[2024-01-24 13:27:46,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,324] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,324] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9ac67ad-8d93-4582-beef-ed2d15751191/dqc_reference
[2024-01-24 13:27:47,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,741] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg4906a8d3-7d76-4342-b2de-6f70fa31098a/GCF_000426525.1_ASM42652v1_genomic.fna.gz | prodigal -d GCF_000426525.1_ASM42652v1_genomic.fna/cds.fna -a GCF_000426525.1_ASM42652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:02,008] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:02,009] [INFO] Task started: HMMsearch
[2024-01-24 13:28:02,009] [INFO] Running command: hmmsearch --tblout GCF_000426525.1_ASM42652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9ac67ad-8d93-4582-beef-ed2d15751191/dqc_reference/reference_markers.hmm GCF_000426525.1_ASM42652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:02,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:02,357] [INFO] Found 6/6 markers.
[2024-01-24 13:28:02,407] [INFO] Query marker FASTA was written to GCF_000426525.1_ASM42652v1_genomic.fna/markers.fasta
[2024-01-24 13:28:02,407] [INFO] Task started: Blastn
[2024-01-24 13:28:02,407] [INFO] Running command: blastn -query GCF_000426525.1_ASM42652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9ac67ad-8d93-4582-beef-ed2d15751191/dqc_reference/reference_markers.fasta -out GCF_000426525.1_ASM42652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:03,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:03,724] [INFO] Selected 26 target genomes.
[2024-01-24 13:28:03,724] [INFO] Target genome list was writen to GCF_000426525.1_ASM42652v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:03,736] [INFO] Task started: fastANI
[2024-01-24 13:28:03,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg4906a8d3-7d76-4342-b2de-6f70fa31098a/GCF_000426525.1_ASM42652v1_genomic.fna.gz --refList GCF_000426525.1_ASM42652v1_genomic.fna/target_genomes.txt --output GCF_000426525.1_ASM42652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:30,368] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:30,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9ac67ad-8d93-4582-beef-ed2d15751191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:30,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9ac67ad-8d93-4582-beef-ed2d15751191/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:30,389] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:30,389] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:30,389] [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 alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	100.0	1610	1610	95	conclusive
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.4798	707	1610	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	80.4526	715	1610	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.3717	712	1610	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.3531	713	1610	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	80.3385	730	1610	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.3175	743	1610	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.1991	730	1610	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.0727	692	1610	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	80.0587	745	1610	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	80.0493	667	1610	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.0022	710	1610	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.9585	675	1610	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	79.9564	714	1610	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	79.8655	660	1610	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.8553	716	1610	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	79.8422	653	1610	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	79.8228	692	1610	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.8163	652	1610	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.778	683	1610	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.6947	726	1610	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.6687	605	1610	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	79.5601	630	1610	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.5513	756	1610	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.486	674	1610	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.9513	640	1610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:30,391] [INFO] DFAST Taxonomy check result was written to GCF_000426525.1_ASM42652v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:30,391] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:30,391] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:30,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9ac67ad-8d93-4582-beef-ed2d15751191/dqc_reference/checkm_data
[2024-01-24 13:28:30,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:30,441] [INFO] Task started: CheckM
[2024-01-24 13:28:30,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000426525.1_ASM42652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000426525.1_ASM42652v1_genomic.fna/checkm_input GCF_000426525.1_ASM42652v1_genomic.fna/checkm_result
[2024-01-24 13:29:44,485] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:44,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:44,509] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:44,509] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:44,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000426525.1_ASM42652v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:44,510] [INFO] Task started: Blastn
[2024-01-24 13:29:44,510] [INFO] Running command: blastn -query GCF_000426525.1_ASM42652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9ac67ad-8d93-4582-beef-ed2d15751191/dqc_reference/reference_markers_gtdb.fasta -out GCF_000426525.1_ASM42652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:46,836] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:46,840] [INFO] Selected 24 target genomes.
[2024-01-24 13:29:46,840] [INFO] Target genome list was writen to GCF_000426525.1_ASM42652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:46,877] [INFO] Task started: fastANI
[2024-01-24 13:29:46,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg4906a8d3-7d76-4342-b2de-6f70fa31098a/GCF_000426525.1_ASM42652v1_genomic.fna.gz --refList GCF_000426525.1_ASM42652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000426525.1_ASM42652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:11,963] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:11,986] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:11,986] [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_000426525.1	s__Nocardioides alkalitolerans	100.0	1610	1610	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_010686755.1	s__Nocardioides zeae	82.5154	941	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.4662	707	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_014266025.1	s__Nocardioides deserti	80.4239	704	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013466785.1	s__Nocardioides marinisabuli	80.3007	718	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014212315.1	s__Nocardioides luti	80.2898	748	1610	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	80.2157	702	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011250565.1	s__Nocardioides sp011250565	80.1462	719	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015024225.1	s__Nocardioides sp015024225	80.0859	742	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_013177455.1	s__Nocardioides sp013177455	80.0164	715	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_013466985.1	s__Nocardioides ungokensis	80.0092	700	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778305.1	s__Nocardioides sp013778305	79.9928	713	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003047265.1	s__Nocardioides terrigena	79.9742	713	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_000620705.1	s__Nocardioides sp000620705	79.945	721	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557055.1	s__Nocardioides sp009557055	79.8984	673	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018275325.1	s__Nocardioides sp018275325	79.8609	710	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	79.8465	666	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017310035.1	s__Nocardioides sp017310035	79.8344	693	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137345.1	s__Nocardioides sp004137345	79.8298	655	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699265.1	s__Nocardioides sp009699265	79.8233	684	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653335.1	s__Nocardioides dokdonensis	79.7845	697	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018459925.1	s__Nocardioides aquaticus	79.6512	698	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506435.1	s__Nocardioides sp902506435	79.5613	712	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752505.1	s__Marmoricola aurantiacus	79.4898	673	1610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:11,990] [INFO] GTDB search result was written to GCF_000426525.1_ASM42652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:11,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:11,995] [INFO] DFAST_QC result json was written to GCF_000426525.1_ASM42652v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:11,996] [INFO] DFAST_QC completed!
[2024-01-24 13:30:11,996] [INFO] Total running time: 0h2m26s