[2024-01-24 13:46:02,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:02,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:02,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d9669a5-c8aa-49f1-b644-a5a0001f10ab/dqc_reference
[2024-01-24 13:46:03,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,485] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c6e0ac1-50cd-455d-893b-4b5ddcc9f731/GCF_021403115.1_ASM2140311v1_genomic.fna.gz | prodigal -d GCF_021403115.1_ASM2140311v1_genomic.fna/cds.fna -a GCF_021403115.1_ASM2140311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:17,134] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:17,134] [INFO] Task started: HMMsearch
[2024-01-24 13:46:17,134] [INFO] Running command: hmmsearch --tblout GCF_021403115.1_ASM2140311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d9669a5-c8aa-49f1-b644-a5a0001f10ab/dqc_reference/reference_markers.hmm GCF_021403115.1_ASM2140311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:17,445] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:17,447] [INFO] Found 6/6 markers.
[2024-01-24 13:46:17,488] [INFO] Query marker FASTA was written to GCF_021403115.1_ASM2140311v1_genomic.fna/markers.fasta
[2024-01-24 13:46:17,488] [INFO] Task started: Blastn
[2024-01-24 13:46:17,488] [INFO] Running command: blastn -query GCF_021403115.1_ASM2140311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d9669a5-c8aa-49f1-b644-a5a0001f10ab/dqc_reference/reference_markers.fasta -out GCF_021403115.1_ASM2140311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:18,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:18,382] [INFO] Selected 26 target genomes.
[2024-01-24 13:46:18,382] [INFO] Target genome list was writen to GCF_021403115.1_ASM2140311v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:18,398] [INFO] Task started: fastANI
[2024-01-24 13:46:18,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6e0ac1-50cd-455d-893b-4b5ddcc9f731/GCF_021403115.1_ASM2140311v1_genomic.fna.gz --refList GCF_021403115.1_ASM2140311v1_genomic.fna/target_genomes.txt --output GCF_021403115.1_ASM2140311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:39,088] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:39,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d9669a5-c8aa-49f1-b644-a5a0001f10ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:39,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d9669a5-c8aa-49f1-b644-a5a0001f10ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:39,108] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:39,108] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:39,108] [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
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	100.0	1456	1458	95	conclusive
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	79.5333	441	1458	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	79.4788	487	1458	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	79.3326	481	1458	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	79.3192	473	1458	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	79.3127	480	1458	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	79.288	426	1458	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	79.1798	519	1458	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	79.1595	502	1458	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	79.145	485	1458	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	79.1418	465	1458	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	79.0385	446	1458	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	79.0093	447	1458	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_000632125.2	76947	76947	type	True	78.7314	365	1458	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_001598535.1	76947	76947	type	True	78.6498	380	1458	95	below_threshold
Sphingobium herbicidovorans	strain=MH	GCA_002080435.1	76947	76947	type	True	78.5668	385	1458	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	78.5514	390	1458	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.9542	308	1458	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	77.8684	319	1458	95	below_threshold
Sphingomonas turrisvirgatae	strain=MCT13	GCA_001721295.1	1888892	1888892	type	True	77.8275	312	1458	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.8194	321	1458	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.7249	414	1458	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	77.5807	328	1458	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.3964	198	1458	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	77.3217	301	1458	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.1453	241	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:39,109] [INFO] DFAST Taxonomy check result was written to GCF_021403115.1_ASM2140311v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:39,110] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:39,110] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:39,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d9669a5-c8aa-49f1-b644-a5a0001f10ab/dqc_reference/checkm_data
[2024-01-24 13:46:39,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:39,155] [INFO] Task started: CheckM
[2024-01-24 13:46:39,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021403115.1_ASM2140311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021403115.1_ASM2140311v1_genomic.fna/checkm_input GCF_021403115.1_ASM2140311v1_genomic.fna/checkm_result
[2024-01-24 13:47:21,758] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:21,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:21,777] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:21,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:21,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021403115.1_ASM2140311v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:21,778] [INFO] Task started: Blastn
[2024-01-24 13:47:21,779] [INFO] Running command: blastn -query GCF_021403115.1_ASM2140311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d9669a5-c8aa-49f1-b644-a5a0001f10ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_021403115.1_ASM2140311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:23,502] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:23,509] [INFO] Selected 28 target genomes.
[2024-01-24 13:47:23,509] [INFO] Target genome list was writen to GCF_021403115.1_ASM2140311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:23,560] [INFO] Task started: fastANI
[2024-01-24 13:47:23,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6e0ac1-50cd-455d-893b-4b5ddcc9f731/GCF_021403115.1_ASM2140311v1_genomic.fna.gz --refList GCF_021403115.1_ASM2140311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021403115.1_ASM2140311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:45,235] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:45,257] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:45,257] [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_014196635.1	s__Sphingobium fontiphilum	79.5353	440	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000264945.2	s__Sphingobium indicum	79.4871	487	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	-
GCF_012927105.1	s__Sphingobium psychrophilum	79.3323	481	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967075.1	s__Sphingobium amiense	79.3124	480	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001650725.1	s__Sphingobium sp001650725	79.312	506	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	79.3104	424	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
GCF_014203965.1	s__Sphingobium sp014203965	79.2647	504	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013375535.1	s__Sphingobium sp013375535	79.2534	485	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355855.1	s__Sphingobium cloacae	79.2384	473	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014197035.1	s__Sphingobium scionense	79.179	520	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	79.1692	482	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCA_002457415.1	s__Sphingobium sp002457415	79.1611	439	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822485.1	s__Sphingobium sp013822485	79.1025	375	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447205.1	s__Sphingobium ummariense	79.0442	446	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445065.1	s__Sphingobium quisquiliarum	79.0049	444	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	97.93	0.83	0.83	3	-
GCF_008692605.1	s__Sphingobium estronivorans	78.9887	449	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248935.1	s__Sphingobium sp003248935	78.7665	406	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899715.1	s__Sphingobium sp001899715	78.6145	414	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122115.1	s__Sphingobium fluviale	78.5041	306	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005485.1	s__Sphingobium algorifonticola	78.4895	376	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304105.1	s__Sphingobium sp017304105	78.4574	355	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603885.1	s__Sphingobium sp018603885	78.2954	420	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744605.1	s__Sphingobium sp017744605	77.9897	299	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721295.1	s__Sphingomonas turrisvirgatae	77.8165	313	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	77.8091	322	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005145025.1	s__Novosphingobium sp005145025	77.7527	315	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	77.719	415	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	77.0156	227	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:45,259] [INFO] GTDB search result was written to GCF_021403115.1_ASM2140311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:45,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:45,265] [INFO] DFAST_QC result json was written to GCF_021403115.1_ASM2140311v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:45,265] [INFO] DFAST_QC completed!
[2024-01-24 13:47:45,265] [INFO] Total running time: 0h1m43s