[2024-01-24 14:14:21,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:21,276] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:21,277] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcef55b0-8d12-4f11-8e66-2ef05d27c2a6/dqc_reference
[2024-01-24 14:14:24,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:24,208] [INFO] Task started: Prodigal
[2024-01-24 14:14:24,208] [INFO] Running command: gunzip -c /var/lib/cwl/stgef0eff5f-e355-4995-a22e-500a4972691c/GCF_012641365.1_ASM1264136v1_genomic.fna.gz | prodigal -d GCF_012641365.1_ASM1264136v1_genomic.fna/cds.fna -a GCF_012641365.1_ASM1264136v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:36,741] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:36,741] [INFO] Task started: HMMsearch
[2024-01-24 14:14:36,741] [INFO] Running command: hmmsearch --tblout GCF_012641365.1_ASM1264136v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcef55b0-8d12-4f11-8e66-2ef05d27c2a6/dqc_reference/reference_markers.hmm GCF_012641365.1_ASM1264136v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:37,147] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:37,150] [INFO] Found 6/6 markers.
[2024-01-24 14:14:37,199] [INFO] Query marker FASTA was written to GCF_012641365.1_ASM1264136v1_genomic.fna/markers.fasta
[2024-01-24 14:14:37,204] [INFO] Task started: Blastn
[2024-01-24 14:14:37,204] [INFO] Running command: blastn -query GCF_012641365.1_ASM1264136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcef55b0-8d12-4f11-8e66-2ef05d27c2a6/dqc_reference/reference_markers.fasta -out GCF_012641365.1_ASM1264136v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:38,506] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:38,511] [INFO] Selected 28 target genomes.
[2024-01-24 14:14:38,512] [INFO] Target genome list was writen to GCF_012641365.1_ASM1264136v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:38,524] [INFO] Task started: fastANI
[2024-01-24 14:14:38,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0eff5f-e355-4995-a22e-500a4972691c/GCF_012641365.1_ASM1264136v1_genomic.fna.gz --refList GCF_012641365.1_ASM1264136v1_genomic.fna/target_genomes.txt --output GCF_012641365.1_ASM1264136v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:02,661] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:02,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcef55b0-8d12-4f11-8e66-2ef05d27c2a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:02,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcef55b0-8d12-4f11-8e66-2ef05d27c2a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:02,688] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:02,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:02,688] [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
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	100.0	1179	1179	95	conclusive
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	77.7166	207	1179	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	77.5774	215	1179	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	77.551	220	1179	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	77.5108	190	1179	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	77.5064	193	1179	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	77.4865	201	1179	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	77.4626	210	1179	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	77.4218	208	1179	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	77.381	199	1179	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	77.3279	192	1179	95	below_threshold
Leeia oryzae	strain=DSM 17879	GCA_000376945.1	356662	356662	type	True	77.3263	233	1179	95	below_threshold
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	77.3099	182	1179	95	below_threshold
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	77.2294	149	1179	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001517245.1	375574	375574	type	True	77.2072	158	1179	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001418035.1	375574	375574	type	True	77.1729	160	1179	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1365	140	1179	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	77.0568	200	1179	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	76.868	156	1179	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	76.8574	107	1179	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	76.6918	138	1179	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	76.6707	140	1179	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.5935	89	1179	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	76.5867	166	1179	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.551	92	1179	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.5228	163	1179	95	below_threshold
Natronospirillum operosum	strain=G-116	GCA_004768465.1	2759953	2759953	type	True	75.9825	52	1179	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	75.5882	98	1179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:02,690] [INFO] DFAST Taxonomy check result was written to GCF_012641365.1_ASM1264136v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:02,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:02,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:02,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcef55b0-8d12-4f11-8e66-2ef05d27c2a6/dqc_reference/checkm_data
[2024-01-24 14:15:02,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:02,732] [INFO] Task started: CheckM
[2024-01-24 14:15:02,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012641365.1_ASM1264136v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012641365.1_ASM1264136v1_genomic.fna/checkm_input GCF_012641365.1_ASM1264136v1_genomic.fna/checkm_result
[2024-01-24 14:15:46,812] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:46,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:46,836] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:46,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:46,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012641365.1_ASM1264136v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:46,837] [INFO] Task started: Blastn
[2024-01-24 14:15:46,837] [INFO] Running command: blastn -query GCF_012641365.1_ASM1264136v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcef55b0-8d12-4f11-8e66-2ef05d27c2a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_012641365.1_ASM1264136v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:50,490] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:50,494] [INFO] Selected 27 target genomes.
[2024-01-24 14:15:50,494] [INFO] Target genome list was writen to GCF_012641365.1_ASM1264136v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:50,522] [INFO] Task started: fastANI
[2024-01-24 14:15:50,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0eff5f-e355-4995-a22e-500a4972691c/GCF_012641365.1_ASM1264136v1_genomic.fna.gz --refList GCF_012641365.1_ASM1264136v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012641365.1_ASM1264136v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:09,732] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:09,795] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:09,796] [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_012641365.1	s__Leeia aquatica	100.0	1179	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Leeiaceae;g__Leeia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003201855.1	s__Rivicola pingtungensis	77.7329	206	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008275125.1	s__Chromobacterium paludis	77.6795	210	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829295.1	s__Vogesella oryzae	77.6115	207	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428465.1	s__Chitinimonas koreensis	77.5634	216	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855565.1	s__Chromobacterium amazonense	77.5247	189	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_016428945.1	s__Chromobacterium sp016428945	77.5179	196	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_900176275.1	s__Andreprevotia lacus	77.4853	201	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202035.1	s__Aquitalea magnusonii	77.459	237	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	99.21	98.53	0.95	0.91	3	-
GCF_018802765.1	s__Paludibacterium sp018802765	77.4093	156	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	77.4035	254	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376945.1	s__Leeia oryzae	77.3263	233	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Leeiaceae;g__Leeia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119825.1	s__Chitinimonas taiwanensis	77.31	182	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	96.92	96.91	0.93	0.93	3	-
GCF_014645535.1	s__Silvimonas iriomotensis	77.2303	148	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855555.1	s__Chromobacterium sphagni	77.0434	201	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
GCF_017814915.1	s__Herbaspirillum sp017814915	76.9219	143	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234745.1	s__JAFAKZ01 sp019234745	76.8871	93	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__JAFAKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013363835.1	s__Azonexus sp013363835	76.5635	98	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549295.1	s__Azonexus sp900549295	76.5418	94	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.93	0.93	2	-
GCF_014042365.1	s__LX47W sp014042365	76.5228	163	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705475.1	s__Azonexus sp016705475	76.4468	69	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.40	98.37	0.84	0.83	3	-
GCF_900109645.1	s__Duganella sp900109645	76.4255	128	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900174485.1	s__Sterolibacterium denitrificans	76.4038	95	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sterolibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715485.1	s__Massilia sp006715485	76.3497	131	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720685.1	s__Zoogloea sp016720685	76.3077	110	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214145.1	s__Desulfobacillus sp016214145	76.1908	105	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842345.1	s__Azonexus sp002842345	76.1036	102	1179	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:09,797] [INFO] GTDB search result was written to GCF_012641365.1_ASM1264136v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:09,798] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:09,803] [INFO] DFAST_QC result json was written to GCF_012641365.1_ASM1264136v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:09,803] [INFO] DFAST_QC completed!
[2024-01-24 14:16:09,803] [INFO] Total running time: 0h1m49s