[2023-06-29 04:01:20,443] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:01:20,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:01:20,445] [INFO] DQC Reference Directory: /var/lib/cwl/stgc031c3ca-0f7c-4402-b478-64b3131f2eab/dqc_reference
[2023-06-29 04:01:21,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:01:21,702] [INFO] Task started: Prodigal
[2023-06-29 04:01:21,702] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd13b5b5-f19e-442c-9d44-d8c14d3ac4a4/GCA_020441665.1_ASM2044166v1_genomic.fna.gz | prodigal -d GCA_020441665.1_ASM2044166v1_genomic.fna/cds.fna -a GCA_020441665.1_ASM2044166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:01:31,127] [INFO] Task succeeded: Prodigal
[2023-06-29 04:01:31,128] [INFO] Task started: HMMsearch
[2023-06-29 04:01:31,128] [INFO] Running command: hmmsearch --tblout GCA_020441665.1_ASM2044166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc031c3ca-0f7c-4402-b478-64b3131f2eab/dqc_reference/reference_markers.hmm GCA_020441665.1_ASM2044166v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:01:31,384] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:01:31,386] [INFO] Found 6/6 markers.
[2023-06-29 04:01:31,423] [INFO] Query marker FASTA was written to GCA_020441665.1_ASM2044166v1_genomic.fna/markers.fasta
[2023-06-29 04:01:31,424] [INFO] Task started: Blastn
[2023-06-29 04:01:31,424] [INFO] Running command: blastn -query GCA_020441665.1_ASM2044166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc031c3ca-0f7c-4402-b478-64b3131f2eab/dqc_reference/reference_markers.fasta -out GCA_020441665.1_ASM2044166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:01:32,354] [INFO] Task succeeded: Blastn
[2023-06-29 04:01:32,359] [INFO] Selected 34 target genomes.
[2023-06-29 04:01:32,359] [INFO] Target genome list was writen to GCA_020441665.1_ASM2044166v1_genomic.fna/target_genomes.txt
[2023-06-29 04:01:32,363] [INFO] Task started: fastANI
[2023-06-29 04:01:32,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd13b5b5-f19e-442c-9d44-d8c14d3ac4a4/GCA_020441665.1_ASM2044166v1_genomic.fna.gz --refList GCA_020441665.1_ASM2044166v1_genomic.fna/target_genomes.txt --output GCA_020441665.1_ASM2044166v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:02:08,570] [INFO] Task succeeded: fastANI
[2023-06-29 04:02:08,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc031c3ca-0f7c-4402-b478-64b3131f2eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:02:08,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc031c3ca-0f7c-4402-b478-64b3131f2eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:02:08,602] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:02:08,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:02:08,603] [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
Salaquimonas pukyongi	strain=RR3-28	GCA_001953055.1	2712698	2712698	type	True	79.0761	483	1023	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.7669	291	1023	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	77.7432	299	1023	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.7283	360	1023	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	77.7121	296	1023	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.6668	324	1023	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	77.6014	318	1023	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	77.5896	341	1023	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.5709	307	1023	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.534	327	1023	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	77.5044	317	1023	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.4973	337	1023	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.4876	342	1023	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	77.4463	271	1023	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	77.3145	246	1023	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	77.3125	340	1023	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.2704	290	1023	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	77.2123	288	1023	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	77.1949	296	1023	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	77.187	259	1023	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.1816	287	1023	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.1448	281	1023	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	77.0567	211	1023	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	76.8094	216	1023	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	76.7857	178	1023	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	76.5837	203	1023	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.5737	217	1023	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.4475	203	1023	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.3069	173	1023	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.2644	173	1023	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	75.9652	147	1023	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	75.9632	147	1023	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.9479	137	1023	95	below_threshold
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	75.8562	112	1023	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:02:08,605] [INFO] DFAST Taxonomy check result was written to GCA_020441665.1_ASM2044166v1_genomic.fna/tc_result.tsv
[2023-06-29 04:02:08,606] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:02:08,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:02:08,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc031c3ca-0f7c-4402-b478-64b3131f2eab/dqc_reference/checkm_data
[2023-06-29 04:02:08,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:02:08,645] [INFO] Task started: CheckM
[2023-06-29 04:02:08,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020441665.1_ASM2044166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020441665.1_ASM2044166v1_genomic.fna/checkm_input GCA_020441665.1_ASM2044166v1_genomic.fna/checkm_result
[2023-06-29 04:02:40,799] [INFO] Task succeeded: CheckM
[2023-06-29 04:02:40,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:02:40,827] [INFO] ===== Completeness check finished =====
[2023-06-29 04:02:40,827] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:02:40,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020441665.1_ASM2044166v1_genomic.fna/markers.fasta)
[2023-06-29 04:02:40,829] [INFO] Task started: Blastn
[2023-06-29 04:02:40,829] [INFO] Running command: blastn -query GCA_020441665.1_ASM2044166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc031c3ca-0f7c-4402-b478-64b3131f2eab/dqc_reference/reference_markers_gtdb.fasta -out GCA_020441665.1_ASM2044166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:02:42,591] [INFO] Task succeeded: Blastn
[2023-06-29 04:02:42,597] [INFO] Selected 32 target genomes.
