[2024-01-24 13:32:18,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dd22155-7ddd-4b86-a215-7538ae68e4ab/dqc_reference
[2024-01-24 13:32:19,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,679] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,679] [INFO] Running command: gunzip -c /var/lib/cwl/stgc83b75ed-0983-4a7e-9c71-8b9fe2103923/GCF_003594875.1_ASM359487v1_genomic.fna.gz | prodigal -d GCF_003594875.1_ASM359487v1_genomic.fna/cds.fna -a GCF_003594875.1_ASM359487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:43,334] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:43,335] [INFO] Task started: HMMsearch
[2024-01-24 13:32:43,335] [INFO] Running command: hmmsearch --tblout GCF_003594875.1_ASM359487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dd22155-7ddd-4b86-a215-7538ae68e4ab/dqc_reference/reference_markers.hmm GCF_003594875.1_ASM359487v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:43,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:43,804] [INFO] Found 6/6 markers.
[2024-01-24 13:32:43,881] [INFO] Query marker FASTA was written to GCF_003594875.1_ASM359487v1_genomic.fna/markers.fasta
[2024-01-24 13:32:43,882] [INFO] Task started: Blastn
[2024-01-24 13:32:43,882] [INFO] Running command: blastn -query GCF_003594875.1_ASM359487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dd22155-7ddd-4b86-a215-7538ae68e4ab/dqc_reference/reference_markers.fasta -out GCF_003594875.1_ASM359487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:45,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:45,457] [INFO] Selected 36 target genomes.
[2024-01-24 13:32:45,458] [INFO] Target genome list was writen to GCF_003594875.1_ASM359487v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:45,478] [INFO] Task started: fastANI
[2024-01-24 13:32:45,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgc83b75ed-0983-4a7e-9c71-8b9fe2103923/GCF_003594875.1_ASM359487v1_genomic.fna.gz --refList GCF_003594875.1_ASM359487v1_genomic.fna/target_genomes.txt --output GCF_003594875.1_ASM359487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:54,008] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:54,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dd22155-7ddd-4b86-a215-7538ae68e4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:54,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dd22155-7ddd-4b86-a215-7538ae68e4ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:54,037] [INFO] Found 35 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:54,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:54,037] [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
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.0208	1391	2970	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	78.9868	1344	2970	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	78.9439	899	2970	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	78.8622	1297	2970	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	78.84	1250	2970	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	78.7856	1204	2970	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	78.7826	1469	2970	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	78.7659	1226	2970	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	78.7178	1102	2970	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	78.7048	1079	2970	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	78.6664	1304	2970	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	78.6579	1040	2970	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	78.6169	1047	2970	95	below_threshold
Microbispora hainanensis	strain=DSM 45428	GCA_006874475.1	568844	568844	type	True	78.5633	1134	2970	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	78.5082	1215	2970	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	78.5	1272	2970	95	below_threshold
Microbispora amethystogenes	strain=NBRC 101907	GCA_016863015.1	1427754	1427754	type	True	78.4626	1090	2970	95	below_threshold
Streptosporangium saharense	strain=CECT 8840	GCA_014203715.1	1706840	1706840	type	True	78.453	1136	2970	95	below_threshold
Microbispora cellulosiformans	strain=Gxj-6	GCA_008728085.1	2614688	2614688	type	True	78.4105	1098	2970	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	78.4094	1230	2970	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	78.3561	1413	2970	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	78.3422	1391	2970	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.3381	1396	2970	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	78.3366	1458	2970	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	78.227	1371	2970	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	78.1895	1006	2970	95	below_threshold
Planotetraspora silvatica	strain=NBRC 100141	GCA_016863315.1	234614	234614	type	True	78.1584	975	2970	95	below_threshold
Actinomadura logoneensis	strain=NEAU-G17	GCA_003428695.1	2293572	2293572	type	True	77.7696	1000	2970	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	77.5867	1143	2970	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	77.5849	973	2970	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	77.557	1036	2970	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	77.5539	1187	2970	95	below_threshold
Calditerricola satsumensis	strain=JCM 14719	GCA_014646935.1	373054	373054	type	True	74.963	69	2970	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	74.8565	403	2970	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	74.7488	377	2970	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:54,041] [INFO] DFAST Taxonomy check result was written to GCF_003594875.1_ASM359487v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:54,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:54,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:54,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dd22155-7ddd-4b86-a215-7538ae68e4ab/dqc_reference/checkm_data
[2024-01-24 13:33:54,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:54,131] [INFO] Task started: CheckM
[2024-01-24 13:33:54,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003594875.1_ASM359487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003594875.1_ASM359487v1_genomic.fna/checkm_input GCF_003594875.1_ASM359487v1_genomic.fna/checkm_result
[2024-01-24 13:35:42,147] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:42,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 8.80%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:42,182] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:42,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:42,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003594875.1_ASM359487v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:42,184] [INFO] Task started: Blastn
[2024-01-24 13:35:42,184] [INFO] Running command: blastn -query GCF_003594875.1_ASM359487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dd22155-7ddd-4b86-a215-7538ae68e4ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_003594875.1_ASM359487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:44,377] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:44,381] [INFO] Selected 33 target genomes.
