[2024-01-24 15:10:40,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg221e61fb-638f-4a46-beb5-f41aad48cc24/dqc_reference
[2024-01-24 15:10:41,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:41,928] [INFO] Task started: Prodigal
[2024-01-24 15:10:41,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg423a4fe9-d6e7-4635-8a48-3e0b29192fe0/GCF_014237875.1_ASM1423787v1_genomic.fna.gz | prodigal -d GCF_014237875.1_ASM1423787v1_genomic.fna/cds.fna -a GCF_014237875.1_ASM1423787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:51,860] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:51,861] [INFO] Task started: HMMsearch
[2024-01-24 15:10:51,861] [INFO] Running command: hmmsearch --tblout GCF_014237875.1_ASM1423787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg221e61fb-638f-4a46-beb5-f41aad48cc24/dqc_reference/reference_markers.hmm GCF_014237875.1_ASM1423787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:52,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:52,146] [INFO] Found 6/6 markers.
[2024-01-24 15:10:52,174] [INFO] Query marker FASTA was written to GCF_014237875.1_ASM1423787v1_genomic.fna/markers.fasta
[2024-01-24 15:10:52,175] [INFO] Task started: Blastn
[2024-01-24 15:10:52,175] [INFO] Running command: blastn -query GCF_014237875.1_ASM1423787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg221e61fb-638f-4a46-beb5-f41aad48cc24/dqc_reference/reference_markers.fasta -out GCF_014237875.1_ASM1423787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:53,190] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:53,193] [INFO] Selected 25 target genomes.
[2024-01-24 15:10:53,193] [INFO] Target genome list was writen to GCF_014237875.1_ASM1423787v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:53,222] [INFO] Task started: fastANI
[2024-01-24 15:10:53,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg423a4fe9-d6e7-4635-8a48-3e0b29192fe0/GCF_014237875.1_ASM1423787v1_genomic.fna.gz --refList GCF_014237875.1_ASM1423787v1_genomic.fna/target_genomes.txt --output GCF_014237875.1_ASM1423787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:12,069] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:12,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg221e61fb-638f-4a46-beb5-f41aad48cc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:12,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg221e61fb-638f-4a46-beb5-f41aad48cc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:12,089] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:12,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:12,089] [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
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	100.0	1099	1099	95	conclusive
Parasphingopyxis algicola	strain=JCM 31719	GCA_013378075.1	2026624	2026624	type	True	80.9826	646	1099	95	below_threshold
Parasphingopyxis lamellibrachiae	strain=DSM 26725	GCA_003385775.1	680125	680125	type	True	79.178	547	1099	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.2044	328	1099	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2001	332	1099	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.0882	366	1099	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.0858	328	1099	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.0271	338	1099	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.0026	327	1099	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.8623	343	1099	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.84	308	1099	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.8303	309	1099	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	77.7401	260	1099	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.7164	309	1099	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.7017	310	1099	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	77.6914	322	1099	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.621	334	1099	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	77.5677	274	1099	95	below_threshold
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	77.5545	281	1099	95	below_threshold
Sphingomonas psychrolutea	strain=CGMCC 1.10106	GCA_014636175.1	1259676	1259676	type	True	77.5318	258	1099	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	77.4264	247	1099	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.3873	216	1099	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	77.3478	272	1099	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	77.1926	264	1099	95	below_threshold
Camelimonas lactis	strain=DSM 22958	GCA_004342915.1	659006	659006	type	True	75.3876	74	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:12,091] [INFO] DFAST Taxonomy check result was written to GCF_014237875.1_ASM1423787v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:12,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:12,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:12,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg221e61fb-638f-4a46-beb5-f41aad48cc24/dqc_reference/checkm_data
[2024-01-24 15:11:12,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:12,131] [INFO] Task started: CheckM
[2024-01-24 15:11:12,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014237875.1_ASM1423787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014237875.1_ASM1423787v1_genomic.fna/checkm_input GCF_014237875.1_ASM1423787v1_genomic.fna/checkm_result
[2024-01-24 15:11:45,066] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:45,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:45,087] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:45,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:45,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014237875.1_ASM1423787v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:45,088] [INFO] Task started: Blastn
[2024-01-24 15:11:45,088] [INFO] Running command: blastn -query GCF_014237875.1_ASM1423787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg221e61fb-638f-4a46-beb5-f41aad48cc24/dqc_reference/reference_markers_gtdb.fasta -out GCF_014237875.1_ASM1423787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:46,901] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:46,905] [INFO] Selected 15 target genomes.
[2024-01-24 15:11:46,905] [INFO] Target genome list was writen to GCF_014237875.1_ASM1423787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:46,917] [INFO] Task started: fastANI
[2024-01-24 15:11:46,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg423a4fe9-d6e7-4635-8a48-3e0b29192fe0/GCF_014237875.1_ASM1423787v1_genomic.fna.gz --refList GCF_014237875.1_ASM1423787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014237875.1_ASM1423787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:57,969] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:57,994] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:57,995] [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_014237875.1	s__Parasphingopyxis sp014237875	100.0	1099	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013378075.1	s__Parasphingopyxis algicola	81.0058	643	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001755.1	s__Parasphingopyxis sp013001755	79.8286	427	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385775.1	s__Parasphingopyxis lamellibrachiae	79.1648	548	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479515.1	s__Parasphingopyxis sp905479515	79.0518	295	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378055.1	s__Parasphingopyxis sp013378055	78.3269	409	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.0834	312	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	77.9921	385	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_001429065.1	s__Rhizorhabdus sp001429065	77.8021	329	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	77.7933	314	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	77.6688	313	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241465.1	s__Sphingomonas echinoides	77.5545	281	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.65	96.65	0.85	0.85	2	-
GCF_001650725.1	s__Sphingobium sp001650725	77.4816	290	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_002813245.1	s__Novosphingobium kunmingense	77.3873	216	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111125.1	s__Sphingobium sp900111125	77.3769	272	1099	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:57,997] [INFO] GTDB search result was written to GCF_014237875.1_ASM1423787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:57,997] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:58,006] [INFO] DFAST_QC result json was written to GCF_014237875.1_ASM1423787v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:58,006] [INFO] DFAST_QC completed!
[2024-01-24 15:11:58,006] [INFO] Total running time: 0h1m17s