[2023-06-29 04:02:42,597] [INFO] Target genome list was writen to GCA_020441665.1_ASM2044166v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:02:42,619] [INFO] Task started: fastANI
[2023-06-29 04:02:42,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd13b5b5-f19e-442c-9d44-d8c14d3ac4a4/GCA_020441665.1_ASM2044166v1_genomic.fna.gz --refList GCA_020441665.1_ASM2044166v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020441665.1_ASM2044166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:03:09,491] [INFO] Task succeeded: fastANI
[2023-06-29 04:03:09,516] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:03:09,516] [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_001953055.1	s__Salaquimonas pukyongi	79.0761	483	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Salaquimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	78.1379	388	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	77.7643	297	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000497755.1	s__Aliihoeflea sp000497755	77.7053	287	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331955.1	s__Roseitalea porphyridii	77.6487	300	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149475.2	s__Roseitalea stylonematis	77.6266	298	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	-
GCF_016839145.1	s__Shinella sp016839145	77.6186	326	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091085.1	s__Mesorhizobium sp019091085	77.6141	341	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341885.1	s__Shinella granuli	77.5987	340	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCA_002698425.1	s__Oricola sp002698425	77.5879	326	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115245.1	s__Mesorhizobium sp900115245	77.5647	326	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439355.1	s__Mesorhizobium sp006439355	77.5633	323	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	77.5187	349	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_001651875.1	s__Sinorhizobium saheli	77.4967	282	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	77.4818	317	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	77.4632	343	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006440735.1	s__Mesorhizobium sp006440735	77.4374	343	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896885.1	s__65-79 sp001896885	77.3458	293	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__65-79	95.0	99.97	99.97	0.97	0.97	2	-
GCA_017642895.1	s__Roseitalea sp017642895	77.289	285	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001696535.1	s__Stappia indica	77.2834	289	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_000378985.1	s__Sinorhizobium sp000378985	77.2615	261	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	77.2144	293	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970795.1	s__Mesorhizobium_E carbonis	77.2035	289	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	77.1925	285	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789575.1	s__Stappia indica_A	77.1451	303	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	77.0914	276	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_001425575.1	s__Leaf443 sp001425575	77.063	243	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466745.1	s__Bosea sp900466745	76.897	243	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_900102525.1	s__Bosea robiniae	76.8063	218	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.62	97.45	0.92	0.88	4	-
GCF_011764485.1	s__Bosea sp011764485	76.7978	219	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144595.1	s__Bosea sp004144595	76.5937	192	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316345.1	s__Corticibacterium sp002316345	76.4924	179	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:03:09,519] [INFO] GTDB search result was written to GCA_020441665.1_ASM2044166v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:03:09,519] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:03:09,525] [INFO] DFAST_QC result json was written to GCA_020441665.1_ASM2044166v1_genomic.fna/dqc_result.json
[2023-06-29 04:03:09,525] [INFO] DFAST_QC completed!
[2023-06-29 04:03:09,526] [INFO] Total running time: 0h1m49s