[2024-01-25 18:55:20,839] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:20,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:20,841] [INFO] DQC Reference Directory: /var/lib/cwl/stge12c3e3f-9714-4a3e-affb-302504af81fb/dqc_reference
[2024-01-25 18:55:22,035] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:22,035] [INFO] Task started: Prodigal
[2024-01-25 18:55:22,036] [INFO] Running command: gunzip -c /var/lib/cwl/stg862f1135-2442-4c4c-97f6-35fbd2ad158f/GCF_003732435.1_ASM373243v1_genomic.fna.gz | prodigal -d GCF_003732435.1_ASM373243v1_genomic.fna/cds.fna -a GCF_003732435.1_ASM373243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:30,925] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:30,926] [INFO] Task started: HMMsearch
[2024-01-25 18:55:30,926] [INFO] Running command: hmmsearch --tblout GCF_003732435.1_ASM373243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge12c3e3f-9714-4a3e-affb-302504af81fb/dqc_reference/reference_markers.hmm GCF_003732435.1_ASM373243v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:31,137] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:31,138] [INFO] Found 6/6 markers.
[2024-01-25 18:55:31,166] [INFO] Query marker FASTA was written to GCF_003732435.1_ASM373243v1_genomic.fna/markers.fasta
[2024-01-25 18:55:31,166] [INFO] Task started: Blastn
[2024-01-25 18:55:31,166] [INFO] Running command: blastn -query GCF_003732435.1_ASM373243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12c3e3f-9714-4a3e-affb-302504af81fb/dqc_reference/reference_markers.fasta -out GCF_003732435.1_ASM373243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:32,109] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:32,112] [INFO] Selected 17 target genomes.
[2024-01-25 18:55:32,112] [INFO] Target genome list was writen to GCF_003732435.1_ASM373243v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:32,123] [INFO] Task started: fastANI
[2024-01-25 18:55:32,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg862f1135-2442-4c4c-97f6-35fbd2ad158f/GCF_003732435.1_ASM373243v1_genomic.fna.gz --refList GCF_003732435.1_ASM373243v1_genomic.fna/target_genomes.txt --output GCF_003732435.1_ASM373243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:43,345] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:43,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge12c3e3f-9714-4a3e-affb-302504af81fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:43,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge12c3e3f-9714-4a3e-affb-302504af81fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:43,356] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:55:43,356] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:43,356] [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
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_003732435.1	634155	634155	type	True	100.0	1068	1069	95	conclusive
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004798975.1	634155	634155	type	True	99.9556	1031	1069	95	conclusive
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004343305.1	634155	634155	type	True	99.9402	1045	1069	95	conclusive
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	78.8539	326	1069	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	78.8516	317	1069	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	78.6681	328	1069	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	78.6363	305	1069	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	78.5676	335	1069	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	78.5289	293	1069	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	78.4394	320	1069	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	78.3176	339	1069	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	78.2863	329	1069	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	78.263	318	1069	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	78.1961	380	1069	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.1359	343	1069	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	77.7056	228	1069	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.4933	236	1069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:43,358] [INFO] DFAST Taxonomy check result was written to GCF_003732435.1_ASM373243v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:43,358] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:43,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:43,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge12c3e3f-9714-4a3e-affb-302504af81fb/dqc_reference/checkm_data
[2024-01-25 18:55:43,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:43,395] [INFO] Task started: CheckM
[2024-01-25 18:55:43,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003732435.1_ASM373243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003732435.1_ASM373243v1_genomic.fna/checkm_input GCF_003732435.1_ASM373243v1_genomic.fna/checkm_result
[2024-01-25 18:56:25,895] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:25,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:25,911] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:25,911] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:25,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003732435.1_ASM373243v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:25,912] [INFO] Task started: Blastn
[2024-01-25 18:56:25,912] [INFO] Running command: blastn -query GCF_003732435.1_ASM373243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12c3e3f-9714-4a3e-affb-302504af81fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003732435.1_ASM373243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:27,785] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:27,790] [INFO] Selected 23 target genomes.
[2024-01-25 18:56:27,790] [INFO] Target genome list was writen to GCF_003732435.1_ASM373243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:27,809] [INFO] Task started: fastANI
[2024-01-25 18:56:27,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg862f1135-2442-4c4c-97f6-35fbd2ad158f/GCF_003732435.1_ASM373243v1_genomic.fna.gz --refList GCF_003732435.1_ASM373243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003732435.1_ASM373243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:43,553] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:43,567] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:43,567] [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_004343305.1	s__Pseudofulvimonas gallinarii	99.9402	1045	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__UBA2363;g__Pseudofulvimonas	95.0	99.97	99.94	0.98	0.98	3	conclusive
GCA_002344355.1	s__Pseudofulvimonas sp002344355	80.1719	549	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__UBA2363;g__Pseudofulvimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCF_003024235.1	s__Arenimonas caeni	78.852	326	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	78.6425	354	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014202935.1	s__Rehaibacterium terrae	78.5977	342	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	78.5959	308	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.5429	362	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002324875.1	s__Luteimonas sp002324875	78.415	301	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_013620825.1	s__Rhodanobacter sp001899565	78.4002	303	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCA_016720345.1	s__Thermomonas sp016720345	78.3476	315	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_900018785.1	s__Xanthomonas_B massiliensis	78.3451	310	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018333835.1	s__Silanimonas sp018333835	78.344	242	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302095.1	s__Thermomonas sp017302095	78.3284	216	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803715.2	s__Luteimonas yindakuii	78.2907	328	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.11	98.11	0.97	0.97	2	-
GCF_001632775.1	s__Dokdonella koreensis	78.2032	380	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	78.1969	370	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014645.1	s__Luteimonas sp001014645	78.1483	346	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641285.1	s__Dyella_A thiooxydans	78.0954	289	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	78.0654	287	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_002307375.1	s__Luteimonas sp002307375	78.0224	308	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182785.1	s__JADKHK01 sp016182785	77.8469	281	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721845.1	s__JADKHK01 sp016721845	77.7515	251	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.21	98.90	0.96	0.94	3	-
GCA_018240505.1	s__Rudaea sp018240505	77.538	238	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rudaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:43,568] [INFO] GTDB search result was written to GCF_003732435.1_ASM373243v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:43,569] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:43,573] [INFO] DFAST_QC result json was written to GCF_003732435.1_ASM373243v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:43,574] [INFO] DFAST_QC completed!
[2024-01-25 18:56:43,574] [INFO] Total running time: 0h1m23s