[2024-01-24 10:47:11,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg57af05d5-415e-45ec-b023-76dae29899e1/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg45d6c423-f6db-49c6-9a60-1a85273df75b/GCF_008087345.1_ASM808734v1_genomic.fna.gz | prodigal -d GCF_008087345.1_ASM808734v1_genomic.fna/cds.fna -a GCF_008087345.1_ASM808734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:32,276] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:32,276] [INFO] Task started: HMMsearch
[2024-01-24 10:47:32,276] [INFO] Running command: hmmsearch --tblout GCF_008087345.1_ASM808734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57af05d5-415e-45ec-b023-76dae29899e1/dqc_reference/reference_markers.hmm GCF_008087345.1_ASM808734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:32,560] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:32,561] [INFO] Found 6/6 markers.
[2024-01-24 10:47:32,604] [INFO] Query marker FASTA was written to GCF_008087345.1_ASM808734v1_genomic.fna/markers.fasta
[2024-01-24 10:47:32,605] [INFO] Task started: Blastn
[2024-01-24 10:47:32,605] [INFO] Running command: blastn -query GCF_008087345.1_ASM808734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57af05d5-415e-45ec-b023-76dae29899e1/dqc_reference/reference_markers.fasta -out GCF_008087345.1_ASM808734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:33,842] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:33,849] [INFO] Selected 30 target genomes.
[2024-01-24 10:47:33,850] [INFO] Target genome list was writen to GCF_008087345.1_ASM808734v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:42,026] [INFO] Task started: fastANI
[2024-01-24 10:47:42,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg45d6c423-f6db-49c6-9a60-1a85273df75b/GCF_008087345.1_ASM808734v1_genomic.fna.gz --refList GCF_008087345.1_ASM808734v1_genomic.fna/target_genomes.txt --output GCF_008087345.1_ASM808734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:09,185] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57af05d5-415e-45ec-b023-76dae29899e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:09,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57af05d5-415e-45ec-b023-76dae29899e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:09,209] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:09,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:09,210] [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 iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	80.2198	748	1585	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.1984	695	1585	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	79.8449	676	1585	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.7434	693	1585	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	79.7363	698	1585	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.6998	590	1585	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.6161	626	1585	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.4791	714	1585	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.4481	716	1585	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.4099	644	1585	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	79.3873	659	1585	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	79.3841	653	1585	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.3298	697	1585	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	79.3118	676	1585	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	79.3018	653	1585	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.3007	639	1585	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.2978	600	1585	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.291	614	1585	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	79.2731	606	1585	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.2515	706	1585	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.2466	614	1585	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	79.2407	615	1585	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	79.2304	652	1585	95	below_threshold
Nocardioides terrae	strain=CGMCC 1.7056	GCA_900112345.1	574651	574651	type	True	79.2131	551	1585	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.1445	678	1585	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	79.1386	550	1585	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	79.1322	636	1585	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	79.0892	614	1585	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	79.0851	706	1585	95	below_threshold
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	79.0319	492	1585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,211] [INFO] DFAST Taxonomy check result was written to GCF_008087345.1_ASM808734v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:09,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:09,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:09,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57af05d5-415e-45ec-b023-76dae29899e1/dqc_reference/checkm_data
[2024-01-24 10:48:09,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:09,264] [INFO] Task started: CheckM
[2024-01-24 10:48:09,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008087345.1_ASM808734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008087345.1_ASM808734v1_genomic.fna/checkm_input GCF_008087345.1_ASM808734v1_genomic.fna/checkm_result
[2024-01-24 10:49:21,487] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:21,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:21,514] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:21,514] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:21,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008087345.1_ASM808734v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:21,515] [INFO] Task started: Blastn
[2024-01-24 10:49:21,515] [INFO] Running command: blastn -query GCF_008087345.1_ASM808734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57af05d5-415e-45ec-b023-76dae29899e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008087345.1_ASM808734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:23,469] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:23,473] [INFO] Selected 18 target genomes.
[2024-01-24 10:49:23,473] [INFO] Target genome list was writen to GCF_008087345.1_ASM808734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:23,493] [INFO] Task started: fastANI
[2024-01-24 10:49:23,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg45d6c423-f6db-49c6-9a60-1a85273df75b/GCF_008087345.1_ASM808734v1_genomic.fna.gz --refList GCF_008087345.1_ASM808734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008087345.1_ASM808734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:40,998] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:41,017] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:41,018] [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_008087345.1	s__Marmoricola_A caldifontis	100.0	1583	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902805865.1	s__Marmoricola_A sp902805865	81.3478	597	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805845.1	s__Marmoricola_A sp902805845	80.8518	622	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011299595.1	s__Marmoricola_A sp011299595	80.6041	753	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	80.2161	750	1585	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_019039255.1	s__JABFXA01 sp019039255	80.1937	696	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	80.1366	630	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_900067705.2	s__Nocardioides_A massiliensis	79.7165	444	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	79.6744	690	1585	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	79.6538	655	1585	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	79.4428	718	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_000720335.1	s__Marmoricola aequoreus	79.2963	654	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	79.2652	604	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725535.1	s__Marmoricola pocheonensis	79.2267	635	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	79.1726	649	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519005.1	s__Nocardioides sp000519005	79.1181	646	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCF_001653335.1	s__Nocardioides dokdonensis	79.0645	617	1585	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046535.1	s__Nocardioides anomalus	79.0541	711	1585	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 10:49:41,019] [INFO] GTDB search result was written to GCF_008087345.1_ASM808734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:41,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:41,024] [INFO] DFAST_QC result json was written to GCF_008087345.1_ASM808734v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:41,025] [INFO] DFAST_QC completed!
[2024-01-24 10:49:41,025] [INFO] Total running time: 0h2m29s