[2024-01-24 11:52:49,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:49,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:49,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgebb8e3e6-5884-4744-ba94-c7d5167e821c/dqc_reference
[2024-01-24 11:52:51,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:51,056] [INFO] Task started: Prodigal
[2024-01-24 11:52:51,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c01cf4f-600e-4df6-973a-a3f569c4f6d5/GCF_009925085.1_ASM992508v1_genomic.fna.gz | prodigal -d GCF_009925085.1_ASM992508v1_genomic.fna/cds.fna -a GCF_009925085.1_ASM992508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:53:04,636] [INFO] Task succeeded: Prodigal
[2024-01-24 11:53:04,636] [INFO] Task started: HMMsearch
[2024-01-24 11:53:04,637] [INFO] Running command: hmmsearch --tblout GCF_009925085.1_ASM992508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebb8e3e6-5884-4744-ba94-c7d5167e821c/dqc_reference/reference_markers.hmm GCF_009925085.1_ASM992508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:53:04,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:53:04,919] [INFO] Found 6/6 markers.
[2024-01-24 11:53:04,964] [INFO] Query marker FASTA was written to GCF_009925085.1_ASM992508v1_genomic.fna/markers.fasta
[2024-01-24 11:53:04,965] [INFO] Task started: Blastn
[2024-01-24 11:53:04,965] [INFO] Running command: blastn -query GCF_009925085.1_ASM992508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebb8e3e6-5884-4744-ba94-c7d5167e821c/dqc_reference/reference_markers.fasta -out GCF_009925085.1_ASM992508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:05,939] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:05,943] [INFO] Selected 21 target genomes.
[2024-01-24 11:53:05,944] [INFO] Target genome list was writen to GCF_009925085.1_ASM992508v1_genomic.fna/target_genomes.txt
[2024-01-24 11:53:05,953] [INFO] Task started: fastANI
[2024-01-24 11:53:05,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c01cf4f-600e-4df6-973a-a3f569c4f6d5/GCF_009925085.1_ASM992508v1_genomic.fna.gz --refList GCF_009925085.1_ASM992508v1_genomic.fna/target_genomes.txt --output GCF_009925085.1_ASM992508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:23,346] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:23,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebb8e3e6-5884-4744-ba94-c7d5167e821c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:23,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebb8e3e6-5884-4744-ba94-c7d5167e821c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:23,376] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:53:23,376] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:53:23,376] [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
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	100.0	1484	1487	95	conclusive
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.5713	580	1487	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.5648	581	1487	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	79.2167	552	1487	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	79.1339	581	1487	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	79.116	573	1487	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.9742	440	1487	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	78.8585	537	1487	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	78.8569	516	1487	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.8174	543	1487	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	78.7863	481	1487	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	78.771	489	1487	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	78.7626	438	1487	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.6556	480	1487	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	78.6015	551	1487	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	78.5044	447	1487	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.4897	438	1487	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	78.4784	497	1487	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.1967	451	1487	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	77.9239	331	1487	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	77.1458	335	1487	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:23,378] [INFO] DFAST Taxonomy check result was written to GCF_009925085.1_ASM992508v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:23,379] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:23,379] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:23,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebb8e3e6-5884-4744-ba94-c7d5167e821c/dqc_reference/checkm_data
[2024-01-24 11:53:23,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:23,426] [INFO] Task started: CheckM
[2024-01-24 11:53:23,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009925085.1_ASM992508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009925085.1_ASM992508v1_genomic.fna/checkm_input GCF_009925085.1_ASM992508v1_genomic.fna/checkm_result
[2024-01-24 11:54:12,029] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:12,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:12,051] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:12,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:12,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009925085.1_ASM992508v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:12,052] [INFO] Task started: Blastn
[2024-01-24 11:54:12,052] [INFO] Running command: blastn -query GCF_009925085.1_ASM992508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebb8e3e6-5884-4744-ba94-c7d5167e821c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009925085.1_ASM992508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:13,905] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:13,909] [INFO] Selected 20 target genomes.
[2024-01-24 11:54:13,910] [INFO] Target genome list was writen to GCF_009925085.1_ASM992508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:13,938] [INFO] Task started: fastANI
[2024-01-24 11:54:13,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c01cf4f-600e-4df6-973a-a3f569c4f6d5/GCF_009925085.1_ASM992508v1_genomic.fna.gz --refList GCF_009925085.1_ASM992508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009925085.1_ASM992508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:30,340] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:30,360] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:30,360] [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
GCA_009925085.1	s__CYK-10 sp009925085	100.0	1484	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CYK-10	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016124195.1	s__CYK-10 sp016124195	80.0324	714	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CYK-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	79.5761	560	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	79.5596	483	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	79.512	605	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057165.1	s__Tabrizicola sp018057165	79.3703	396	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013693875.1	s__SSD5 sp013693875	79.1739	611	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SSD5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	79.138	581	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793705.1	s__Tabrizicola sp016793705	79.0445	579	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	78.9071	549	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792905.1	s__Tabrizicola sp016792905	78.8055	534	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271655.1	s__Gemmobacter caeruleus	78.7669	548	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	78.5985	552	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869835.1	s__KMS-5 sp016869835	78.5851	418	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003290025.1	s__Pseudogemmobacter bohemicus	78.5486	447	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002358085.1	s__Thioclava arenosa	78.1927	317	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794355.1	s__ETT8 sp002794355	78.1081	412	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002356635.1	s__QY30 sp002356635	78.0894	375	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QY30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	77.9011	359	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_016765775.1	s__Pseudorhodobacter sp016765775	77.8046	398	1487	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:30,362] [INFO] GTDB search result was written to GCF_009925085.1_ASM992508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:30,363] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:30,367] [INFO] DFAST_QC result json was written to GCF_009925085.1_ASM992508v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:30,367] [INFO] DFAST_QC completed!
[2024-01-24 11:54:30,368] [INFO] Total running time: 0h1m41s