[2024-01-24 13:19:13,094] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:13,096] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:13,096] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2287cda-03b9-4538-ab76-883051c03a36/dqc_reference
[2024-01-24 13:19:14,327] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,328] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,328] [INFO] Running command: gunzip -c /var/lib/cwl/stgba2b5405-33f1-4435-ae29-80b4c5f41bc0/GCF_013607875.1_ASM1360787v1_genomic.fna.gz | prodigal -d GCF_013607875.1_ASM1360787v1_genomic.fna/cds.fna -a GCF_013607875.1_ASM1360787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:26,133] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:26,134] [INFO] Task started: HMMsearch
[2024-01-24 13:19:26,134] [INFO] Running command: hmmsearch --tblout GCF_013607875.1_ASM1360787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2287cda-03b9-4538-ab76-883051c03a36/dqc_reference/reference_markers.hmm GCF_013607875.1_ASM1360787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:26,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:26,419] [INFO] Found 6/6 markers.
[2024-01-24 13:19:26,465] [INFO] Query marker FASTA was written to GCF_013607875.1_ASM1360787v1_genomic.fna/markers.fasta
[2024-01-24 13:19:26,465] [INFO] Task started: Blastn
[2024-01-24 13:19:26,466] [INFO] Running command: blastn -query GCF_013607875.1_ASM1360787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2287cda-03b9-4538-ab76-883051c03a36/dqc_reference/reference_markers.fasta -out GCF_013607875.1_ASM1360787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:27,508] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:27,512] [INFO] Selected 25 target genomes.
[2024-01-24 13:19:27,513] [INFO] Target genome list was writen to GCF_013607875.1_ASM1360787v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:27,524] [INFO] Task started: fastANI
[2024-01-24 13:19:27,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgba2b5405-33f1-4435-ae29-80b4c5f41bc0/GCF_013607875.1_ASM1360787v1_genomic.fna.gz --refList GCF_013607875.1_ASM1360787v1_genomic.fna/target_genomes.txt --output GCF_013607875.1_ASM1360787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:45,595] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:45,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2287cda-03b9-4538-ab76-883051c03a36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:45,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2287cda-03b9-4538-ab76-883051c03a36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:45,621] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:45,622] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:45,622] [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
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	84.7357	899	1263	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	83.2939	849	1263	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.8613	419	1263	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	78.788	423	1263	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.6462	460	1263	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	78.5365	426	1263	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.5181	442	1263	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.4915	345	1263	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	78.3695	349	1263	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.3374	378	1263	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.3218	406	1263	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	78.2587	406	1263	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.25	388	1263	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	78.2293	363	1263	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.1932	320	1263	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	78.1684	349	1263	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.0407	324	1263	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	77.9103	362	1263	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	77.8899	356	1263	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	77.8899	358	1263	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.889	355	1263	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.862	321	1263	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	77.8433	326	1263	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.7145	334	1263	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	77.5807	281	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:45,624] [INFO] DFAST Taxonomy check result was written to GCF_013607875.1_ASM1360787v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:45,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:45,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:45,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2287cda-03b9-4538-ab76-883051c03a36/dqc_reference/checkm_data
[2024-01-24 13:19:45,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:45,667] [INFO] Task started: CheckM
[2024-01-24 13:19:45,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013607875.1_ASM1360787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013607875.1_ASM1360787v1_genomic.fna/checkm_input GCF_013607875.1_ASM1360787v1_genomic.fna/checkm_result
[2024-01-24 13:20:23,331] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:23,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:23,354] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:23,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:23,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013607875.1_ASM1360787v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:23,355] [INFO] Task started: Blastn
[2024-01-24 13:20:23,355] [INFO] Running command: blastn -query GCF_013607875.1_ASM1360787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2287cda-03b9-4538-ab76-883051c03a36/dqc_reference/reference_markers_gtdb.fasta -out GCF_013607875.1_ASM1360787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:25,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:25,286] [INFO] Selected 9 target genomes.
[2024-01-24 13:20:25,286] [INFO] Target genome list was writen to GCF_013607875.1_ASM1360787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:25,318] [INFO] Task started: fastANI
[2024-01-24 13:20:25,318] [INFO] Running command: fastANI --query /var/lib/cwl/stgba2b5405-33f1-4435-ae29-80b4c5f41bc0/GCF_013607875.1_ASM1360787v1_genomic.fna.gz --refList GCF_013607875.1_ASM1360787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013607875.1_ASM1360787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:34,204] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:34,215] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:34,216] [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_013607875.1	s__Blastomonas ursincola	100.0	1262	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.82	97.14	0.88	0.79	7	conclusive
GCA_001555775.1	s__Blastomonas delafieldii_A	93.3414	1016	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	99.74	98.25	0.90	0.81	22	-
GCA_000503195.1	s__Blastomonas sp000503195	91.3364	1010	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	97.00	97.00	0.84	0.84	2	-
GCF_003201955.1	s__Blastomonas natatoria	87.9343	978	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786215.1	s__Blastomonas sp000786215	85.7392	953	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331245.1	s__Blastomonas sp000331245	85.0944	897	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003431825.1	s__Blastomonas fulva	84.7646	896	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	98.01	97.97	0.88	0.85	3	-
GCF_000744895.1	s__Erythrobacter sp000744895	77.6217	339	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483135.1	s__UBA7672 sp002483135	77.4867	107	1263	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:34,217] [INFO] GTDB search result was written to GCF_013607875.1_ASM1360787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:34,218] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:34,242] [INFO] DFAST_QC result json was written to GCF_013607875.1_ASM1360787v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:34,243] [INFO] DFAST_QC completed!
[2024-01-24 13:20:34,243] [INFO] Total running time: 0h1m21s