[2023-06-19 08:35:39,595] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:35:39,598] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:35:39,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d9e94ad-20f3-4b35-821f-ca3793f9b295/dqc_reference
[2023-06-19 08:35:40,880] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:35:40,882] [INFO] Task started: Prodigal
[2023-06-19 08:35:40,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg51b75cb8-7597-48de-b6fd-707fbfaec31e/GCA_018269075.1_ASM1826907v1_genomic.fna.gz | prodigal -d GCA_018269075.1_ASM1826907v1_genomic.fna/cds.fna -a GCA_018269075.1_ASM1826907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:35:55,744] [INFO] Task succeeded: Prodigal
[2023-06-19 08:35:55,745] [INFO] Task started: HMMsearch
[2023-06-19 08:35:55,745] [INFO] Running command: hmmsearch --tblout GCA_018269075.1_ASM1826907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d9e94ad-20f3-4b35-821f-ca3793f9b295/dqc_reference/reference_markers.hmm GCA_018269075.1_ASM1826907v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:35:56,107] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:35:56,109] [INFO] Found 6/6 markers.
[2023-06-19 08:35:56,186] [INFO] Query marker FASTA was written to GCA_018269075.1_ASM1826907v1_genomic.fna/markers.fasta
[2023-06-19 08:35:56,187] [INFO] Task started: Blastn
[2023-06-19 08:35:56,187] [INFO] Running command: blastn -query GCA_018269075.1_ASM1826907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9e94ad-20f3-4b35-821f-ca3793f9b295/dqc_reference/reference_markers.fasta -out GCA_018269075.1_ASM1826907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:35:56,835] [INFO] Task succeeded: Blastn
[2023-06-19 08:35:56,839] [INFO] Selected 31 target genomes.
[2023-06-19 08:35:56,839] [INFO] Target genome list was writen to GCA_018269075.1_ASM1826907v1_genomic.fna/target_genomes.txt
[2023-06-19 08:35:56,845] [INFO] Task started: fastANI
[2023-06-19 08:35:56,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg51b75cb8-7597-48de-b6fd-707fbfaec31e/GCA_018269075.1_ASM1826907v1_genomic.fna.gz --refList GCA_018269075.1_ASM1826907v1_genomic.fna/target_genomes.txt --output GCA_018269075.1_ASM1826907v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:36:21,284] [INFO] Task succeeded: fastANI
[2023-06-19 08:36:21,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d9e94ad-20f3-4b35-821f-ca3793f9b295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:36:21,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d9e94ad-20f3-4b35-821f-ca3793f9b295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:36:21,310] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:36:21,310] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:36:21,311] [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
Rhizobium metallidurans	strain=DSM 26575	GCA_014196505.1	1265931	1265931	type	True	74.9057	68	2385	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.8777	98	2385	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	74.8622	65	2385	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	74.848	61	2385	95	below_threshold
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	74.8064	111	2385	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	74.7975	70	2385	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	74.7936	106	2385	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	74.7422	104	2385	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	74.7363	116	2385	95	below_threshold
Burkholderia ambifaria	strain=AMMD	GCA_000959545.1	152480	152480	type	True	74.7253	250	2385	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	74.7197	71	2385	95	below_threshold
Burkholderia ambifaria	strain=AMMD	GCA_000203915.1	152480	152480	type	True	74.7136	255	2385	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	74.7096	82	2385	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.7095	257	2385	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.7093	328	2385	95	below_threshold
Actinomadura rubteroloni	strain=RB29	GCA_002911665.1	1926885	1926885	type	True	74.7047	235	2385	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.6957	159	2385	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	74.691	151	2385	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	74.69	50	2385	95	below_threshold
Actinomadura rayongensis	strain=DSM 102126	GCA_009831215.1	1429076	1429076	type	True	74.6707	241	2385	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	74.6328	82	2385	95	below_threshold
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	74.6232	257	2385	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	74.6161	87	2385	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	74.6161	194	2385	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:36:21,313] [INFO] DFAST Taxonomy check result was written to GCA_018269075.1_ASM1826907v1_genomic.fna/tc_result.tsv
[2023-06-19 08:36:21,315] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:36:21,315] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:36:21,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d9e94ad-20f3-4b35-821f-ca3793f9b295/dqc_reference/checkm_data
[2023-06-19 08:36:21,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:36:21,394] [INFO] Task started: CheckM
[2023-06-19 08:36:21,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018269075.1_ASM1826907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018269075.1_ASM1826907v1_genomic.fna/checkm_input GCA_018269075.1_ASM1826907v1_genomic.fna/checkm_result
[2023-06-19 08:37:06,398] [INFO] Task succeeded: CheckM
[2023-06-19 08:37:06,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:37:06,431] [INFO] ===== Completeness check finished =====
[2023-06-19 08:37:06,431] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:37:06,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018269075.1_ASM1826907v1_genomic.fna/markers.fasta)
[2023-06-19 08:37:06,432] [INFO] Task started: Blastn
[2023-06-19 08:37:06,432] [INFO] Running command: blastn -query GCA_018269075.1_ASM1826907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9e94ad-20f3-4b35-821f-ca3793f9b295/dqc_reference/reference_markers_gtdb.fasta -out GCA_018269075.1_ASM1826907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:37:07,323] [INFO] Task succeeded: Blastn
[2023-06-19 08:37:07,331] [INFO] Selected 21 target genomes.
