[2023-06-27 17:27:12,297] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:27:12,305] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:27:12,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgea940a67-790f-4b53-bad6-b00af1e1c256/dqc_reference
[2023-06-27 17:27:14,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:27:14,393] [INFO] Task started: Prodigal
[2023-06-27 17:27:14,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg75a5c326-82ac-4f0f-8ff0-9f5a34626e7b/GCA_002083445.1_ASM208344v1_genomic.fna.gz | prodigal -d GCA_002083445.1_ASM208344v1_genomic.fna/cds.fna -a GCA_002083445.1_ASM208344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:27:23,673] [INFO] Task succeeded: Prodigal
[2023-06-27 17:27:23,674] [INFO] Task started: HMMsearch
[2023-06-27 17:27:23,674] [INFO] Running command: hmmsearch --tblout GCA_002083445.1_ASM208344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea940a67-790f-4b53-bad6-b00af1e1c256/dqc_reference/reference_markers.hmm GCA_002083445.1_ASM208344v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:27:23,874] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:27:23,876] [INFO] Found 6/6 markers.
[2023-06-27 17:27:23,904] [INFO] Query marker FASTA was written to GCA_002083445.1_ASM208344v1_genomic.fna/markers.fasta
[2023-06-27 17:27:23,904] [INFO] Task started: Blastn
[2023-06-27 17:27:23,904] [INFO] Running command: blastn -query GCA_002083445.1_ASM208344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea940a67-790f-4b53-bad6-b00af1e1c256/dqc_reference/reference_markers.fasta -out GCA_002083445.1_ASM208344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:27:24,685] [INFO] Task succeeded: Blastn
[2023-06-27 17:27:24,690] [INFO] Selected 32 target genomes.
[2023-06-27 17:27:24,690] [INFO] Target genome list was writen to GCA_002083445.1_ASM208344v1_genomic.fna/target_genomes.txt
[2023-06-27 17:27:24,693] [INFO] Task started: fastANI
[2023-06-27 17:27:24,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg75a5c326-82ac-4f0f-8ff0-9f5a34626e7b/GCA_002083445.1_ASM208344v1_genomic.fna.gz --refList GCA_002083445.1_ASM208344v1_genomic.fna/target_genomes.txt --output GCA_002083445.1_ASM208344v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:27:52,058] [INFO] Task succeeded: fastANI
[2023-06-27 17:27:52,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea940a67-790f-4b53-bad6-b00af1e1c256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:27:52,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea940a67-790f-4b53-bad6-b00af1e1c256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:27:52,081] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:27:52,081] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 17:27:52,082] [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
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.7608	130	993	95	below_threshold
Rhabdaerophilum calidifontis	strain=SYSU G02060	GCA_008641065.1	2604328	2604328	type	True	76.6146	138	993	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.5549	151	993	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	76.4748	128	993	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.4608	134	993	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	76.4537	172	993	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	76.4351	146	993	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.3218	130	993	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	76.3075	66	993	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	76.2968	146	993	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	76.2575	103	993	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.24	100	993	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.2309	108	993	95	below_threshold
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	76.2017	122	993	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.1863	88	993	95	below_threshold
Methylobacterium symbioticum	strain=SB0023/3	GCA_902141845.1	2584084	2584084	type	True	76.1554	90	993	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	76.1483	140	993	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.1444	115	993	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	76.115	133	993	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.0853	102	993	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_003258905.1	1080	1080	type	True	76.0695	69	993	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	76.0695	69	993	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_016584015.1	1080	1080	type	True	76.0695	69	993	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.0586	103	993	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	76.0418	98	993	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	76.0326	128	993	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	76.0024	149	993	95	below_threshold
Nitrobacter hamburgensis	strain=X14	GCA_000013885.1	912	912	type	True	75.9144	69	993	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	75.846	88	993	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	75.8037	69	993	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	75.7754	107	993	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_018398275.1	28210	28210	type	True	75.7503	109	993	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 17:27:52,084] [INFO] DFAST Taxonomy check result was written to GCA_002083445.1_ASM208344v1_genomic.fna/tc_result.tsv
[2023-06-27 17:27:52,084] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:27:52,085] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:27:52,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea940a67-790f-4b53-bad6-b00af1e1c256/dqc_reference/checkm_data
[2023-06-27 17:27:52,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:27:52,115] [INFO] Task started: CheckM
[2023-06-27 17:27:52,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002083445.1_ASM208344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002083445.1_ASM208344v1_genomic.fna/checkm_input GCA_002083445.1_ASM208344v1_genomic.fna/checkm_result
[2023-06-27 17:28:23,376] [INFO] Task succeeded: CheckM
[2023-06-27 17:28:23,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:28:23,402] [INFO] ===== Completeness check finished =====
[2023-06-27 17:28:23,402] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:28:23,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002083445.1_ASM208344v1_genomic.fna/markers.fasta)
[2023-06-27 17:28:23,403] [INFO] Task started: Blastn
[2023-06-27 17:28:23,403] [INFO] Running command: blastn -query GCA_002083445.1_ASM208344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea940a67-790f-4b53-bad6-b00af1e1c256/dqc_reference/reference_markers_gtdb.fasta -out GCA_002083445.1_ASM208344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:28:24,844] [INFO] Task succeeded: Blastn
[2023-06-27 17:28:24,848] [INFO] Selected 29 target genomes.
