[2024-01-24 15:26:33,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg1417c98e-2aea-4965-862e-0c0988518453/dqc_reference
[2024-01-24 15:26:35,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:35,759] [INFO] Task started: Prodigal
[2024-01-24 15:26:35,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg68991288-e105-4b44-8ab7-995fac24c70f/GCF_008761635.1_ASM876163v1_genomic.fna.gz | prodigal -d GCF_008761635.1_ASM876163v1_genomic.fna/cds.fna -a GCF_008761635.1_ASM876163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:46,947] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:46,947] [INFO] Task started: HMMsearch
[2024-01-24 15:26:46,948] [INFO] Running command: hmmsearch --tblout GCF_008761635.1_ASM876163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1417c98e-2aea-4965-862e-0c0988518453/dqc_reference/reference_markers.hmm GCF_008761635.1_ASM876163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:47,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:47,244] [INFO] Found 6/6 markers.
[2024-01-24 15:26:47,286] [INFO] Query marker FASTA was written to GCF_008761635.1_ASM876163v1_genomic.fna/markers.fasta
[2024-01-24 15:26:47,286] [INFO] Task started: Blastn
[2024-01-24 15:26:47,286] [INFO] Running command: blastn -query GCF_008761635.1_ASM876163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1417c98e-2aea-4965-862e-0c0988518453/dqc_reference/reference_markers.fasta -out GCF_008761635.1_ASM876163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:48,537] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:48,541] [INFO] Selected 23 target genomes.
[2024-01-24 15:26:48,541] [INFO] Target genome list was writen to GCF_008761635.1_ASM876163v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:48,666] [INFO] Task started: fastANI
[2024-01-24 15:26:48,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg68991288-e105-4b44-8ab7-995fac24c70f/GCF_008761635.1_ASM876163v1_genomic.fna.gz --refList GCF_008761635.1_ASM876163v1_genomic.fna/target_genomes.txt --output GCF_008761635.1_ASM876163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:09,850] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:09,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1417c98e-2aea-4965-862e-0c0988518453/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:09,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1417c98e-2aea-4965-862e-0c0988518453/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:09,873] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:09,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:09,873] [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 cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	100.0	1332	1332	95	conclusive
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.1421	709	1332	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.9495	718	1332	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.7812	721	1332	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	80.5469	676	1332	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.5046	703	1332	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	80.4908	660	1332	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	80.4791	663	1332	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.4132	679	1332	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.393	672	1332	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.3417	704	1332	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.3121	687	1332	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	80.1962	616	1332	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.1815	621	1332	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.1667	648	1332	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.1633	650	1332	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.103	617	1332	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.9969	659	1332	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	79.9966	608	1332	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.9906	642	1332	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	79.9803	665	1332	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	79.9202	585	1332	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.8167	662	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:09,875] [INFO] DFAST Taxonomy check result was written to GCF_008761635.1_ASM876163v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:09,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:09,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:09,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1417c98e-2aea-4965-862e-0c0988518453/dqc_reference/checkm_data
[2024-01-24 15:27:09,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:09,918] [INFO] Task started: CheckM
[2024-01-24 15:27:09,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008761635.1_ASM876163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008761635.1_ASM876163v1_genomic.fna/checkm_input GCF_008761635.1_ASM876163v1_genomic.fna/checkm_result
[2024-01-24 15:28:13,747] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:13,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:13,764] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:13,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:13,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008761635.1_ASM876163v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:13,766] [INFO] Task started: Blastn
[2024-01-24 15:28:13,766] [INFO] Running command: blastn -query GCF_008761635.1_ASM876163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1417c98e-2aea-4965-862e-0c0988518453/dqc_reference/reference_markers_gtdb.fasta -out GCF_008761635.1_ASM876163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:15,738] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:15,742] [INFO] Selected 23 target genomes.
[2024-01-24 15:28:15,742] [INFO] Target genome list was writen to GCF_008761635.1_ASM876163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:15,762] [INFO] Task started: fastANI
[2024-01-24 15:28:15,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg68991288-e105-4b44-8ab7-995fac24c70f/GCF_008761635.1_ASM876163v1_genomic.fna.gz --refList GCF_008761635.1_ASM876163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008761635.1_ASM876163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:37,445] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:37,471] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:37,472] [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_008761635.1	s__Nocardioides cynanchi	100.0	1332	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017354415.1	s__Nocardioides sp017354415	82.0674	695	1332	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	81.0999	715	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.9265	722	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	80.7787	722	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	80.5248	666	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.4908	705	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103935.1	s__Nocardioides szechwanensis	80.4882	661	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013778305.1	s__Nocardioides sp013778305	80.4616	676	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015024225.1	s__Nocardioides sp015024225	80.4608	665	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_004564375.1	s__Nocardioides euryhalodurans	80.4478	678	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	80.4374	718	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902805925.1	s__Nocardioides sp902805925	80.4297	546	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	80.3003	688	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013408145.1	s__Nocardioides marinus	80.214	614	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_003057875.1	s__Nocardioides currus	80.2068	643	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	80.1978	677	1332	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	80.178	620	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121585.1	s__Nocardioides speluncae	80.129	624	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	80.0868	618	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017916455.1	s__Nocardioides sp017916455	80.0632	594	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_009823805.1	s__Nocardioides sp009823805	79.9554	668	1332	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	79.8746	661	1332	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 15:28:37,473] [INFO] GTDB search result was written to GCF_008761635.1_ASM876163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:37,474] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:37,479] [INFO] DFAST_QC result json was written to GCF_008761635.1_ASM876163v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:37,479] [INFO] DFAST_QC completed!
[2024-01-24 15:28:37,479] [INFO] Total running time: 0h2m4s