[2024-01-24 14:22:04,339] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg911152ac-c0e1-4962-9074-39148e3a9742/dqc_reference
[2024-01-24 14:22:05,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,706] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,706] [INFO] Running command: gunzip -c /var/lib/cwl/stg88e07287-7cbd-43ba-bacc-ecc77909f15b/GCF_009828065.1_ASM982806v1_genomic.fna.gz | prodigal -d GCF_009828065.1_ASM982806v1_genomic.fna/cds.fna -a GCF_009828065.1_ASM982806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:14,688] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:14,688] [INFO] Task started: HMMsearch
[2024-01-24 14:22:14,689] [INFO] Running command: hmmsearch --tblout GCF_009828065.1_ASM982806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg911152ac-c0e1-4962-9074-39148e3a9742/dqc_reference/reference_markers.hmm GCF_009828065.1_ASM982806v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:14,953] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:14,954] [INFO] Found 6/6 markers.
[2024-01-24 14:22:14,984] [INFO] Query marker FASTA was written to GCF_009828065.1_ASM982806v1_genomic.fna/markers.fasta
[2024-01-24 14:22:14,984] [INFO] Task started: Blastn
[2024-01-24 14:22:14,985] [INFO] Running command: blastn -query GCF_009828065.1_ASM982806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg911152ac-c0e1-4962-9074-39148e3a9742/dqc_reference/reference_markers.fasta -out GCF_009828065.1_ASM982806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:16,092] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:16,095] [INFO] Selected 27 target genomes.
[2024-01-24 14:22:16,096] [INFO] Target genome list was writen to GCF_009828065.1_ASM982806v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:16,120] [INFO] Task started: fastANI
[2024-01-24 14:22:16,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg88e07287-7cbd-43ba-bacc-ecc77909f15b/GCF_009828065.1_ASM982806v1_genomic.fna.gz --refList GCF_009828065.1_ASM982806v1_genomic.fna/target_genomes.txt --output GCF_009828065.1_ASM982806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:33,345] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:33,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg911152ac-c0e1-4962-9074-39148e3a9742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:33,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg911152ac-c0e1-4962-9074-39148e3a9742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:33,369] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:33,370] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:33,370] [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
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	80.2125	453	1022	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	80.1877	467	1022	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.8513	467	1022	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	79.7501	429	1022	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.4475	386	1022	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	79.4339	469	1022	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	79.1757	392	1022	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	79.1302	382	1022	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	79.0946	382	1022	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.0914	347	1022	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	79.0224	380	1022	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	79.0202	360	1022	95	below_threshold
Novosphingobium piscinae	strain=KCTC 42194	GCA_014230355.1	1507448	1507448	type	True	78.9539	394	1022	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.9128	396	1022	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.8357	354	1022	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.7258	339	1022	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.7235	368	1022	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	78.6931	403	1022	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.6527	351	1022	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.5737	348	1022	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	78.5601	375	1022	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	78.5238	324	1022	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	78.48	329	1022	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.3783	283	1022	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.3731	298	1022	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	78.3449	366	1022	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	78.0331	299	1022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:33,372] [INFO] DFAST Taxonomy check result was written to GCF_009828065.1_ASM982806v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:33,372] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:33,373] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:33,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg911152ac-c0e1-4962-9074-39148e3a9742/dqc_reference/checkm_data
[2024-01-24 14:22:33,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:33,406] [INFO] Task started: CheckM
[2024-01-24 14:22:33,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828065.1_ASM982806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828065.1_ASM982806v1_genomic.fna/checkm_input GCF_009828065.1_ASM982806v1_genomic.fna/checkm_result
[2024-01-24 14:23:03,381] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:03,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:03,406] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:03,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:03,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828065.1_ASM982806v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:03,407] [INFO] Task started: Blastn
[2024-01-24 14:23:03,408] [INFO] Running command: blastn -query GCF_009828065.1_ASM982806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg911152ac-c0e1-4962-9074-39148e3a9742/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828065.1_ASM982806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:05,342] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:05,345] [INFO] Selected 19 target genomes.
[2024-01-24 14:23:05,345] [INFO] Target genome list was writen to GCF_009828065.1_ASM982806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:05,359] [INFO] Task started: fastANI
[2024-01-24 14:23:05,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg88e07287-7cbd-43ba-bacc-ecc77909f15b/GCF_009828065.1_ASM982806v1_genomic.fna.gz --refList GCF_009828065.1_ASM982806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828065.1_ASM982806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:18,379] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:18,401] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:18,401] [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_009828065.1	s__Croceibacterium soli	100.0	1021	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011320115.1	s__Croceibacterium segetis	81.7854	581	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827435.1	s__Croceibacterium salegens	80.9229	558	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279825.1	s__Croceibacterium sp002279825	80.6348	541	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCA_017308255.1	s__Croceibacterium sp001897135	80.3684	533	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001427865.1	s__Croceibacterium sp001427865	80.1217	519	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744315.1	s__Croceibacterium sp017744315	80.0428	525	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.8179	470	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018599195.1	s__Croceibacterium sp018599195	79.5094	472	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	79.4358	387	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	79.1225	404	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644315.1	s__Tsuneonella deserti	79.0014	362	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113255.1	s__Novosphingobium sp900113255	78.9648	373	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.9551	363	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230315.1	s__Novosphingobium flavum	78.9348	394	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	78.8229	388	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001557115.1	s__Erythrobacter sp001557115	78.5586	370	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.84	99.84	0.90	0.90	2	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.526	362	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791705.1	s__Novosphingobium sp013791705	78.2636	280	1022	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.87	99.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:18,403] [INFO] GTDB search result was written to GCF_009828065.1_ASM982806v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:18,403] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:18,408] [INFO] DFAST_QC result json was written to GCF_009828065.1_ASM982806v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:18,408] [INFO] DFAST_QC completed!
[2024-01-24 14:23:18,408] [INFO] Total running time: 0h1m14s