[2024-01-24 11:43:53,144] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,146] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d91a266-d3a0-4d36-af0b-88df01d593d5/dqc_reference
[2024-01-24 11:43:54,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,377] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg00bf34b7-7557-45d8-925b-0e08e8c97805/GCF_003121585.1_ASM312158v1_genomic.fna.gz | prodigal -d GCF_003121585.1_ASM312158v1_genomic.fna/cds.fna -a GCF_003121585.1_ASM312158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:09,792] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:09,793] [INFO] Task started: HMMsearch
[2024-01-24 11:44:09,793] [INFO] Running command: hmmsearch --tblout GCF_003121585.1_ASM312158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d91a266-d3a0-4d36-af0b-88df01d593d5/dqc_reference/reference_markers.hmm GCF_003121585.1_ASM312158v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:10,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:10,048] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg00bf34b7-7557-45d8-925b-0e08e8c97805/GCF_003121585.1_ASM312158v1_genomic.fna.gz]
[2024-01-24 11:44:10,093] [INFO] Query marker FASTA was written to GCF_003121585.1_ASM312158v1_genomic.fna/markers.fasta
[2024-01-24 11:44:10,093] [INFO] Task started: Blastn
[2024-01-24 11:44:10,093] [INFO] Running command: blastn -query GCF_003121585.1_ASM312158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d91a266-d3a0-4d36-af0b-88df01d593d5/dqc_reference/reference_markers.fasta -out GCF_003121585.1_ASM312158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:11,322] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:11,326] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:11,326] [INFO] Target genome list was writen to GCF_003121585.1_ASM312158v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:11,334] [INFO] Task started: fastANI
[2024-01-24 11:44:11,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg00bf34b7-7557-45d8-925b-0e08e8c97805/GCF_003121585.1_ASM312158v1_genomic.fna.gz --refList GCF_003121585.1_ASM312158v1_genomic.fna/target_genomes.txt --output GCF_003121585.1_ASM312158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:32,396] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:32,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d91a266-d3a0-4d36-af0b-88df01d593d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:32,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d91a266-d3a0-4d36-af0b-88df01d593d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:32,412] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:32,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:32,413] [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
Nocardioides speluncae	strain=YIM ART13	GCA_003121585.1	2670337	2670337	type	True	100.0	1877	1878	95	conclusive
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.8108	768	1878	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.6043	650	1878	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.5865	702	1878	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.5409	732	1878	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	80.3281	783	1878	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	80.2366	680	1878	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.2223	704	1878	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.205	708	1878	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.1124	750	1878	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.0809	802	1878	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.9993	664	1878	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	79.959	703	1878	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	79.8558	632	1878	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.729	673	1878	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	79.7226	642	1878	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.7122	607	1878	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.6596	650	1878	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	79.5258	593	1878	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.511	672	1878	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	79.0024	659	1878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:32,414] [INFO] DFAST Taxonomy check result was written to GCF_003121585.1_ASM312158v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:32,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:32,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:32,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d91a266-d3a0-4d36-af0b-88df01d593d5/dqc_reference/checkm_data
[2024-01-24 11:44:32,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:32,467] [INFO] Task started: CheckM
[2024-01-24 11:44:32,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003121585.1_ASM312158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003121585.1_ASM312158v1_genomic.fna/checkm_input GCF_003121585.1_ASM312158v1_genomic.fna/checkm_result
[2024-01-24 11:45:17,974] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:17,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,994] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:17,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:17,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003121585.1_ASM312158v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:17,995] [INFO] Task started: Blastn
[2024-01-24 11:45:17,995] [INFO] Running command: blastn -query GCF_003121585.1_ASM312158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d91a266-d3a0-4d36-af0b-88df01d593d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003121585.1_ASM312158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:19,895] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:19,899] [INFO] Selected 22 target genomes.
[2024-01-24 11:45:19,899] [INFO] Target genome list was writen to GCF_003121585.1_ASM312158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:19,914] [INFO] Task started: fastANI
[2024-01-24 11:45:19,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg00bf34b7-7557-45d8-925b-0e08e8c97805/GCF_003121585.1_ASM312158v1_genomic.fna.gz --refList GCF_003121585.1_ASM312158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003121585.1_ASM312158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:41,838] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:41,855] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:41,856] [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_003121585.1	s__Nocardioides speluncae	100.0	1877	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.8529	748	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.8115	769	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.6182	698	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	80.601	650	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	80.5349	733	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	80.4077	741	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014191495.1	s__Nocardioides soli	80.3098	786	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_013778305.1	s__Nocardioides sp013778305	80.2724	745	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003047285.1	s__Nocardioides allogilvus	80.2623	677	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.72	98.72	0.92	0.92	2	-
GCF_900103935.1	s__Nocardioides szechwanensis	80.2473	732	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014266025.1	s__Nocardioides deserti	80.1999	709	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011250565.1	s__Nocardioides sp011250565	80.197	717	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564375.1	s__Nocardioides euryhalodurans	80.0632	656	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	80.0505	684	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815725.1	s__Nocardioides sp013815725	79.9946	409	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057875.1	s__Nocardioides currus	79.97	702	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	79.9239	680	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	79.73	597	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054165.1	s__Nocardioides sp003054165	79.6185	702	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865585.1	s__Nocardioides houyundeii	79.5037	596	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCF_000426525.1	s__Nocardioides alkalitolerans	78.9867	661	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:41,857] [INFO] GTDB search result was written to GCF_003121585.1_ASM312158v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:41,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:41,861] [INFO] DFAST_QC result json was written to GCF_003121585.1_ASM312158v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:41,862] [INFO] DFAST_QC completed!
[2024-01-24 11:45:41,862] [INFO] Total running time: 0h1m49s