[2023-06-19 08:37:07,331] [INFO] Target genome list was writen to GCA_018269075.1_ASM1826907v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:37:07,343] [INFO] Task started: fastANI
[2023-06-19 08:37:07,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg51b75cb8-7597-48de-b6fd-707fbfaec31e/GCA_018269075.1_ASM1826907v1_genomic.fna.gz --refList GCA_018269075.1_ASM1826907v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018269075.1_ASM1826907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:37:27,572] [INFO] Task succeeded: fastANI
[2023-06-19 08:37:27,602] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:37:27,602] [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_018269075.1	s__JAFDVJ01 sp018269075	100.0	2370	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JAFDVJ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016715115.1	s__JAFDVJ01 sp016715115	77.5118	618	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JAFDVJ01	95.0	98.64	98.61	0.89	0.88	3	-
GCA_017983495.1	s__OLB17 sp017983495	76.1846	206	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	99.99	99.99	0.98	0.98	2	-
GCA_016712045.1	s__OLB17 sp016712045	76.1559	183	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005790265.1	s__SXVE01 sp005790265	76.1548	236	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__SXVE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700075.1	s__OLB17 sp016700075	76.1294	113	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805935.1	s__GCA-002050365 sp902805935	76.0834	260	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__GCA-002050365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826795.1	s__OLB17 sp902826795	76.0424	179	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716365.1	s__OLB17 sp016716365	76.0192	208	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713675.1	s__OLB17 sp016713675	76.0002	185	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	99.38	99.27	0.97	0.96	3	-
GCA_016700175.1	s__QQUY01 sp016700175	75.9726	200	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QQUY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140875.1	s__OLB17 sp013140875	75.9257	157	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718135.1	s__OLB17 sp016718135	75.8471	128	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	99.08	98.78	0.94	0.93	3	-
GCA_019247865.1	s__JACMLC01 sp019247865	75.7878	153	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACMLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247455.1	s__OLB17 sp019247455	75.7314	102	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379075.1	s__OLB17 sp014379075	75.6286	126	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__OLB17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050455.1	s__GCA-002050365 sp002050455	75.2658	73	2385	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__GCA-002050365	95.0	99.57	99.57	0.85	0.85	2	-
GCA_016861185.1	s__DSNY01 sp016861185	74.8797	171	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004105.1	s__Gemmatimonas sp013004105	74.8491	63	2385	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284255.1	s__Rubrivivax gelatinosus_A	74.799	183	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCA_903886975.1	s__Propionivibrio sp903886975	74.6638	56	2385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:37:27,604] [INFO] GTDB search result was written to GCA_018269075.1_ASM1826907v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:37:27,605] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:37:27,613] [INFO] DFAST_QC result json was written to GCA_018269075.1_ASM1826907v1_genomic.fna/dqc_result.json
[2023-06-19 08:37:27,613] [INFO] DFAST_QC completed!
[2023-06-19 08:37:27,613] [INFO] Total running time: 0h1m48s