[2024-01-24 10:47:06,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg33b0542a-ff77-4653-a28f-a8a05fc85ba5/dqc_reference
[2024-01-24 10:47:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,105] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb2795d2-2b47-493a-95cb-525a63f0c4dd/GCF_003002095.1_ASM300209v1_genomic.fna.gz | prodigal -d GCF_003002095.1_ASM300209v1_genomic.fna/cds.fna -a GCF_003002095.1_ASM300209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:30,409] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:30,409] [INFO] Task started: HMMsearch
[2024-01-24 10:47:30,409] [INFO] Running command: hmmsearch --tblout GCF_003002095.1_ASM300209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33b0542a-ff77-4653-a28f-a8a05fc85ba5/dqc_reference/reference_markers.hmm GCF_003002095.1_ASM300209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:30,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:30,771] [INFO] Found 6/6 markers.
[2024-01-24 10:47:30,836] [INFO] Query marker FASTA was written to GCF_003002095.1_ASM300209v1_genomic.fna/markers.fasta
[2024-01-24 10:47:30,837] [INFO] Task started: Blastn
[2024-01-24 10:47:30,837] [INFO] Running command: blastn -query GCF_003002095.1_ASM300209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b0542a-ff77-4653-a28f-a8a05fc85ba5/dqc_reference/reference_markers.fasta -out GCF_003002095.1_ASM300209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:32,134] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:32,138] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:32,138] [INFO] Target genome list was writen to GCF_003002095.1_ASM300209v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:32,168] [INFO] Task started: fastANI
[2024-01-24 10:47:32,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb2795d2-2b47-493a-95cb-525a63f0c4dd/GCF_003002095.1_ASM300209v1_genomic.fna.gz --refList GCF_003002095.1_ASM300209v1_genomic.fna/target_genomes.txt --output GCF_003002095.1_ASM300209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:09,822] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33b0542a-ff77-4653-a28f-a8a05fc85ba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:09,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33b0542a-ff77-4653-a28f-a8a05fc85ba5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:09,841] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:09,842] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:09,842] [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
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	78.6952	736	2314	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	78.5152	1054	2314	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	78.4817	757	2314	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	78.4711	768	2314	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	78.4679	756	2314	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	78.4429	721	2314	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	78.4134	778	2314	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	78.3553	659	2314	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	78.3348	790	2314	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	78.3112	1040	2314	95	below_threshold
Nocardiopsis algeriensis	strain=CECT 8712	GCA_014203695.1	1478215	1478215	type	True	78.3043	674	2314	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	78.2711	892	2314	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	78.1865	927	2314	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	78.1813	876	2314	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	77.8812	950	2314	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	77.8794	617	2314	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	77.7803	765	2314	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	77.6405	732	2314	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	77.3223	1028	2314	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	77.2354	983	2314	95	below_threshold
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	77.105	804	2314	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	77.0846	1022	2314	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	77.0378	970	2314	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	76.9131	890	2314	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	76.4022	676	2314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,843] [INFO] DFAST Taxonomy check result was written to GCF_003002095.1_ASM300209v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:09,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:09,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:09,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33b0542a-ff77-4653-a28f-a8a05fc85ba5/dqc_reference/checkm_data
[2024-01-24 10:48:09,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:09,907] [INFO] Task started: CheckM
[2024-01-24 10:48:09,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002095.1_ASM300209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002095.1_ASM300209v1_genomic.fna/checkm_input GCF_003002095.1_ASM300209v1_genomic.fna/checkm_result
[2024-01-24 10:49:31,527] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:31,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:31,547] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:31,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:31,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002095.1_ASM300209v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:31,548] [INFO] Task started: Blastn
[2024-01-24 10:49:31,548] [INFO] Running command: blastn -query GCF_003002095.1_ASM300209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b0542a-ff77-4653-a28f-a8a05fc85ba5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002095.1_ASM300209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:33,464] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:33,467] [INFO] Selected 19 target genomes.
[2024-01-24 10:49:33,467] [INFO] Target genome list was writen to GCF_003002095.1_ASM300209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:33,500] [INFO] Task started: fastANI
[2024-01-24 10:49:33,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb2795d2-2b47-493a-95cb-525a63f0c4dd/GCF_003002095.1_ASM300209v1_genomic.fna.gz --refList GCF_003002095.1_ASM300209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002095.1_ASM300209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:03,163] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:03,178] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:03,178] [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_003002095.1	s__Allonocardiopsis opalescens	100.0	2314	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allonocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013408795.1	s__Spinactinospora alkalitolerans	78.9807	974	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	78.8118	1059	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	78.7573	1002	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517975.1	s__Thermobifida cellulosilytica	78.6492	745	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728995.1	s__Streptomonospora sp009728995	78.6143	925	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	78.5508	907	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_014200805.1	s__Nocardiopsis_A composta	78.4469	1072	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167435.1	s__Marinactinospora thermotolerans	78.4132	799	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	78.4057	780	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341245.1	s__Nocardiopsis_A halophila	78.3488	879	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	98.23	98.23	0.90	0.90	2	-
GCF_000341105.1	s__Nocardiopsis_A potens	78.3138	1040	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341185.1	s__Nocardiopsis_A chromatogenes	78.2017	924	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018316655.1	s__Nocardiopsis sp018316655	78.0535	975	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380095.1	s__WHSL01 sp009380095	77.7707	729	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__WHSL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006363815.1	s__Thermomonospora catenispora	77.6325	734	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289645.1	s__Actinomadura_D craniellae	77.4729	894	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863395.1	s__Sphaerisporangium rufum	77.2358	987	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	77.0369	972	2314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:03,180] [INFO] GTDB search result was written to GCF_003002095.1_ASM300209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:03,180] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:03,186] [INFO] DFAST_QC result json was written to GCF_003002095.1_ASM300209v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:03,186] [INFO] DFAST_QC completed!
[2024-01-24 10:50:03,187] [INFO] Total running time: 0h2m57s