[2023-06-27 17:28:24,848] [INFO] Target genome list was writen to GCA_002083445.1_ASM208344v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:28:24,859] [INFO] Task started: fastANI
[2023-06-27 17:28:24,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg75a5c326-82ac-4f0f-8ff0-9f5a34626e7b/GCA_002083445.1_ASM208344v1_genomic.fna.gz --refList GCA_002083445.1_ASM208344v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002083445.1_ASM208344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:28:46,536] [INFO] Task succeeded: fastANI
[2023-06-27 17:28:46,557] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:28:46,558] [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_002365175.1	s__UBA4765 sp002365175	99.924	953	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__UBA4765;g__UBA4765	95.0	99.31	95.36	0.97	0.94	8	conclusive
GCF_003046185.1	s__Phreatobacter oligotrophus	76.5549	151	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002982075.1	s__Labrys okinawensis	76.4804	136	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Labraceae;g__Labrys	95.0	98.61	98.61	0.96	0.96	2	-
GCA_000017645.1	s__Xanthobacter autotrophicus	76.4539	105	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	76.444	124	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102525.1	s__Bosea robiniae	76.4351	146	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.62	97.45	0.92	0.88	4	-
GCA_016716745.1	s__GCA-013693735 sp016716745	76.4336	158	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005160265.1	s__Phreatobacter sp005160265	76.4057	154	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012971745.1	s__ORNL1 sp012971745	76.3791	135	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__ORNL1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970465.2	s__Devosia_A insulae	76.3075	66	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390555.1	s__Ancylobacter_B oerskovii	76.3021	147	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	76.2714	100	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	76.2575	103	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517025.1	s__Pinisolibacter sp012517025	76.2426	81	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364685.1	s__Xanthobacter sp008364685	76.24	100	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898965.1	s__28-YEA-48 sp001898965	76.2375	131	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016219575.1	s__Bradyrhizobium sp016219575	76.2334	126	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635325.1	s__Azorhizobium oxalatiphilum	76.1889	123	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304555.1	s__JAFKKS01 sp017304555	76.1843	77	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__JAFKKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	76.0993	136	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102695.1	s__Afifella marina	76.0695	69	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	99.99	99.99	1.00	0.99	5	-
GCF_000010525.1	s__Azorhizobium caulinodans	76.0326	128	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCF_015624485.1	s__Bradyrhizobium sp015624485	76.0193	139	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907975.1	s__Methylopila capsulata	76.0056	91	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Methylopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173755.1	s__Methylobacterium terrae	76.004	115	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307495.1	s__Devosia_A sp017307495	75.8672	62	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCF_018130505.1	s__Bradyrhizobium tropiciagri_B	75.81	131	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655535.1	s__Methyloferula sp015655535	75.6877	50	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methyloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006376685.1	s__Ochrobactrum_B teleogrylli	75.3622	64	993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.13	98.09	0.91	0.90	5	-
--------------------------------------------------------------------------------
[2023-06-27 17:28:46,560] [INFO] GTDB search result was written to GCA_002083445.1_ASM208344v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:28:46,560] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:28:46,566] [INFO] DFAST_QC result json was written to GCA_002083445.1_ASM208344v1_genomic.fna/dqc_result.json
[2023-06-27 17:28:46,566] [INFO] DFAST_QC completed!
[2023-06-27 17:28:46,566] [INFO] Total running time: 0h1m34s