[2024-01-24 14:05:48,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:48,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:48,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcce4aed-88f5-4684-8e06-ecb6b79cd63f/dqc_reference
[2024-01-24 14:05:50,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,069] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg4608d51c-d32b-4dc4-a897-569ea5b228af/GCF_014644315.1_ASM1464431v1_genomic.fna.gz | prodigal -d GCF_014644315.1_ASM1464431v1_genomic.fna/cds.fna -a GCF_014644315.1_ASM1464431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:58,375] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:58,375] [INFO] Task started: HMMsearch
[2024-01-24 14:05:58,375] [INFO] Running command: hmmsearch --tblout GCF_014644315.1_ASM1464431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcce4aed-88f5-4684-8e06-ecb6b79cd63f/dqc_reference/reference_markers.hmm GCF_014644315.1_ASM1464431v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:58,640] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:58,641] [INFO] Found 6/6 markers.
[2024-01-24 14:05:58,671] [INFO] Query marker FASTA was written to GCF_014644315.1_ASM1464431v1_genomic.fna/markers.fasta
[2024-01-24 14:05:58,671] [INFO] Task started: Blastn
[2024-01-24 14:05:58,671] [INFO] Running command: blastn -query GCF_014644315.1_ASM1464431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcce4aed-88f5-4684-8e06-ecb6b79cd63f/dqc_reference/reference_markers.fasta -out GCF_014644315.1_ASM1464431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:59,581] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:59,585] [INFO] Selected 18 target genomes.
[2024-01-24 14:05:59,586] [INFO] Target genome list was writen to GCF_014644315.1_ASM1464431v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:59,592] [INFO] Task started: fastANI
[2024-01-24 14:05:59,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg4608d51c-d32b-4dc4-a897-569ea5b228af/GCF_014644315.1_ASM1464431v1_genomic.fna.gz --refList GCF_014644315.1_ASM1464431v1_genomic.fna/target_genomes.txt --output GCF_014644315.1_ASM1464431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:11,577] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:11,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcce4aed-88f5-4684-8e06-ecb6b79cd63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:11,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcce4aed-88f5-4684-8e06-ecb6b79cd63f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:11,599] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:11,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:11,600] [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 deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	100.0	920	920	95	conclusive
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	82.4167	619	920	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	80.594	504	920	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	80.568	509	920	95	below_threshold
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	80.5314	515	920	95	below_threshold
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	80.2197	484	920	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.6128	410	920	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.5841	421	920	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.5103	411	920	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.9865	382	920	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.8858	359	920	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	78.7639	312	920	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.6821	326	920	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.45	357	920	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.4232	366	920	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.4072	309	920	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	78.3134	316	920	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.087	302	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:11,602] [INFO] DFAST Taxonomy check result was written to GCF_014644315.1_ASM1464431v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:11,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:11,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:11,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcce4aed-88f5-4684-8e06-ecb6b79cd63f/dqc_reference/checkm_data
[2024-01-24 14:06:11,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:11,638] [INFO] Task started: CheckM
[2024-01-24 14:06:11,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644315.1_ASM1464431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644315.1_ASM1464431v1_genomic.fna/checkm_input GCF_014644315.1_ASM1464431v1_genomic.fna/checkm_result
[2024-01-24 14:06:42,198] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:42,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,218] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:42,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:42,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644315.1_ASM1464431v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:42,220] [INFO] Task started: Blastn
[2024-01-24 14:06:42,220] [INFO] Running command: blastn -query GCF_014644315.1_ASM1464431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcce4aed-88f5-4684-8e06-ecb6b79cd63f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644315.1_ASM1464431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:43,796] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:43,800] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:43,800] [INFO] Target genome list was writen to GCF_014644315.1_ASM1464431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:43,822] [INFO] Task started: fastANI
[2024-01-24 14:06:43,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg4608d51c-d32b-4dc4-a897-569ea5b228af/GCF_014644315.1_ASM1464431v1_genomic.fna.gz --refList GCF_014644315.1_ASM1464431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644315.1_ASM1464431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:54,093] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:54,111] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:54,112] [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_014644315.1	s__Tsuneonella deserti	100.0	920	920	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	82.4385	617	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007065885.1	s__Tsuneonella sp007065885	81.2224	541	920	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	80.7037	501	920	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	80.594	504	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441535.1	s__Tsuneonella troitsensis	80.5427	514	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827495.1	s__Tsuneonella aeria	80.2197	484	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	79.8005	398	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.5934	412	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.5837	421	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	79.1558	357	920	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	79.1533	373	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230305.1	s__Novosphingobium aerophilum	78.7639	312	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	98.68	98.68	0.90	0.90	2	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.7062	338	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	78.6905	347	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.4554	358	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018828205.1	s__Qipengyuania sp018828205	78.4103	300	920	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,113] [INFO] GTDB search result was written to GCF_014644315.1_ASM1464431v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:54,114] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:54,118] [INFO] DFAST_QC result json was written to GCF_014644315.1_ASM1464431v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:54,119] [INFO] DFAST_QC completed!
[2024-01-24 14:06:54,119] [INFO] Total running time: 0h1m5s