[2024-01-25 20:14:50,352] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,353] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea75222-c244-4236-9016-bbf99b33d4ac/dqc_reference
[2024-01-25 20:14:51,431] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,431] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,432] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbe3cd66-0443-417c-87e8-777ac461a96d/GCF_030814015.1_ASM3081401v1_genomic.fna.gz | prodigal -d GCF_030814015.1_ASM3081401v1_genomic.fna/cds.fna -a GCF_030814015.1_ASM3081401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:03,062] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:03,062] [INFO] Task started: HMMsearch
[2024-01-25 20:15:03,063] [INFO] Running command: hmmsearch --tblout GCF_030814015.1_ASM3081401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea75222-c244-4236-9016-bbf99b33d4ac/dqc_reference/reference_markers.hmm GCF_030814015.1_ASM3081401v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:03,356] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:03,357] [INFO] Found 6/6 markers.
[2024-01-25 20:15:03,397] [INFO] Query marker FASTA was written to GCF_030814015.1_ASM3081401v1_genomic.fna/markers.fasta
[2024-01-25 20:15:03,397] [INFO] Task started: Blastn
[2024-01-25 20:15:03,397] [INFO] Running command: blastn -query GCF_030814015.1_ASM3081401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea75222-c244-4236-9016-bbf99b33d4ac/dqc_reference/reference_markers.fasta -out GCF_030814015.1_ASM3081401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:04,384] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:04,391] [INFO] Selected 30 target genomes.
[2024-01-25 20:15:04,391] [INFO] Target genome list was writen to GCF_030814015.1_ASM3081401v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:04,408] [INFO] Task started: fastANI
[2024-01-25 20:15:04,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe3cd66-0443-417c-87e8-777ac461a96d/GCF_030814015.1_ASM3081401v1_genomic.fna.gz --refList GCF_030814015.1_ASM3081401v1_genomic.fna/target_genomes.txt --output GCF_030814015.1_ASM3081401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:32,248] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:32,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea75222-c244-4236-9016-bbf99b33d4ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:32,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea75222-c244-4236-9016-bbf99b33d4ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:32,265] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:15:32,265] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:15:32,265] [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
Amorphus coralli	strain=DSM 19760	GCA_000374525.1	340680	340680	type	True	81.1509	848	1565	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	78.0976	417	1565	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	78.0063	413	1565	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.9646	384	1565	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.7156	434	1565	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.7004	310	1565	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.6988	341	1565	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	77.5983	436	1565	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	77.5848	414	1565	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.5799	352	1565	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.5377	313	1565	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.5157	356	1565	95	below_threshold
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	77.4032	439	1565	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.2645	236	1565	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	77.2331	297	1565	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.2204	351	1565	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.2155	374	1565	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.1889	320	1565	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	77.1852	304	1565	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	77.1662	289	1565	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	77.1316	301	1565	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	77.1171	312	1565	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.114	314	1565	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	77.0785	227	1565	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	77.0095	316	1565	95	below_threshold
Bradyrhizobium uaiense	strain=UFLA03-164	GCA_010811875.1	2594946	2594946	type	True	76.9874	294	1565	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.9623	348	1565	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.9121	284	1565	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.9043	298	1565	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	76.7657	165	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:32,267] [INFO] DFAST Taxonomy check result was written to GCF_030814015.1_ASM3081401v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:32,268] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:32,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:32,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea75222-c244-4236-9016-bbf99b33d4ac/dqc_reference/checkm_data
[2024-01-25 20:15:32,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:32,312] [INFO] Task started: CheckM
[2024-01-25 20:15:32,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814015.1_ASM3081401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814015.1_ASM3081401v1_genomic.fna/checkm_input GCF_030814015.1_ASM3081401v1_genomic.fna/checkm_result
[2024-01-25 20:16:11,843] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:11,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:11,884] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:11,884] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:11,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814015.1_ASM3081401v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:11,886] [INFO] Task started: Blastn
[2024-01-25 20:16:11,886] [INFO] Running command: blastn -query GCF_030814015.1_ASM3081401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea75222-c244-4236-9016-bbf99b33d4ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814015.1_ASM3081401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:13,973] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:13,976] [INFO] Selected 28 target genomes.
[2024-01-25 20:16:13,977] [INFO] Target genome list was writen to GCF_030814015.1_ASM3081401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:13,999] [INFO] Task started: fastANI
[2024-01-25 20:16:13,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbe3cd66-0443-417c-87e8-777ac461a96d/GCF_030814015.1_ASM3081401v1_genomic.fna.gz --refList GCF_030814015.1_ASM3081401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814015.1_ASM3081401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:38,865] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:38,881] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:16:38,881] [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_000374525.1	s__Amorphus coralli	81.1225	852	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	78.0097	412	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_900185725.1	s__Stappia sp900185725	77.9797	409	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_001696535.1	s__Stappia indica	77.9552	408	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_003610575.1	s__Stappia sp003610575	77.9177	392	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_009789575.1	s__Stappia indica_A	77.9045	414	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	77.8825	391	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900231165.1	s__Hartmannibacter diazotrophicus	77.824	319	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Hartmannibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148505.1	s__Pseudoxanthobacter soli	77.7075	391	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	77.689	431	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_013839525.1	s__Mongoliimonas rhizosphaerae	77.6186	360	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421645.1	s__Aurantimonas coralicida	77.6023	337	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_016411865.1	s__Acuticoccus sp016411865	77.5706	415	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	77.5058	357	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187085.1	s__Pseudorhodoplanes sp019187085	77.505	234	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	98.90	98.90	0.85	0.85	2	-
GCA_017305835.1	s__RCIO01 sp017305835	77.4615	370	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517025.1	s__Pinisolibacter sp012517025	77.4593	271	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	77.4428	335	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258595.1	s__Acuticoccus sediminis	77.3938	441	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722295.1	s__Stappia sp002722295	77.382	303	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
GCF_009910705.1	s__Microvirga sp009910705	77.3497	238	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014904745.1	s__Oricola sp014904745	77.2994	302	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826895.1	s__Hongsoonwoonella sp009826895	77.2855	244	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482425.1	s__Bradyrhizobium japonicum_B	77.1449	289	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518665.1	s__Microvirga flocculans	77.0897	225	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018131075.1	s__Bradyrhizobium sp018131075	76.8463	238	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133345.1	s__Pseudolabrys sp003133345	76.5264	168	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	96.45	96.45	0.86	0.86	2	-
GCA_019237215.1	s__VAZQ01 sp019237215	76.3992	154	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__VAZQ01	95.0	98.63	98.51	0.77	0.77	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:38,882] [INFO] GTDB search result was written to GCF_030814015.1_ASM3081401v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:38,883] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:38,888] [INFO] DFAST_QC result json was written to GCF_030814015.1_ASM3081401v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:38,888] [INFO] DFAST_QC completed!
[2024-01-25 20:16:38,888] [INFO] Total running time: 0h1m49s