[2024-01-25 18:47:05,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:05,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:05,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg80e73d32-fd57-4273-a2c4-40a758440a43/dqc_reference
[2024-01-25 18:47:06,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:06,691] [INFO] Task started: Prodigal
[2024-01-25 18:47:06,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgb476fe3f-bf0d-494e-b9c6-8be54e246116/GCF_016025255.1_ASM1602525v1_genomic.fna.gz | prodigal -d GCF_016025255.1_ASM1602525v1_genomic.fna/cds.fna -a GCF_016025255.1_ASM1602525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:13,064] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:13,065] [INFO] Task started: HMMsearch
[2024-01-25 18:47:13,065] [INFO] Running command: hmmsearch --tblout GCF_016025255.1_ASM1602525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80e73d32-fd57-4273-a2c4-40a758440a43/dqc_reference/reference_markers.hmm GCF_016025255.1_ASM1602525v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:13,276] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:13,277] [INFO] Found 6/6 markers.
[2024-01-25 18:47:13,300] [INFO] Query marker FASTA was written to GCF_016025255.1_ASM1602525v1_genomic.fna/markers.fasta
[2024-01-25 18:47:13,300] [INFO] Task started: Blastn
[2024-01-25 18:47:13,300] [INFO] Running command: blastn -query GCF_016025255.1_ASM1602525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e73d32-fd57-4273-a2c4-40a758440a43/dqc_reference/reference_markers.fasta -out GCF_016025255.1_ASM1602525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:14,132] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:14,135] [INFO] Selected 26 target genomes.
[2024-01-25 18:47:14,135] [INFO] Target genome list was writen to GCF_016025255.1_ASM1602525v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:14,161] [INFO] Task started: fastANI
[2024-01-25 18:47:14,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgb476fe3f-bf0d-494e-b9c6-8be54e246116/GCF_016025255.1_ASM1602525v1_genomic.fna.gz --refList GCF_016025255.1_ASM1602525v1_genomic.fna/target_genomes.txt --output GCF_016025255.1_ASM1602525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:31,325] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:31,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80e73d32-fd57-4273-a2c4-40a758440a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:31,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80e73d32-fd57-4273-a2c4-40a758440a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:31,340] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:47:31,340] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:47:31,341] [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
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	79.5287	430	807	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	79.2537	387	807	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	79.1706	411	807	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.9852	347	807	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	78.9269	375	807	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	78.6964	293	807	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	78.5245	294	807	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.5031	289	807	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.4961	298	807	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	78.455	265	807	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	78.3938	316	807	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.3604	247	807	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.3162	298	807	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.2458	261	807	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.2039	220	807	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.1729	310	807	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.0739	274	807	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.0673	277	807	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	78.0238	275	807	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.0173	265	807	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.8234	262	807	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.8173	270	807	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	77.6202	187	807	95	below_threshold
Erythrobacter neustonensis	strain=DSM 9434	GCA_001663175.1	1112	1112	type	True	77.4938	166	807	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	77.1892	167	807	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	77.1462	168	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:31,344] [INFO] DFAST Taxonomy check result was written to GCF_016025255.1_ASM1602525v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:31,344] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:31,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:31,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80e73d32-fd57-4273-a2c4-40a758440a43/dqc_reference/checkm_data
[2024-01-25 18:47:31,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:31,373] [INFO] Task started: CheckM
[2024-01-25 18:47:31,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016025255.1_ASM1602525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016025255.1_ASM1602525v1_genomic.fna/checkm_input GCF_016025255.1_ASM1602525v1_genomic.fna/checkm_result
[2024-01-25 18:47:55,114] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:55,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:55,133] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:55,133] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:55,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016025255.1_ASM1602525v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:55,133] [INFO] Task started: Blastn
[2024-01-25 18:47:55,133] [INFO] Running command: blastn -query GCF_016025255.1_ASM1602525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80e73d32-fd57-4273-a2c4-40a758440a43/dqc_reference/reference_markers_gtdb.fasta -out GCF_016025255.1_ASM1602525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:56,729] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:56,732] [INFO] Selected 15 target genomes.
[2024-01-25 18:47:56,732] [INFO] Target genome list was writen to GCF_016025255.1_ASM1602525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:56,746] [INFO] Task started: fastANI
[2024-01-25 18:47:56,746] [INFO] Running command: fastANI --query /var/lib/cwl/stgb476fe3f-bf0d-494e-b9c6-8be54e246116/GCF_016025255.1_ASM1602525v1_genomic.fna.gz --refList GCF_016025255.1_ASM1602525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016025255.1_ASM1602525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:07,124] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:07,133] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:07,134] [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_016025255.1	s__Allosphingosinicella sp016025255	100.0	807	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003012815.1	s__Allosphingosinicella vermicomposti	83.1292	574	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	79.5466	428	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	79.3486	414	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	79.2794	385	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	78.9259	373	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCF_003012735.1	s__Allosphingosinicella deserti	78.9152	376	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135585.1	s__Allosphingosinicella sp004135585	78.7834	387	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	78.6931	371	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005865.1	s__Rhizorhabdus crocodyli	78.6058	284	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883305.1	s__Allosphingosinicella sp005883305	78.6011	353	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151485.1	s__Allosphingosinicella sp004151485	78.5667	324	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	78.4703	264	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456115.1	s__Sphingobium baderi_A	78.2656	219	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934325.1	s__Erythrobacter sp903934325	77.5388	179	807	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:07,136] [INFO] GTDB search result was written to GCF_016025255.1_ASM1602525v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:07,137] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:07,140] [INFO] DFAST_QC result json was written to GCF_016025255.1_ASM1602525v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:07,140] [INFO] DFAST_QC completed!
[2024-01-25 18:48:07,140] [INFO] Total running time: 0h1m2s