] Task started: CheckM
[2024-01-24 13:43:29,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024496245.1_ASM2449624v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024496245.1_ASM2449624v1_genomic.fna/checkm_input GCF_024496245.1_ASM2449624v1_genomic.fna/checkm_result
[2024-01-24 13:44:02,610] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:02,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:02,628] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:02,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:02,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024496245.1_ASM2449624v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:02,629] [INFO] Task started: Blastn
[2024-01-24 13:44:02,629] [INFO] Running command: blastn -query GCF_024496245.1_ASM2449624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga05ce9af-1746-43b1-9538-2e1d857eb7d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024496245.1_ASM2449624v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:04,303] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:04,307] [INFO] Selected 19 target genomes.
[2024-01-24 13:44:04,308] [INFO] Target genome list was writen to GCF_024496245.1_ASM2449624v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:04,392] [INFO] Task started: fastANI
[2024-01-24 13:44:04,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgd59599a7-3bb1-4865-9efe-36cc6e6a1aac/GCF_024496245.1_ASM2449624v1_genomic.fna.gz --refList GCF_024496245.1_ASM2449624v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024496245.1_ASM2449624v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:20,549] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:20,570] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:44:20,570] [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_000786205.1	s__Sphingomonas sp000786205	88.3206	762	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144715.1	s__Sphingomonas sp005144715	81.8169	629	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346325.1	s__Sphingomonas japonica	81.1624	605	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014199325.1	s__Sphingomonas yantingensis	80.7315	632	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	-
GCF_002351485.1	s__Sphingomonas spermidinifaciens	80.6743	638	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	80.2768	627	1143	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	80.2355	560	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_006439055.1	s__Sphingomonas glacialis_A	80.1638	611	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425385.1	s__Sphingomonas sp001425385	80.1141	549	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.44	96.89	0.96	0.93	3	-
GCF_003946805.1	s__Sphingomonas sp003946805	79.9955	562	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	79.9111	596	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_014653575.1	s__Sphingomonas glacialis	79.9038	578	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_003050705.1	s__Sphingomonas aurantiaca	79.8049	568	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.29	95.02	0.87	0.86	4	-
GCA_006438735.1	s__Sphingomonas koreensis_A	79.7191	538	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.05	96.05	0.80	0.80	2	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	79.5723	580	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281485.1	s__Sphingomonas sp002281485	79.5435	443	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241465.1	s__Sphingomonas echinoides	79.4204	521	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.65	96.65	0.85	0.85	2	-
GCF_001990265.1	s__Sphingopyxis sp001990265	78.6527	415	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	78.0033	275	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:20,572] [INFO] GTDB search result was written to GCF_024496245.1_ASM2449624v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:20,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:20,577] [INFO] DFAST_QC result json was written to GCF_024496245.1_ASM2449624v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:20,577] [INFO] DFAST_QC completed!
[2024-01-24 13:44:20,577] [INFO] Total running time: 0h1m23s