[2024-01-24 13:55:13,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:13,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:13,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg19f2f3ad-8731-43c4-b69c-9d32cfc77f1b/dqc_reference
[2024-01-24 13:55:14,958] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:14,959] [INFO] Task started: Prodigal
[2024-01-24 13:55:14,959] [INFO] Running command: gunzip -c /var/lib/cwl/stga0f64f86-fd80-4dca-8289-47fe30f823c7/GCF_014681765.1_ASM1468176v1_genomic.fna.gz | prodigal -d GCF_014681765.1_ASM1468176v1_genomic.fna/cds.fna -a GCF_014681765.1_ASM1468176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:29,385] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:29,386] [INFO] Task started: HMMsearch
[2024-01-24 13:55:29,386] [INFO] Running command: hmmsearch --tblout GCF_014681765.1_ASM1468176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19f2f3ad-8731-43c4-b69c-9d32cfc77f1b/dqc_reference/reference_markers.hmm GCF_014681765.1_ASM1468176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:29,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:29,663] [INFO] Found 6/6 markers.
[2024-01-24 13:55:29,703] [INFO] Query marker FASTA was written to GCF_014681765.1_ASM1468176v1_genomic.fna/markers.fasta
[2024-01-24 13:55:29,704] [INFO] Task started: Blastn
[2024-01-24 13:55:29,704] [INFO] Running command: blastn -query GCF_014681765.1_ASM1468176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19f2f3ad-8731-43c4-b69c-9d32cfc77f1b/dqc_reference/reference_markers.fasta -out GCF_014681765.1_ASM1468176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:30,703] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:30,707] [INFO] Selected 21 target genomes.
[2024-01-24 13:55:30,708] [INFO] Target genome list was writen to GCF_014681765.1_ASM1468176v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:30,719] [INFO] Task started: fastANI
[2024-01-24 13:55:30,720] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f64f86-fd80-4dca-8289-47fe30f823c7/GCF_014681765.1_ASM1468176v1_genomic.fna.gz --refList GCF_014681765.1_ASM1468176v1_genomic.fna/target_genomes.txt --output GCF_014681765.1_ASM1468176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:47,699] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:47,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19f2f3ad-8731-43c4-b69c-9d32cfc77f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:47,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19f2f3ad-8731-43c4-b69c-9d32cfc77f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:47,717] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:55:47,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:47,718] [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
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	100.0	1415	1415	95	conclusive
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	99.9417	1335	1415	95	conclusive
Roseibaca ekhonensis	strain=CECT 7235	GCA_900499075.1	254356	254356	type	True	78.6395	357	1415	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.2951	420	1415	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.9866	344	1415	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.952	385	1415	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	77.913	358	1415	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	77.8629	423	1415	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	77.8301	408	1415	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.817	343	1415	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.7639	338	1415	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7637	336	1415	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.7258	340	1415	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	77.661	368	1415	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.6474	429	1415	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	77.4829	304	1415	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.4689	349	1415	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	77.455	295	1415	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.4129	292	1415	95	below_threshold
Roseinatronobacter thiooxidans	strain=DSM 13087	GCA_003254005.1	121821	121821	type	True	77.3286	333	1415	95	below_threshold
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	77.3229	341	1415	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:47,720] [INFO] DFAST Taxonomy check result was written to GCF_014681765.1_ASM1468176v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:47,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:47,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:47,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19f2f3ad-8731-43c4-b69c-9d32cfc77f1b/dqc_reference/checkm_data
[2024-01-24 13:55:47,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:47,766] [INFO] Task started: CheckM
[2024-01-24 13:55:47,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014681765.1_ASM1468176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014681765.1_ASM1468176v1_genomic.fna/checkm_input GCF_014681765.1_ASM1468176v1_genomic.fna/checkm_result
[2024-01-24 13:56:34,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:34,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:34,216] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:34,216] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:34,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014681765.1_ASM1468176v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:34,217] [INFO] Task started: Blastn
[2024-01-24 13:56:34,217] [INFO] Running command: blastn -query GCF_014681765.1_ASM1468176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19f2f3ad-8731-43c4-b69c-9d32cfc77f1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014681765.1_ASM1468176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:35,961] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:35,966] [INFO] Selected 26 target genomes.
[2024-01-24 13:56:35,966] [INFO] Target genome list was writen to GCF_014681765.1_ASM1468176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:36,026] [INFO] Task started: fastANI
[2024-01-24 13:56:36,027] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f64f86-fd80-4dca-8289-47fe30f823c7/GCF_014681765.1_ASM1468176v1_genomic.fna.gz --refList GCF_014681765.1_ASM1468176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014681765.1_ASM1468176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:53,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:53,495] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:53,496] [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_014681765.1	s__Roseicitreum antarcticum	100.0	1415	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicitreum	95.0	99.98	99.98	0.97	0.97	2	conclusive
GCA_013415485.1	s__PUOA01 sp003567395	78.274	423	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	98.54	98.26	0.95	0.89	5	-
GCA_003551925.1	s__PUOA01 sp003551925	78.1113	321	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121115.1	s__PUOA01 sp007121115	78.0727	355	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	99.30	99.15	0.84	0.78	4	-
GCF_000429765.1	s__Wagnerdoeblera nectariphila	77.924	356	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122215.1	s__Pararhodobacter marinus	77.8384	407	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303295.1	s__Pararhodobacter sp017303295	77.7783	394	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	77.7443	338	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016653255.1	s__Rhodobaculum claviforme	77.7351	319	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	77.7215	280	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129775.1	s__Rhodobaculum sp007129775	77.7061	258	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	77.7059	347	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.642	316	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908405.1	s__Roseinatronobacter sp009908405	77.6416	297	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	77.634	306	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811755.1	s__Pararhodobacter sp017811755	77.6264	358	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124615.1	s__Solirhodobacter sp016124615	77.5603	361	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	77.4446	296	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	77.4228	324	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704435.1	s__JAAKGP01 sp016704435	77.3872	305	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCF_004015795.1	s__Falsirhodobacter deserti	77.3612	210	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959935.1	s__Falsirhodobacter xinxiangensis	77.3468	292	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692585.1	s__Roseinatronobacter sp007692585	77.3035	287	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937725.1	s__Roseinatronobacter sp016937725	77.2934	245	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007116445.1	s__Roseinatronobacter sp007116445	77.1556	187	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869875.1	s__Paracoccus sp016869875	77.0235	179	1415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:53,497] [INFO] GTDB search result was written to GCF_014681765.1_ASM1468176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:53,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:53,502] [INFO] DFAST_QC result json was written to GCF_014681765.1_ASM1468176v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:53,503] [INFO] DFAST_QC completed!
[2024-01-24 13:56:53,503] [INFO] Total running time: 0h1m40s