[2024-01-24 14:13:18,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc5e9143-039e-41e4-a748-597d444c74d2/dqc_reference
[2024-01-24 14:13:20,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:20,022] [INFO] Task started: Prodigal
[2024-01-24 14:13:20,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg157ee1e0-d792-463c-92f7-66d13698909c/GCF_002269345.1_ASM226934v1_genomic.fna.gz | prodigal -d GCF_002269345.1_ASM226934v1_genomic.fna/cds.fna -a GCF_002269345.1_ASM226934v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:28,853] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:28,853] [INFO] Task started: HMMsearch
[2024-01-24 14:13:28,853] [INFO] Running command: hmmsearch --tblout GCF_002269345.1_ASM226934v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc5e9143-039e-41e4-a748-597d444c74d2/dqc_reference/reference_markers.hmm GCF_002269345.1_ASM226934v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:29,092] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:29,094] [INFO] Found 6/6 markers.
[2024-01-24 14:13:29,127] [INFO] Query marker FASTA was written to GCF_002269345.1_ASM226934v1_genomic.fna/markers.fasta
[2024-01-24 14:13:29,127] [INFO] Task started: Blastn
[2024-01-24 14:13:29,128] [INFO] Running command: blastn -query GCF_002269345.1_ASM226934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc5e9143-039e-41e4-a748-597d444c74d2/dqc_reference/reference_markers.fasta -out GCF_002269345.1_ASM226934v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:30,125] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:30,128] [INFO] Selected 20 target genomes.
[2024-01-24 14:13:30,129] [INFO] Target genome list was writen to GCF_002269345.1_ASM226934v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:30,140] [INFO] Task started: fastANI
[2024-01-24 14:13:30,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg157ee1e0-d792-463c-92f7-66d13698909c/GCF_002269345.1_ASM226934v1_genomic.fna.gz --refList GCF_002269345.1_ASM226934v1_genomic.fna/target_genomes.txt --output GCF_002269345.1_ASM226934v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:42,236] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:42,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc5e9143-039e-41e4-a748-597d444c74d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:42,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc5e9143-039e-41e4-a748-597d444c74d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:42,254] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:42,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:42,255] [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
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	80.3686	493	900	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.9483	464	900	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.7324	452	900	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.7186	432	900	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	79.7089	399	900	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.5563	438	900	95	below_threshold
Tsuneonella suprasediminis	strain=Ery12	GCA_003605755.1	2306996	2306996	type	True	79.4643	458	900	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	79.4373	452	900	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.3749	434	900	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	79.0873	386	900	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	79.0834	382	900	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.0327	399	900	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	79.0199	374	900	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	79.0124	385	900	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	78.9942	389	900	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.9893	379	900	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.9798	378	900	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.8107	369	900	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.7775	375	900	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.447	343	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:42,256] [INFO] DFAST Taxonomy check result was written to GCF_002269345.1_ASM226934v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:42,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:42,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:42,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc5e9143-039e-41e4-a748-597d444c74d2/dqc_reference/checkm_data
[2024-01-24 14:13:42,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:42,289] [INFO] Task started: CheckM
[2024-01-24 14:13:42,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002269345.1_ASM226934v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002269345.1_ASM226934v1_genomic.fna/checkm_input GCF_002269345.1_ASM226934v1_genomic.fna/checkm_result
[2024-01-24 14:14:11,171] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:11,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:11,204] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:11,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:11,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002269345.1_ASM226934v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:11,205] [INFO] Task started: Blastn
[2024-01-24 14:14:11,205] [INFO] Running command: blastn -query GCF_002269345.1_ASM226934v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc5e9143-039e-41e4-a748-597d444c74d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002269345.1_ASM226934v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:12,903] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:12,907] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:12,908] [INFO] Target genome list was writen to GCF_002269345.1_ASM226934v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:12,927] [INFO] Task started: fastANI
[2024-01-24 14:14:12,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg157ee1e0-d792-463c-92f7-66d13698909c/GCF_002269345.1_ASM226934v1_genomic.fna.gz --refList GCF_002269345.1_ASM226934v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002269345.1_ASM226934v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:23,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:23,420] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:23,420] [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_002269345.1	s__Tsuneonella mangrovi	100.0	900	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003958625.1	s__Tsuneonella rigui	80.3605	494	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698205.1	s__Tsuneonella dongtanensis	80.1317	466	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	79.9573	464	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	79.9215	435	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	79.5554	438	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.5462	438	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003605755.1	s__Tsuneonella suprasediminis	79.4857	456	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002870965.1	s__Tsuneonella flava	79.4502	450	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	99.01	98.03	0.92	0.87	3	-
GCF_009827435.1	s__Croceibacterium salegens	79.417	405	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125555.1	s__Erythrobacter sp016125555	79.1714	434	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	79.0886	396	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	79.0834	382	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.0766	350	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	79.0126	385	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011054555.1	s__Erythrobacter sp011054555	78.9334	325	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000756795.1	s__Qipengyuania vulgaris_A	78.8784	326	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	78.7909	210	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:23,422] [INFO] GTDB search result was written to GCF_002269345.1_ASM226934v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:23,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:23,427] [INFO] DFAST_QC result json was written to GCF_002269345.1_ASM226934v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:23,427] [INFO] DFAST_QC completed!
[2024-01-24 14:14:23,427] [INFO] Total running time: 0h1m5s