[2024-01-25 20:15:35,695] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:35,700] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:35,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgb89de705-a68e-4836-9bc0-b805d5a6b57c/dqc_reference
[2024-01-25 20:15:36,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:36,836] [INFO] Task started: Prodigal
[2024-01-25 20:15:36,836] [INFO] Running command: gunzip -c /var/lib/cwl/stga1265708-7684-41ef-8016-a835c65e42e1/GCF_016863235.1_ASM1686323v1_genomic.fna.gz | prodigal -d GCF_016863235.1_ASM1686323v1_genomic.fna/cds.fna -a GCF_016863235.1_ASM1686323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:57,265] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:57,265] [INFO] Task started: HMMsearch
[2024-01-25 20:15:57,265] [INFO] Running command: hmmsearch --tblout GCF_016863235.1_ASM1686323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb89de705-a68e-4836-9bc0-b805d5a6b57c/dqc_reference/reference_markers.hmm GCF_016863235.1_ASM1686323v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:57,566] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:57,568] [INFO] Found 6/6 markers.
[2024-01-25 20:15:57,627] [INFO] Query marker FASTA was written to GCF_016863235.1_ASM1686323v1_genomic.fna/markers.fasta
[2024-01-25 20:15:57,627] [INFO] Task started: Blastn
[2024-01-25 20:15:57,627] [INFO] Running command: blastn -query GCF_016863235.1_ASM1686323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb89de705-a68e-4836-9bc0-b805d5a6b57c/dqc_reference/reference_markers.fasta -out GCF_016863235.1_ASM1686323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:58,941] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:58,945] [INFO] Selected 22 target genomes.
[2024-01-25 20:15:58,945] [INFO] Target genome list was writen to GCF_016863235.1_ASM1686323v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:58,951] [INFO] Task started: fastANI
[2024-01-25 20:15:58,951] [INFO] Running command: fastANI --query /var/lib/cwl/stga1265708-7684-41ef-8016-a835c65e42e1/GCF_016863235.1_ASM1686323v1_genomic.fna.gz --refList GCF_016863235.1_ASM1686323v1_genomic.fna/target_genomes.txt --output GCF_016863235.1_ASM1686323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:43,067] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:43,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb89de705-a68e-4836-9bc0-b805d5a6b57c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:43,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb89de705-a68e-4836-9bc0-b805d5a6b57c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:43,081] [INFO] Found 21 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:16:43,081] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:16:43,081] [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
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	100.0	2511	2518	95	inconclusive
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	99.9858	2498	2518	95	inconclusive
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	95.9948	2167	2518	95	inconclusive
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	86.1913	1757	2518	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	86.1392	1751	2518	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	86.1088	1765	2518	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	86.0516	1788	2518	95	below_threshold
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	84.68	1597	2518	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	84.635	1543	2518	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	83.8093	1455	2518	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.7258	1517	2518	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.7915	905	2518	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.5441	1382	2518	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.2758	1349	2518	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	80.2414	1347	2518	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	80.1344	1227	2518	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	79.8877	1335	2518	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	76.8306	746	2518	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	76.7549	805	2518	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	76.5462	653	2518	95	below_threshold
Amycolatopsis endophytica	strain=DSM 104006	GCA_013410405.1	860233	860233	type	True	76.2651	568	2518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:43,083] [INFO] DFAST Taxonomy check result was written to GCF_016863235.1_ASM1686323v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:43,083] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:43,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:43,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb89de705-a68e-4836-9bc0-b805d5a6b57c/dqc_reference/checkm_data
[2024-01-25 20:16:43,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:43,158] [INFO] Task started: CheckM
[2024-01-25 20:16:43,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863235.1_ASM1686323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863235.1_ASM1686323v1_genomic.fna/checkm_input GCF_016863235.1_ASM1686323v1_genomic.fna/checkm_result
[2024-01-25 20:17:52,784] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:52,785] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:52,806] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:52,806] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:52,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863235.1_ASM1686323v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:52,807] [INFO] Task started: Blastn
[2024-01-25 20:17:52,807] [INFO] Running command: blastn -query GCF_016863235.1_ASM1686323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb89de705-a68e-4836-9bc0-b805d5a6b57c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863235.1_ASM1686323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:54,970] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:54,972] [INFO] Selected 15 target genomes.
[2024-01-25 20:17:54,973] [INFO] Target genome list was writen to GCF_016863235.1_ASM1686323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:54,995] [INFO] Task started: fastANI
[2024-01-25 20:17:54,995] [INFO] Running command: fastANI --query /var/lib/cwl/stga1265708-7684-41ef-8016-a835c65e42e1/GCF_016863235.1_ASM1686323v1_genomic.fna.gz --refList GCF_016863235.1_ASM1686323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863235.1_ASM1686323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:25,703] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:25,714] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:25,715] [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
GCA_014647935.1	s__Planomonospora parontospora	95.8531	2129	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	conclusive
GCF_015711645.1	s__Planomonospora sp015711645	92.9217	1898	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	87.0009	1774	2518	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	86.5882	1776	2518	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_016863135.1	s__Planobispora longispora	86.2178	1752	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863175.1	s__Planobispora siamensis	86.0793	1783	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	86.0615	1772	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_900113865.1	s__Streptosporangium canum	84.71	1592	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_000024865.1	s__Streptosporangium roseum	84.5142	1695	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409935.1	s__Streptosporangium sandarakinum	83.7819	1459	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.6379	1532	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_003236385.1	s__Desertactinospora gelatinilytica	80.0871	1002	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Desertactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017592665.1	s__NEAU-GS5 sp017592665	79.1997	1126	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__NEAU-GS5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410405.1	s__Amycolatopsis endophytica	76.265	570	2518	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	75.3734	404	2518	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:25,716] [INFO] GTDB search result was written to GCF_016863235.1_ASM1686323v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:25,717] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:25,720] [INFO] DFAST_QC result json was written to GCF_016863235.1_ASM1686323v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:25,721] [INFO] DFAST_QC completed!
[2024-01-25 20:18:25,721] [INFO] Total running time: 0h2m50s