[2024-01-25 17:40:35,545] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:35,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:35,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg03bedbfb-997d-4faa-9850-d7fdb94775a9/dqc_reference
[2024-01-25 17:40:36,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:36,756] [INFO] Task started: Prodigal
[2024-01-25 17:40:36,756] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5eb38be-74f0-4276-910b-9686fb24d490/GCF_017963645.1_ASM1796364v1_genomic.fna.gz | prodigal -d GCF_017963645.1_ASM1796364v1_genomic.fna/cds.fna -a GCF_017963645.1_ASM1796364v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:47,315] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:47,315] [INFO] Task started: HMMsearch
[2024-01-25 17:40:47,315] [INFO] Running command: hmmsearch --tblout GCF_017963645.1_ASM1796364v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03bedbfb-997d-4faa-9850-d7fdb94775a9/dqc_reference/reference_markers.hmm GCF_017963645.1_ASM1796364v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:47,539] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:47,540] [INFO] Found 6/6 markers.
[2024-01-25 17:40:47,575] [INFO] Query marker FASTA was written to GCF_017963645.1_ASM1796364v1_genomic.fna/markers.fasta
[2024-01-25 17:40:47,575] [INFO] Task started: Blastn
[2024-01-25 17:40:47,575] [INFO] Running command: blastn -query GCF_017963645.1_ASM1796364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03bedbfb-997d-4faa-9850-d7fdb94775a9/dqc_reference/reference_markers.fasta -out GCF_017963645.1_ASM1796364v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:48,466] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:48,469] [INFO] Selected 27 target genomes.
[2024-01-25 17:40:48,470] [INFO] Target genome list was writen to GCF_017963645.1_ASM1796364v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:48,487] [INFO] Task started: fastANI
[2024-01-25 17:40:48,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eb38be-74f0-4276-910b-9686fb24d490/GCF_017963645.1_ASM1796364v1_genomic.fna.gz --refList GCF_017963645.1_ASM1796364v1_genomic.fna/target_genomes.txt --output GCF_017963645.1_ASM1796364v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:13,000] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:13,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03bedbfb-997d-4faa-9850-d7fdb94775a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:13,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03bedbfb-997d-4faa-9850-d7fdb94775a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:13,016] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:13,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:13,016] [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
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	100.0	1381	1383	95	conclusive
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	77.2641	305	1383	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.0709	238	1383	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.8056	223	1383	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	76.7935	171	1383	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.5226	365	1383	95	below_threshold
Algihabitans albus	strain=HHTR 118	GCA_003572205.1	2164067	2164067	type	True	76.4867	172	1383	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.4785	364	1383	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.4641	195	1383	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.4495	279	1383	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	76.4354	180	1383	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.4097	319	1383	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	76.4078	162	1383	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.4023	215	1383	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.3548	264	1383	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.3305	252	1383	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.2798	265	1383	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.2522	164	1383	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.2439	198	1383	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1289	212	1383	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.0958	208	1383	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	76.0657	171	1383	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	76.0319	170	1383	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	75.9791	136	1383	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	75.9602	216	1383	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	75.7114	155	1383	95	below_threshold
Sphingomonas montana	strain=W16RD	GCA_001956315.1	1843236	1843236	type	True	75.6224	118	1383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:13,017] [INFO] DFAST Taxonomy check result was written to GCF_017963645.1_ASM1796364v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:13,018] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:13,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:13,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03bedbfb-997d-4faa-9850-d7fdb94775a9/dqc_reference/checkm_data
[2024-01-25 17:41:13,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:13,074] [INFO] Task started: CheckM
[2024-01-25 17:41:13,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017963645.1_ASM1796364v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017963645.1_ASM1796364v1_genomic.fna/checkm_input GCF_017963645.1_ASM1796364v1_genomic.fna/checkm_result
[2024-01-25 17:41:44,820] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:44,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:44,840] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:44,840] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:44,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017963645.1_ASM1796364v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:44,841] [INFO] Task started: Blastn
[2024-01-25 17:41:44,841] [INFO] Running command: blastn -query GCF_017963645.1_ASM1796364v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03bedbfb-997d-4faa-9850-d7fdb94775a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017963645.1_ASM1796364v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:46,625] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:46,629] [INFO] Selected 24 target genomes.
[2024-01-25 17:41:46,629] [INFO] Target genome list was writen to GCF_017963645.1_ASM1796364v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:46,643] [INFO] Task started: fastANI
[2024-01-25 17:41:46,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eb38be-74f0-4276-910b-9686fb24d490/GCF_017963645.1_ASM1796364v1_genomic.fna.gz --refList GCF_017963645.1_ASM1796364v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017963645.1_ASM1796364v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:42:10,182] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:10,197] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:42:10,197] [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_017963645.1	s__Marivibrio halodurans	100.0	1381	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Marivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017792345.1	s__GCA-2696645 sp017792345	77.6346	376	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCA_012926505.1	s__GCA-2696645 sp012926505	77.2649	304	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.802	219	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.5467	215	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003119115.1	s__Azospirillum sp003119115	76.5365	289	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_004005845.1	s__Hwanghaeella grinnelliae	76.511	194	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003572205.1	s__Algihabitans albus	76.4864	172	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423485.1	s__Azospirillum oleiclasticum	76.4496	279	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000312425.1	s__Reyranella massiliensis	76.3815	162	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	76.3762	173	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.3685	277	1383	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_000429625.1	s__Azospirillum halopraeferens	76.3456	249	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	76.343	229	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	76.3086	199	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	76.2767	266	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297405.1	s__Reyranella sp004297405	76.2411	167	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932745.1	s__Xanthobacter sp012932745	76.1903	170	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	97.23	97.23	0.90	0.90	2	-
GCA_011620265.1	s__Albidovulum sp011620265	76.1406	140	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250275.1	s__Alpha-05 sp003250275	76.0776	138	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	76.0195	217	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	75.9129	277	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975005.1	s__17J80-11 sp010975005	75.7487	132	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195115.1	s__JACQAI01 sp016195115	75.3611	156	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__JACQAI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:42:10,199] [INFO] GTDB search result was written to GCF_017963645.1_ASM1796364v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:42:10,199] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:42:10,203] [INFO] DFAST_QC result json was written to GCF_017963645.1_ASM1796364v1_genomic.fna/dqc_result.json
[2024-01-25 17:42:10,203] [INFO] DFAST_QC completed!
[2024-01-25 17:42:10,204] [INFO] Total running time: 0h1m35s