[2024-01-24 13:21:11,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d991612-7560-4cdf-9d8d-58dea19a9a65/dqc_reference
[2024-01-24 13:21:12,211] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,212] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,212] [INFO] Running command: gunzip -c /var/lib/cwl/stgc10f8535-f3d6-4351-a180-7c7c3db68f3c/GCF_009792355.1_ASM979235v1_genomic.fna.gz | prodigal -d GCF_009792355.1_ASM979235v1_genomic.fna/cds.fna -a GCF_009792355.1_ASM979235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:24,537] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:24,538] [INFO] Task started: HMMsearch
[2024-01-24 13:21:24,538] [INFO] Running command: hmmsearch --tblout GCF_009792355.1_ASM979235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d991612-7560-4cdf-9d8d-58dea19a9a65/dqc_reference/reference_markers.hmm GCF_009792355.1_ASM979235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:24,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:24,814] [INFO] Found 6/6 markers.
[2024-01-24 13:21:24,850] [INFO] Query marker FASTA was written to GCF_009792355.1_ASM979235v1_genomic.fna/markers.fasta
[2024-01-24 13:21:24,850] [INFO] Task started: Blastn
[2024-01-24 13:21:24,850] [INFO] Running command: blastn -query GCF_009792355.1_ASM979235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d991612-7560-4cdf-9d8d-58dea19a9a65/dqc_reference/reference_markers.fasta -out GCF_009792355.1_ASM979235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:25,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:25,733] [INFO] Selected 34 target genomes.
[2024-01-24 13:21:25,733] [INFO] Target genome list was writen to GCF_009792355.1_ASM979235v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:25,778] [INFO] Task started: fastANI
[2024-01-24 13:21:25,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgc10f8535-f3d6-4351-a180-7c7c3db68f3c/GCF_009792355.1_ASM979235v1_genomic.fna.gz --refList GCF_009792355.1_ASM979235v1_genomic.fna/target_genomes.txt --output GCF_009792355.1_ASM979235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:47,506] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:47,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d991612-7560-4cdf-9d8d-58dea19a9a65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:47,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d991612-7560-4cdf-9d8d-58dea19a9a65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:47,528] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:21:47,529] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:21:47,529] [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
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	76.7824	148	1288	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	76.7371	151	1288	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	76.5913	118	1288	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	76.4383	98	1288	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	76.4342	60	1288	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.4275	58	1288	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	76.4173	104	1288	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.3938	59	1288	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	76.2777	109	1288	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.272	104	1288	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	76.2645	104	1288	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	76.2132	152	1288	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	76.1803	136	1288	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	76.1739	85	1288	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	76.1616	147	1288	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.1243	107	1288	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	76.1003	93	1288	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	76.0819	87	1288	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.0739	123	1288	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009372075.1	1439888	1439888	type	True	75.9976	87	1288	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.9882	125	1288	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	75.9813	88	1288	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	75.9774	88	1288	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.924	116	1288	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	75.9181	98	1288	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	75.8411	100	1288	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.7962	132	1288	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.7273	95	1288	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_900187365.1	1074	1074	suspected-type	True	75.7017	97	1288	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	75.6925	97	1288	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.6441	113	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:47,531] [INFO] DFAST Taxonomy check result was written to GCF_009792355.1_ASM979235v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:47,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:47,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:47,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d991612-7560-4cdf-9d8d-58dea19a9a65/dqc_reference/checkm_data
[2024-01-24 13:21:47,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:47,571] [INFO] Task started: CheckM
[2024-01-24 13:21:47,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009792355.1_ASM979235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009792355.1_ASM979235v1_genomic.fna/checkm_input GCF_009792355.1_ASM979235v1_genomic.fna/checkm_result
[2024-01-24 13:22:27,073] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:27,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:27,095] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:27,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:27,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009792355.1_ASM979235v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:27,096] [INFO] Task started: Blastn
[2024-01-24 13:22:27,096] [INFO] Running command: blastn -query GCF_009792355.1_ASM979235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d991612-7560-4cdf-9d8d-58dea19a9a65/dqc_reference/reference_markers_gtdb.fasta -out GCF_009792355.1_ASM979235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:28,812] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:28,815] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:28,816] [INFO] Target genome list was writen to GCF_009792355.1_ASM979235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:28,851] [INFO] Task started: fastANI
[2024-01-24 13:22:28,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgc10f8535-f3d6-4351-a180-7c7c3db68f3c/GCF_009792355.1_ASM979235v1_genomic.fna.gz --refList GCF_009792355.1_ASM979235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009792355.1_ASM979235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:40,012] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:40,031] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:40,031] [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_009792355.1	s__Terricaulis silvestris	100.0	1287	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003242075.1	s__Terricaulis sp003242075	80.8066	634	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703335.1	s__Terricaulis sp016703335	80.2311	587	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	97.50	97.50	0.87	0.87	2	-
GCA_900696695.1	s__Terricaulis sp900696695	80.1499	555	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	99.53	99.53	0.91	0.91	2	-
GCA_001464425.1	s__Terricaulis sp001464425	79.8863	585	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378995.1	s__Terricaulis sp014378995	79.7546	543	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791365.1	s__Terricaulis sp016791365	79.7034	586	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303355.1	s__Terricaulis sp017303355	79.6123	600	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791385.1	s__Terricaulis sp016791385	79.3729	461	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001679665.1	s__Terricaulis sp001679665	79.072	528	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241475.1	s__Terricaulis sp018241475	78.483	337	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791325.1	s__Terricaulis sp016791325	78.4753	261	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793775.1	s__Sphingopyxis sp016793775	75.7624	96	1288	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:40,033] [INFO] GTDB search result was written to GCF_009792355.1_ASM979235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:40,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:40,041] [INFO] DFAST_QC result json was written to GCF_009792355.1_ASM979235v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:40,041] [INFO] DFAST_QC completed!
[2024-01-24 13:22:40,041] [INFO] Total running time: 0h1m29s