[2024-01-24 11:20:18,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:18,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:18,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f574d77-5237-49db-a36d-f4d920108173/dqc_reference
[2024-01-24 11:20:19,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:19,793] [INFO] Task started: Prodigal
[2024-01-24 11:20:19,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dcd0448-d891-475b-9b94-3c1941cf7407/GCF_016863175.1_ASM1686317v1_genomic.fna.gz | prodigal -d GCF_016863175.1_ASM1686317v1_genomic.fna/cds.fna -a GCF_016863175.1_ASM1686317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:43,738] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:43,739] [INFO] Task started: HMMsearch
[2024-01-24 11:20:43,739] [INFO] Running command: hmmsearch --tblout GCF_016863175.1_ASM1686317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f574d77-5237-49db-a36d-f4d920108173/dqc_reference/reference_markers.hmm GCF_016863175.1_ASM1686317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:44,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:44,212] [INFO] Found 6/6 markers.
[2024-01-24 11:20:44,284] [INFO] Query marker FASTA was written to GCF_016863175.1_ASM1686317v1_genomic.fna/markers.fasta
[2024-01-24 11:20:44,284] [INFO] Task started: Blastn
[2024-01-24 11:20:44,284] [INFO] Running command: blastn -query GCF_016863175.1_ASM1686317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f574d77-5237-49db-a36d-f4d920108173/dqc_reference/reference_markers.fasta -out GCF_016863175.1_ASM1686317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:45,616] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:45,620] [INFO] Selected 15 target genomes.
[2024-01-24 11:20:45,621] [INFO] Target genome list was writen to GCF_016863175.1_ASM1686317v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:45,627] [INFO] Task started: fastANI
[2024-01-24 11:20:45,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dcd0448-d891-475b-9b94-3c1941cf7407/GCF_016863175.1_ASM1686317v1_genomic.fna.gz --refList GCF_016863175.1_ASM1686317v1_genomic.fna/target_genomes.txt --output GCF_016863175.1_ASM1686317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:19,219] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:19,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f574d77-5237-49db-a36d-f4d920108173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:19,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f574d77-5237-49db-a36d-f4d920108173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:19,237] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:21:19,237] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:21:19,237] [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
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	100.0	3002	3010	95	inconclusive
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	95.0973	2534	3010	95	inconclusive
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	87.9011	2167	3010	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	87.8179	2065	3010	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	87.7983	2088	3010	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	86.0031	1788	3010	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	85.8212	1887	3010	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	84.4467	1734	3010	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	83.5544	1525	3010	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.6894	1052	3010	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.5724	1559	3010	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	80.2762	1499	3010	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	80.1211	1391	3010	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	80.0225	1543	3010	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.7074	1135	3010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:19,239] [INFO] DFAST Taxonomy check result was written to GCF_016863175.1_ASM1686317v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:19,239] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:19,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:19,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f574d77-5237-49db-a36d-f4d920108173/dqc_reference/checkm_data
[2024-01-24 11:21:19,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:19,320] [INFO] Task started: CheckM
[2024-01-24 11:21:19,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863175.1_ASM1686317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863175.1_ASM1686317v1_genomic.fna/checkm_input GCF_016863175.1_ASM1686317v1_genomic.fna/checkm_result
[2024-01-24 11:23:10,484] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:10,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.60%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:10,519] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:10,520] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:10,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863175.1_ASM1686317v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:10,521] [INFO] Task started: Blastn
[2024-01-24 11:23:10,521] [INFO] Running command: blastn -query GCF_016863175.1_ASM1686317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f574d77-5237-49db-a36d-f4d920108173/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863175.1_ASM1686317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:12,610] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:12,614] [INFO] Selected 10 target genomes.
[2024-01-24 11:23:12,615] [INFO] Target genome list was writen to GCF_016863175.1_ASM1686317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:12,624] [INFO] Task started: fastANI
[2024-01-24 11:23:12,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dcd0448-d891-475b-9b94-3c1941cf7407/GCF_016863175.1_ASM1686317v1_genomic.fna.gz --refList GCF_016863175.1_ASM1686317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863175.1_ASM1686317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:36,490] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:36,504] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:23:36,505] [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_016863175.1	s__Planobispora siamensis	100.0	3002	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	inconclusive
GCF_016863195.1	s__Planobispora takensis	95.1231	2531	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	inconclusive
GCF_016863135.1	s__Planobispora longispora	87.8993	2167	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	87.8145	2048	3010	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_014648175.1	s__Planobispora rosea	87.7832	2091	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_015711605.1	s__Planomonospora_A sp015711605	87.5378	2070	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014647935.1	s__Planomonospora parontospora	85.8686	1839	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
GCF_015711645.1	s__Planomonospora sp015711645	85.8177	1760	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	84.427	1738	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_014203795.1	s__Streptosporangium album	83.5438	1526	3010	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:36,506] [INFO] GTDB search result was written to GCF_016863175.1_ASM1686317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:36,507] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:36,510] [INFO] DFAST_QC result json was written to GCF_016863175.1_ASM1686317v1_genomic.fna/dqc_result.json
[2024-01-24 11:23:36,511] [INFO] DFAST_QC completed!
[2024-01-24 11:23:36,511] [INFO] Total running time: 0h3m18s