[2023-06-28 12:49:07,219] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:07,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:07,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg745a3cb1-0af5-4290-baff-426f497cedad/dqc_reference
[2023-06-28 12:49:08,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:08,549] [INFO] Task started: Prodigal
[2023-06-28 12:49:08,550] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e1673f8-8dd5-45bc-b206-d8029b6ddcb7/GCA_017987825.1_ASM1798782v1_genomic.fna.gz | prodigal -d GCA_017987825.1_ASM1798782v1_genomic.fna/cds.fna -a GCA_017987825.1_ASM1798782v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:14,583] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:14,584] [INFO] Task started: HMMsearch
[2023-06-28 12:49:14,584] [INFO] Running command: hmmsearch --tblout GCA_017987825.1_ASM1798782v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg745a3cb1-0af5-4290-baff-426f497cedad/dqc_reference/reference_markers.hmm GCA_017987825.1_ASM1798782v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:14,820] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:14,821] [INFO] Found 6/6 markers.
[2023-06-28 12:49:14,844] [INFO] Query marker FASTA was written to GCA_017987825.1_ASM1798782v1_genomic.fna/markers.fasta
[2023-06-28 12:49:14,845] [INFO] Task started: Blastn
[2023-06-28 12:49:14,845] [INFO] Running command: blastn -query GCA_017987825.1_ASM1798782v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg745a3cb1-0af5-4290-baff-426f497cedad/dqc_reference/reference_markers.fasta -out GCA_017987825.1_ASM1798782v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:15,748] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:15,752] [INFO] Selected 28 target genomes.
[2023-06-28 12:49:15,753] [INFO] Target genome list was writen to GCA_017987825.1_ASM1798782v1_genomic.fna/target_genomes.txt
[2023-06-28 12:49:15,753] [INFO] Task started: fastANI
[2023-06-28 12:49:15,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e1673f8-8dd5-45bc-b206-d8029b6ddcb7/GCA_017987825.1_ASM1798782v1_genomic.fna.gz --refList GCA_017987825.1_ASM1798782v1_genomic.fna/target_genomes.txt --output GCA_017987825.1_ASM1798782v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:49:32,685] [INFO] Task succeeded: fastANI
[2023-06-28 12:49:32,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg745a3cb1-0af5-4290-baff-426f497cedad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:49:32,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg745a3cb1-0af5-4290-baff-426f497cedad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:49:32,706] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:49:32,706] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:49:32,707] [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
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	84.2456	445	607	95	below_threshold
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	77.8857	184	607	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	77.7848	181	607	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	77.7038	134	607	95	below_threshold
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	77.6521	168	607	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	77.5371	133	607	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	77.4639	187	607	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	77.4171	123	607	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	77.4094	74	607	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	77.363	135	607	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	77.3319	76	607	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	77.2345	127	607	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	77.2307	123	607	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.1386	145	607	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.124	137	607	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	77.0543	140	607	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	77.0306	140	607	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	76.8976	105	607	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	76.7773	111	607	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	76.5967	91	607	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	76.5264	87	607	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	76.4548	108	607	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	76.208	64	607	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:49:32,710] [INFO] DFAST Taxonomy check result was written to GCA_017987825.1_ASM1798782v1_genomic.fna/tc_result.tsv
[2023-06-28 12:49:32,711] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:49:32,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:49:32,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg745a3cb1-0af5-4290-baff-426f497cedad/dqc_reference/checkm_data
[2023-06-28 12:49:32,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:49:32,746] [INFO] Task started: CheckM
[2023-06-28 12:49:32,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017987825.1_ASM1798782v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017987825.1_ASM1798782v1_genomic.fna/checkm_input GCA_017987825.1_ASM1798782v1_genomic.fna/checkm_result
[2023-06-28 12:49:57,039] [INFO] Task succeeded: CheckM
[2023-06-28 12:49:57,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.67%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:49:57,068] [INFO] ===== Completeness check finished =====
[2023-06-28 12:49:57,069] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:49:57,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017987825.1_ASM1798782v1_genomic.fna/markers.fasta)
[2023-06-28 12:49:57,069] [INFO] Task started: Blastn
[2023-06-28 12:49:57,070] [INFO] Running command: blastn -query GCA_017987825.1_ASM1798782v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg745a3cb1-0af5-4290-baff-426f497cedad/dqc_reference/reference_markers_gtdb.fasta -out GCA_017987825.1_ASM1798782v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:58,567] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:58,573] [INFO] Selected 12 target genomes.
[2023-06-28 12:49:58,574] [INFO] Target genome list was writen to GCA_017987825.1_ASM1798782v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:49:58,585] [INFO] Task started: fastANI
[2023-06-28 12:49:58,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e1673f8-8dd5-45bc-b206-d8029b6ddcb7/GCA_017987825.1_ASM1798782v1_genomic.fna.gz --refList GCA_017987825.1_ASM1798782v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017987825.1_ASM1798782v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:05,189] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:05,198] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:05,198] [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
GCA_017987825.1	s__Sphingorhabdus_B sp017987825	100.0	602	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016707885.1	s__Sphingorhabdus_B sp016707885	85.6605	445	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367235.1	s__Sphingorhabdus_B sp003367235	84.2052	446	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720115.1	s__Sphingorhabdus_B sp016720115	83.3882	438	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.85	99.81	0.95	0.95	3	-
GCA_016721875.1	s__Sphingorhabdus_B sp016721875	80.5767	297	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.47	99.39	0.95	0.94	3	-
GCF_009768975.1	s__Sphingorhabdus_B lacus	77.924	182	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297725.1	s__Sphingorhabdus_B sp013297725	77.795	193	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769755.1	s__Sphingorhabdus_B profundilacus	77.7848	181	607	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:05,200] [INFO] GTDB search result was written to GCA_017987825.1_ASM1798782v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:05,201] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:05,223] [INFO] DFAST_QC result json was written to GCA_017987825.1_ASM1798782v1_genomic.fna/dqc_result.json
[2023-06-28 12:50:05,223] [INFO] DFAST_QC completed!
[2023-06-28 12:50:05,224] [INFO] Total running time: 0h0m58s