[2024-01-24 14:14:19,502] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:19,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:19,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg99932ef9-5000-4aee-bf0f-a242f5c278a6/dqc_reference
[2024-01-24 14:14:20,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:20,830] [INFO] Task started: Prodigal
[2024-01-24 14:14:20,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg8842ded2-5956-4a39-99b3-9a9f82d6920b/GCF_019737615.1_ASM1973761v1_genomic.fna.gz | prodigal -d GCF_019737615.1_ASM1973761v1_genomic.fna/cds.fna -a GCF_019737615.1_ASM1973761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:32,770] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:32,771] [INFO] Task started: HMMsearch
[2024-01-24 14:14:32,771] [INFO] Running command: hmmsearch --tblout GCF_019737615.1_ASM1973761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99932ef9-5000-4aee-bf0f-a242f5c278a6/dqc_reference/reference_markers.hmm GCF_019737615.1_ASM1973761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:33,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:33,054] [INFO] Found 6/6 markers.
[2024-01-24 14:14:33,098] [INFO] Query marker FASTA was written to GCF_019737615.1_ASM1973761v1_genomic.fna/markers.fasta
[2024-01-24 14:14:33,098] [INFO] Task started: Blastn
[2024-01-24 14:14:33,098] [INFO] Running command: blastn -query GCF_019737615.1_ASM1973761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99932ef9-5000-4aee-bf0f-a242f5c278a6/dqc_reference/reference_markers.fasta -out GCF_019737615.1_ASM1973761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:34,105] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:34,108] [INFO] Selected 28 target genomes.
[2024-01-24 14:14:34,108] [INFO] Target genome list was writen to GCF_019737615.1_ASM1973761v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:34,122] [INFO] Task started: fastANI
[2024-01-24 14:14:34,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg8842ded2-5956-4a39-99b3-9a9f82d6920b/GCF_019737615.1_ASM1973761v1_genomic.fna.gz --refList GCF_019737615.1_ASM1973761v1_genomic.fna/target_genomes.txt --output GCF_019737615.1_ASM1973761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:55,595] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:55,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99932ef9-5000-4aee-bf0f-a242f5c278a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:55,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99932ef9-5000-4aee-bf0f-a242f5c278a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:55,618] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:55,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:55,619] [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 xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	100.0	1340	1340	95	conclusive
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	79.0775	445	1340	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	78.8051	410	1340	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.7827	429	1340	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	78.766	403	1340	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	78.7305	399	1340	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	78.7208	426	1340	95	below_threshold
Sphingobium fluviale	strain=CHR27	GCA_004122115.1	2506423	2506423	type	True	78.6309	303	1340	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	78.5759	367	1340	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	78.5705	375	1340	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	78.55	388	1340	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.4275	359	1340	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	78.3375	320	1340	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.2969	389	1340	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.2749	373	1340	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	78.2551	414	1340	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	78.2423	262	1340	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	78.2137	364	1340	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.1991	302	1340	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	78.1075	312	1340	95	below_threshold
Sphingobium algorifonticola	strain=TLA-22	GCA_004005485.1	2008318	2008318	type	True	78.0623	341	1340	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	78.0129	311	1340	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.9804	314	1340	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.9528	323	1340	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.8995	370	1340	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.8942	339	1340	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.7249	318	1340	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.7097	246	1340	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:55,621] [INFO] DFAST Taxonomy check result was written to GCF_019737615.1_ASM1973761v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:55,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:55,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:55,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99932ef9-5000-4aee-bf0f-a242f5c278a6/dqc_reference/checkm_data
[2024-01-24 14:14:55,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:55,662] [INFO] Task started: CheckM
[2024-01-24 14:14:55,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019737615.1_ASM1973761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019737615.1_ASM1973761v1_genomic.fna/checkm_input GCF_019737615.1_ASM1973761v1_genomic.fna/checkm_result
[2024-01-24 14:15:33,255] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:33,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:33,273] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:33,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:33,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019737615.1_ASM1973761v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:33,274] [INFO] Task started: Blastn
[2024-01-24 14:15:33,274] [INFO] Running command: blastn -query GCF_019737615.1_ASM1973761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99932ef9-5000-4aee-bf0f-a242f5c278a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019737615.1_ASM1973761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:35,176] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:35,179] [INFO] Selected 10 target genomes.
[2024-01-24 14:15:35,179] [INFO] Target genome list was writen to GCF_019737615.1_ASM1973761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:35,192] [INFO] Task started: fastANI
[2024-01-24 14:15:35,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg8842ded2-5956-4a39-99b3-9a9f82d6920b/GCF_019737615.1_ASM1973761v1_genomic.fna.gz --refList GCF_019737615.1_ASM1973761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019737615.1_ASM1973761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:43,493] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:43,502] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:15:43,503] [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_018603885.1	s__Sphingobium sp018603885	82.6468	886	1340	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	82.4125	634	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304655.1	s__Sphingobium sp017304655	81.9587	767	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283515.1	s__Sphingobium sp000283515	81.0199	724	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.32	96.27	0.90	0.89	5	-
GCA_001899715.1	s__Sphingobium sp001899715	80.8718	675	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201265.1	s__Sphingobium sp014201265	80.5819	629	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	3	-
GCA_018823325.1	s__Sphingobium sp018823325	80.5	599	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	0.97	0.94	4	-
GCA_017745115.1	s__Sphingobium sp017745115	79.9577	448	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	78.1934	421	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	77.9012	369	1340	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:43,504] [INFO] GTDB search result was written to GCF_019737615.1_ASM1973761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:43,505] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:43,509] [INFO] DFAST_QC result json was written to GCF_019737615.1_ASM1973761v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:43,509] [INFO] DFAST_QC completed!
[2024-01-24 14:15:43,510] [INFO] Total running time: 0h1m24s