[2024-01-24 13:10:01,140] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:01,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:01,142] [INFO] DQC Reference Directory: /var/lib/cwl/stg35a715f9-3b52-47d6-aa7c-ae7c46705b00/dqc_reference
[2024-01-24 13:10:02,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:02,485] [INFO] Task started: Prodigal
[2024-01-24 13:10:02,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a20ba5d-38cb-4884-a3a6-9f12cda7c79a/GCF_003173035.1_ASM317303v1_genomic.fna.gz | prodigal -d GCF_003173035.1_ASM317303v1_genomic.fna/cds.fna -a GCF_003173035.1_ASM317303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:14,668] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:14,668] [INFO] Task started: HMMsearch
[2024-01-24 13:10:14,669] [INFO] Running command: hmmsearch --tblout GCF_003173035.1_ASM317303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35a715f9-3b52-47d6-aa7c-ae7c46705b00/dqc_reference/reference_markers.hmm GCF_003173035.1_ASM317303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:15,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:15,007] [INFO] Found 6/6 markers.
[2024-01-24 13:10:15,051] [INFO] Query marker FASTA was written to GCF_003173035.1_ASM317303v1_genomic.fna/markers.fasta
[2024-01-24 13:10:15,051] [INFO] Task started: Blastn
[2024-01-24 13:10:15,051] [INFO] Running command: blastn -query GCF_003173035.1_ASM317303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35a715f9-3b52-47d6-aa7c-ae7c46705b00/dqc_reference/reference_markers.fasta -out GCF_003173035.1_ASM317303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:16,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:16,036] [INFO] Selected 20 target genomes.
[2024-01-24 13:10:16,037] [INFO] Target genome list was writen to GCF_003173035.1_ASM317303v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:16,065] [INFO] Task started: fastANI
[2024-01-24 13:10:16,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a20ba5d-38cb-4884-a3a6-9f12cda7c79a/GCF_003173035.1_ASM317303v1_genomic.fna.gz --refList GCF_003173035.1_ASM317303v1_genomic.fna/target_genomes.txt --output GCF_003173035.1_ASM317303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:35,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:35,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35a715f9-3b52-47d6-aa7c-ae7c46705b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:35,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35a715f9-3b52-47d6-aa7c-ae7c46705b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:35,529] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:35,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:35,530] [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
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	100.0	1468	1472	95	conclusive
Zavarzinia compransoris	strain=DSM 1231	GCA_004362995.1	1264899	1264899	type	True	83.8986	967	1472	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	83.8616	968	1472	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.0541	315	1472	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	77.0128	376	1472	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.906	230	1472	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.8341	265	1472	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.8306	305	1472	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.7712	466	1472	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.6611	234	1472	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	76.6345	175	1472	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.6261	357	1472	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.6064	286	1472	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.6063	287	1472	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	76.5592	247	1472	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	76.5302	195	1472	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	76.4906	105	1472	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.4402	297	1472	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.3862	219	1472	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.355	285	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:35,532] [INFO] DFAST Taxonomy check result was written to GCF_003173035.1_ASM317303v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:35,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:35,533] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:35,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35a715f9-3b52-47d6-aa7c-ae7c46705b00/dqc_reference/checkm_data
[2024-01-24 13:10:35,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:35,577] [INFO] Task started: CheckM
[2024-01-24 13:10:35,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003173035.1_ASM317303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003173035.1_ASM317303v1_genomic.fna/checkm_input GCF_003173035.1_ASM317303v1_genomic.fna/checkm_result
[2024-01-24 13:11:15,734] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:15,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:15,757] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:15,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:15,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003173035.1_ASM317303v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:15,758] [INFO] Task started: Blastn
[2024-01-24 13:11:15,758] [INFO] Running command: blastn -query GCF_003173035.1_ASM317303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35a715f9-3b52-47d6-aa7c-ae7c46705b00/dqc_reference/reference_markers_gtdb.fasta -out GCF_003173035.1_ASM317303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:17,639] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:17,643] [INFO] Selected 16 target genomes.
[2024-01-24 13:11:17,643] [INFO] Target genome list was writen to GCF_003173035.1_ASM317303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:17,654] [INFO] Task started: fastANI
[2024-01-24 13:11:17,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a20ba5d-38cb-4884-a3a6-9f12cda7c79a/GCF_003173035.1_ASM317303v1_genomic.fna.gz --refList GCF_003173035.1_ASM317303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003173035.1_ASM317303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:33,638] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:33,663] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:33,664] [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_003173035.1	s__Zavarzinia aquatilis	100.0	1468	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003173055.1	s__Zavarzinia compransoris	83.8203	973	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003590945.1	s__Zavarzinia sp003590945	81.2668	914	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	77.1452	375	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	77.1179	409	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046185.1	s__Phreatobacter oligotrophus	77.0632	278	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	77.0304	318	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	77.0269	407	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	77.0047	333	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.9053	367	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	76.8644	262	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCF_014196925.1	s__Chelatococcus_A caeni	76.8231	306	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_017876095.1	s__Azospirillum agricola	76.7935	462	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	76.467	295	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359855.1	s__Parvibaculum sp014359855	76.4327	120	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	76.3665	178	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:33,666] [INFO] GTDB search result was written to GCF_003173035.1_ASM317303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:33,666] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:33,670] [INFO] DFAST_QC result json was written to GCF_003173035.1_ASM317303v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:33,670] [INFO] DFAST_QC completed!
[2024-01-24 13:11:33,671] [INFO] Total running time: 0h1m33s