[2024-01-25 18:53:50,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:50,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:50,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdc6ed90-be28-4400-91e7-b08e7270118b/dqc_reference
[2024-01-25 18:53:51,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:51,796] [INFO] Task started: Prodigal
[2024-01-25 18:53:51,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgae927c8c-75ae-4520-a4c0-eedab527fdaf/GCF_016863435.1_ASM1686343v1_genomic.fna.gz | prodigal -d GCF_016863435.1_ASM1686343v1_genomic.fna/cds.fna -a GCF_016863435.1_ASM1686343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:21,677] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:21,678] [INFO] Task started: HMMsearch
[2024-01-25 18:54:21,678] [INFO] Running command: hmmsearch --tblout GCF_016863435.1_ASM1686343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdc6ed90-be28-4400-91e7-b08e7270118b/dqc_reference/reference_markers.hmm GCF_016863435.1_ASM1686343v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:22,150] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:22,152] [INFO] Found 6/6 markers.
[2024-01-25 18:54:22,218] [INFO] Query marker FASTA was written to GCF_016863435.1_ASM1686343v1_genomic.fna/markers.fasta
[2024-01-25 18:54:22,218] [INFO] Task started: Blastn
[2024-01-25 18:54:22,218] [INFO] Running command: blastn -query GCF_016863435.1_ASM1686343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc6ed90-be28-4400-91e7-b08e7270118b/dqc_reference/reference_markers.fasta -out GCF_016863435.1_ASM1686343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:23,368] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:23,378] [INFO] Selected 25 target genomes.
[2024-01-25 18:54:23,378] [INFO] Target genome list was writen to GCF_016863435.1_ASM1686343v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:23,427] [INFO] Task started: fastANI
[2024-01-25 18:54:23,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgae927c8c-75ae-4520-a4c0-eedab527fdaf/GCF_016863435.1_ASM1686343v1_genomic.fna.gz --refList GCF_016863435.1_ASM1686343v1_genomic.fna/target_genomes.txt --output GCF_016863435.1_ASM1686343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:12,340] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:12,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdc6ed90-be28-4400-91e7-b08e7270118b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:12,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdc6ed90-be28-4400-91e7-b08e7270118b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:12,355] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:55:12,355] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:55:12,355] [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 lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	79.4765	837	2913	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	79.3614	1074	2913	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	79.3591	1100	2913	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	79.332	1052	2913	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	79.3272	1069	2913	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	79.3166	956	2913	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	79.2852	1021	2913	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	79.2611	969	2913	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.2473	709	2913	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	79.2393	1076	2913	95	below_threshold
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	79.2387	1078	2913	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	79.2338	990	2913	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	79.229	975	2913	95	below_threshold
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	79.1549	1071	2913	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.145	1108	2913	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	79.0335	921	2913	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.0191	1064	2913	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.8959	1093	2913	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	78.8925	947	2913	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	78.7842	1058	2913	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	78.7834	1054	2913	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	78.6837	1130	2913	95	below_threshold
Acrocarpospora pleiomorpha	strain=NBRC 16267	GCA_009687885.1	90975	90975	type	True	78.6177	887	2913	95	below_threshold
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	78.5003	894	2913	95	below_threshold
Acrocarpospora macrocephala	strain=NBRC 16266	GCA_009687865.1	150177	150177	type	True	78.3257	925	2913	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:12,357] [INFO] DFAST Taxonomy check result was written to GCF_016863435.1_ASM1686343v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:12,357] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:12,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:12,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdc6ed90-be28-4400-91e7-b08e7270118b/dqc_reference/checkm_data
[2024-01-25 18:55:12,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:12,437] [INFO] Task started: CheckM
[2024-01-25 18:55:12,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863435.1_ASM1686343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863435.1_ASM1686343v1_genomic.fna/checkm_input GCF_016863435.1_ASM1686343v1_genomic.fna/checkm_result
[2024-01-25 18:56:46,990] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:46,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 15.74%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2024-01-25 18:56:47,016] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:47,016] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:47,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863435.1_ASM1686343v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:47,017] [INFO] Task started: Blastn
[2024-01-25 18:56:47,017] [INFO] Running command: blastn -query GCF_016863435.1_ASM1686343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdc6ed90-be28-4400-91e7-b08e7270118b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863435.1_ASM1686343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:48,891] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:48,894] [INFO] Selected 19 target genomes.
[2024-01-25 18:56:48,894] [INFO] Target genome list was writen to GCF_016863435.1_ASM1686343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:48,917] [INFO] Task started: fastANI
[2024-01-25 18:56:48,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgae927c8c-75ae-4520-a4c0-eedab527fdaf/GCF_016863435.1_ASM1686343v1_genomic.fna.gz --refList GCF_016863435.1_ASM1686343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863435.1_ASM1686343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:26,256] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:26,267] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:26,268] [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_016863435.1	s__Sinosporangium siamense	100.0	2911	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sinosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900100605.1	s__Sinosporangium album	82.9237	1434	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sinosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	79.5815	1016	2913	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_014203605.1	s__Planomonospora_A venezuelensis	79.3993	1088	2913	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_014207745.1	s__Nonomuraea muscovyensis	79.3722	1097	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	79.3581	1045	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863195.1	s__Planobispora takensis	79.3545	1060	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	79.3532	1032	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_014646355.1	s__Nonomuraea cavernae	79.3144	958	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711645.1	s__Planomonospora sp015711645	79.2484	984	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202315.1	s__Thermocatellispora tengchongensis	79.1459	1224	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermocatellispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873535.1	s__Nonomuraea africana	79.1285	1079	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646695.1	s__Sphaerisporangium melleum	79.067	916	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_018531465.1	s__Sphaerisporangium sp018531465	78.949	1039	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	78.768	1253	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_900108335.1	s__Nonomuraea solani	78.6998	1127	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687885.1	s__Acrocarpospora pleiomorpha	78.5866	891	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862995.1	s__Acrocarpospora phusangensis	78.5134	891	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687865.1	s__Acrocarpospora macrocephala	78.2992	931	2913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:26,269] [INFO] GTDB search result was written to GCF_016863435.1_ASM1686343v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:26,269] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:26,273] [INFO] DFAST_QC result json was written to GCF_016863435.1_ASM1686343v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:26,273] [INFO] DFAST_QC completed!
[2024-01-25 18:57:26,273] [INFO] Total running time: 0h3m36s