[2024-01-24 13:35:44,382] [INFO] Target genome list was writen to GCF_003594875.1_ASM359487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:44,517] [INFO] Task started: fastANI
[2024-01-24 13:35:44,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgc83b75ed-0983-4a7e-9c71-8b9fe2103923/GCF_003594875.1_ASM359487v1_genomic.fna.gz --refList GCF_003594875.1_ASM359487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003594875.1_ASM359487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:42,888] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:42,915] [INFO] Found 32 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:42,916] [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_003594875.1	s__Bailinhaonella thermotolerans	100.0	2968	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bailinhaonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014203605.1	s__Planomonospora_A venezuelensis	79.0338	1306	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	78.9419	1276	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	78.8976	1289	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	78.8971	1207	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_013283785.1	s__Nonomuraea sp013283785	78.8894	1395	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725485.1	s__Nonomuraea candida	78.8276	1451	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873535.1	s__Nonomuraea africana	78.7644	1258	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204985.1	s__Streptosporangium becharense	78.7262	1096	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014202315.1	s__Thermocatellispora tengchongensis	78.7186	1476	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermocatellispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	78.6928	1296	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_014647835.1	s__Microbispora aerata	78.6722	1035	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016863035.1	s__Microbispora corallina	78.5379	1197	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	-
GCF_006874475.1	s__Microbispora hainanensis	78.5139	1147	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	95.41	95.40	0.85	0.85	4	-
GCF_008017515.1	s__Nonomuraea sp008017515	78.4937	1283	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863015.1	s__Microbispora amethystogenes	78.4161	1103	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.43	97.43	0.91	0.91	2	-
GCF_014200435.1	s__Sphaerisporangium krabiense	78.4092	1229	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014203235.1	s__Nonomuraea endophytica	78.3861	1377	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	78.3611	1408	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	78.347	1453	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760925.1	s__Nonomuraea typhae	78.3351	1398	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863315.1	s__Planotetraspora silvatica	78.1421	980	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planotetraspora	95.2969	N/A	N/A	N/A	N/A	1	-
GCF_000518265.1	s__Spirillospora oligospora	77.5932	1141	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374305.1	s__Spirillospora flavalba	77.5298	990	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348335.1	s__Spirillospora bangladeshensis	77.5238	1048	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	77.3744	1162	2970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015658775.1	s__UBA3125 sp015658775	75.4371	93	2970	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.89	98.89	0.81	0.81	2	-
GCA_007693335.1	s__SKSP01 sp007693335	75.1709	190	2970	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646935.1	s__Calditerricola satsumensis	74.9738	68	2970	d__Bacteria;p__Firmicutes;c__Bacilli;o__Calditerricolales;f__Calditerricolaceae;g__Calditerricola	95.0	99.92	99.92	0.99	0.99	2	-
GCA_019120395.1	s__Gemmiger faecigallinarum	74.8287	96	2970	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235265.1	s__JACRLI01 sp016235265	74.7572	231	2970	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__JACRLI01;g__JACRLI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826705.1	s__CADEFY01 sp902826705	74.7304	165	2970	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__RBG-16-71-46;g__CADEFY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:42,922] [INFO] GTDB search result was written to GCF_003594875.1_ASM359487v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:42,922] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:42,929] [INFO] DFAST_QC result json was written to GCF_003594875.1_ASM359487v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:42,929] [INFO] DFAST_QC completed!
[2024-01-24 13:36:42,929] [INFO] Total running time: 0h4m25s