[2024-01-24 13:40:35,024] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,025] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg03e24959-df60-4ebc-b5dd-3d3173754252/dqc_reference
[2024-01-24 13:40:36,477] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,478] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg76bfb3d3-51e4-40d4-9827-5ead695181a7/GCF_001625325.1_ASM162532v1_genomic.fna.gz | prodigal -d GCF_001625325.1_ASM162532v1_genomic.fna/cds.fna -a GCF_001625325.1_ASM162532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,840] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,841] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,841] [INFO] Running command: hmmsearch --tblout GCF_001625325.1_ASM162532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03e24959-df60-4ebc-b5dd-3d3173754252/dqc_reference/reference_markers.hmm GCF_001625325.1_ASM162532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,133] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,171] [INFO] Query marker FASTA was written to GCF_001625325.1_ASM162532v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,171] [INFO] Task started: Blastn
[2024-01-24 13:40:49,172] [INFO] Running command: blastn -query GCF_001625325.1_ASM162532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03e24959-df60-4ebc-b5dd-3d3173754252/dqc_reference/reference_markers.fasta -out GCF_001625325.1_ASM162532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,053] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,056] [INFO] Selected 31 target genomes.
[2024-01-24 13:40:50,057] [INFO] Target genome list was writen to GCF_001625325.1_ASM162532v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,088] [INFO] Task started: fastANI
[2024-01-24 13:40:50,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg76bfb3d3-51e4-40d4-9827-5ead695181a7/GCF_001625325.1_ASM162532v1_genomic.fna.gz --refList GCF_001625325.1_ASM162532v1_genomic.fna/target_genomes.txt --output GCF_001625325.1_ASM162532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:10,211] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:10,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03e24959-df60-4ebc-b5dd-3d3173754252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:10,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03e24959-df60-4ebc-b5dd-3d3173754252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:10,238] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:10,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:10,239] [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
Caenibius tardaugens	strain=NBRC 16725	GCA_003860345.1	169176	169176	type	True	78.8429	416	1212	95	below_threshold
Caenibius tardaugens	strain=NBRC 16725	GCA_000466945.1	169176	169176	type	True	78.8037	409	1212	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	78.4804	195	1212	95	below_threshold
Altericroceibacterium spongiae	strain=HN-Y73	GCA_003610805.1	2320269	2320269	type	True	78.391	159	1212	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.1307	155	1212	95	below_threshold
Novosphingobium indicum	strain=CGMCC 1.6784	GCA_014645195.1	462949	462949	type	True	78.1149	211	1212	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.0361	197	1212	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.9884	218	1212	95	below_threshold
Novosphingobium malaysiense	strain=MUSC 273	GCA_000802225.1	1348853	1348853	type	True	77.8905	219	1212	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.8485	144	1212	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.7314	203	1212	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	77.7261	199	1212	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.6634	174	1212	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.6484	206	1212	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	77.6332	199	1212	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	77.6083	157	1212	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.6013	163	1212	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	77.5811	205	1212	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	77.5796	200	1212	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	77.5386	170	1212	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.5241	144	1212	95	below_threshold
Novosphingobium meiothermophilum	strain=SYSU G00007	GCA_003171715.1	2202251	2202251	type	True	77.517	186	1212	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.4981	182	1212	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000192575.1	378548	378548	type	True	77.4224	188	1212	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	77.3839	146	1212	95	below_threshold
Qipengyuania psychrotolerans	strain=1XM2-8	GCA_019711355.1	2867238	2867238	type	True	77.3687	142	1212	95	below_threshold
Novosphingobium hassiacum	strain=DSM 14552	GCA_014196055.1	173676	173676	type	True	77.3366	177	1212	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	77.3108	145	1212	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	77.309	186	1212	95	below_threshold
Novosphingobium sediminicola	strain=DSM 27057	GCA_014196525.1	563162	563162	type	True	77.2277	160	1212	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	76.9911	122	1212	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:10,243] [INFO] DFAST Taxonomy check result was written to GCF_001625325.1_ASM162532v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:10,245] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:10,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:10,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03e24959-df60-4ebc-b5dd-3d3173754252/dqc_reference/checkm_data
[2024-01-24 13:41:10,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:10,286] [INFO] Task started: CheckM
[2024-01-24 13:41:10,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001625325.1_ASM162532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001625325.1_ASM162532v1_genomic.fna/checkm_input GCF_001625325.1_ASM162532v1_genomic.fna/checkm_result
[2024-01-24 13:41:49,888] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:49,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,908] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:49,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:49,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001625325.1_ASM162532v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:49,911] [INFO] Task started: Blastn
[2024-01-24 13:41:49,911] [INFO] Running command: blastn -query GCF_001625325.1_ASM162532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03e24959-df60-4ebc-b5dd-3d3173754252/dqc_reference/reference_markers_gtdb.fasta -out GCF_001625325.1_ASM162532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:51,485] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:51,490] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:51,490] [INFO] Target genome list was writen to GCF_001625325.1_ASM162532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:51,515] [INFO] Task started: fastANI
[2024-01-24 13:41:51,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg76bfb3d3-51e4-40d4-9827-5ead695181a7/GCF_001625325.1_ASM162532v1_genomic.fna.gz --refList GCF_001625325.1_ASM162532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001625325.1_ASM162532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:07,111] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,134] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:07,134] [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_001625325.1	s__Caenibius estronivorus	100.0	1211	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003860345.1	s__Caenibius tardaugens	78.8639	414	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002870965.1	s__Tsuneonella flava	78.4596	196	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	99.01	98.03	0.92	0.87	3	-
GCF_003569745.1	s__Croceibacterium sp003569745	78.454	235	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305965.1	s__Caenibius sp001305965	78.3106	248	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145025.1	s__Novosphingobium sp005145025	78.3094	211	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014975.1	s__Novosphingobium sp002336885	78.1378	206	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCF_014645195.1	s__Novosphingobium indicum	78.1084	212	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.92	97.92	0.77	0.77	2	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.0574	197	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855555.1	s__Novosphingobium sp002855555	78.0479	184	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725355.1	s__Novosphingobium sp001725355	77.9703	209	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302615.1	s__Novosphingobium sp017302615	77.9048	209	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802225.1	s__Novosphingobium malaysiense	77.8849	220	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698205.1	s__Tsuneonella dongtanensis	77.851	150	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001635685.1	s__Qipengyuania sp001635685	77.7325	174	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.58	97.35	0.92	0.89	12	-
GCF_009827305.1	s__Croceibacterium xixiisoli	77.7228	205	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.6376	246	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_003724185.1	s__Erythrobacter sp003724185	77.634	163	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	77.6144	158	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002149965.1	s__Novosphingobium panipatense	77.5923	200	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.24	97.74	0.85	0.82	3	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	77.5343	171	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	77.5313	145	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001516125.1	s__Erythrobacter sp001516125	77.5074	135	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	77.2372	165	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240895.1	s__Novosphingobium sp018240895	77.0035	156	1212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,136] [INFO] GTDB search result was written to GCF_001625325.1_ASM162532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:07,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:07,141] [INFO] DFAST_QC result json was written to GCF_001625325.1_ASM162532v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:07,142] [INFO] DFAST_QC completed!
[2024-01-24 13:42:07,142] [INFO] Total running time: 0h1m32s