[2024-01-24 11:05:49,425] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,427] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg0de6d5c8-c250-4052-9a6c-06f91547f29b/dqc_reference
[2024-01-24 11:05:51,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,279] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf263088-7cff-4f44-87fb-316e1a9c6d3b/GCF_000802385.1_ASM80238v1_genomic.fna.gz | prodigal -d GCF_000802385.1_ASM80238v1_genomic.fna/cds.fna -a GCF_000802385.1_ASM80238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:01,975] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:01,975] [INFO] Task started: HMMsearch
[2024-01-24 11:06:01,975] [INFO] Running command: hmmsearch --tblout GCF_000802385.1_ASM80238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0de6d5c8-c250-4052-9a6c-06f91547f29b/dqc_reference/reference_markers.hmm GCF_000802385.1_ASM80238v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:02,177] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:02,178] [INFO] Found 6/6 markers.
[2024-01-24 11:06:02,207] [INFO] Query marker FASTA was written to GCF_000802385.1_ASM80238v1_genomic.fna/markers.fasta
[2024-01-24 11:06:02,208] [INFO] Task started: Blastn
[2024-01-24 11:06:02,208] [INFO] Running command: blastn -query GCF_000802385.1_ASM80238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de6d5c8-c250-4052-9a6c-06f91547f29b/dqc_reference/reference_markers.fasta -out GCF_000802385.1_ASM80238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:03,049] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:03,052] [INFO] Selected 22 target genomes.
[2024-01-24 11:06:03,052] [INFO] Target genome list was writen to GCF_000802385.1_ASM80238v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:03,082] [INFO] Task started: fastANI
[2024-01-24 11:06:03,082] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf263088-7cff-4f44-87fb-316e1a9c6d3b/GCF_000802385.1_ASM80238v1_genomic.fna.gz --refList GCF_000802385.1_ASM80238v1_genomic.fna/target_genomes.txt --output GCF_000802385.1_ASM80238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:17,021] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:17,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0de6d5c8-c250-4052-9a6c-06f91547f29b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:17,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0de6d5c8-c250-4052-9a6c-06f91547f29b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:17,037] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:17,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:17,037] [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
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	100.0	1157	1157	95	conclusive
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	87.5013	867	1157	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.8524	372	1157	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.7274	239	1157	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.6673	345	1157	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.5611	334	1157	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	78.5552	384	1157	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.5366	353	1157	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	78.53	410	1157	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.4212	329	1157	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.3803	308	1157	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.3306	319	1157	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.195	341	1157	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.095	301	1157	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.9891	306	1157	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	77.9371	240	1157	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	77.7993	279	1157	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	77.7936	290	1157	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	77.7795	269	1157	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	77.5834	295	1157	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	77.5263	296	1157	95	below_threshold
Tsuneonella suprasediminis	strain=Ery12	GCA_003605755.1	2306996	2306996	type	True	77.3267	220	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:17,039] [INFO] DFAST Taxonomy check result was written to GCF_000802385.1_ASM80238v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:17,039] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:17,039] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:17,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0de6d5c8-c250-4052-9a6c-06f91547f29b/dqc_reference/checkm_data
[2024-01-24 11:06:17,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:17,073] [INFO] Task started: CheckM
[2024-01-24 11:06:17,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000802385.1_ASM80238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000802385.1_ASM80238v1_genomic.fna/checkm_input GCF_000802385.1_ASM80238v1_genomic.fna/checkm_result
[2024-01-24 11:06:53,913] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:53,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:53,931] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:53,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:53,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000802385.1_ASM80238v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:53,932] [INFO] Task started: Blastn
[2024-01-24 11:06:53,932] [INFO] Running command: blastn -query GCF_000802385.1_ASM80238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de6d5c8-c250-4052-9a6c-06f91547f29b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000802385.1_ASM80238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:55,468] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:55,471] [INFO] Selected 19 target genomes.
[2024-01-24 11:06:55,471] [INFO] Target genome list was writen to GCF_000802385.1_ASM80238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:55,534] [INFO] Task started: fastANI
[2024-01-24 11:06:55,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf263088-7cff-4f44-87fb-316e1a9c6d3b/GCF_000802385.1_ASM80238v1_genomic.fna.gz --refList GCF_000802385.1_ASM80238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000802385.1_ASM80238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:08,689] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:08,704] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:08,704] [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_000802385.1	s__Croceibacterium mercuriale	100.0	1157	1157	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_003660445.1	s__Croceibacterium ferulae	87.5013	867	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359685.1	s__Croceibacterium sp014359685	80.1212	332	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683845.1	s__Croceibacterium sp001683845	79.6141	407	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	79.5408	452	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	79.0233	420	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.5985	306	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.5528	343	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744315.1	s__Croceibacterium sp017744315	78.5481	345	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.5418	352	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	78.4798	327	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320115.1	s__Croceibacterium segetis	78.2904	336	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	78.2512	313	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	78.2467	320	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	78.0834	302	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001519075.1	s__Novosphingobium fuchskuhlense	77.768	270	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017163935.1	s__Novosphingobium sp017163935	77.6988	338	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421355.1	s__Sphingomonas sp001421355	77.5649	295	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_003946805.1	s__Sphingomonas sp003946805	77.4284	316	1157	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:08,706] [INFO] GTDB search result was written to GCF_000802385.1_ASM80238v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:08,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:08,710] [INFO] DFAST_QC result json was written to GCF_000802385.1_ASM80238v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:08,710] [INFO] DFAST_QC completed!
[2024-01-24 11:07:08,710] [INFO] Total running time: 0h1m19s