[2024-01-24 15:10:20,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,103] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f7070d4-a113-4224-92c2-50b455e9256f/dqc_reference
[2024-01-24 15:10:22,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,720] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,720] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4f90be0-ba15-494e-8a8e-c32e0ca12e09/GCF_013186535.1_ASM1318653v1_genomic.fna.gz | prodigal -d GCF_013186535.1_ASM1318653v1_genomic.fna/cds.fna -a GCF_013186535.1_ASM1318653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:02,506] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:02,507] [INFO] Task started: HMMsearch
[2024-01-24 15:11:02,507] [INFO] Running command: hmmsearch --tblout GCF_013186535.1_ASM1318653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f7070d4-a113-4224-92c2-50b455e9256f/dqc_reference/reference_markers.hmm GCF_013186535.1_ASM1318653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:03,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:03,175] [INFO] Found 6/6 markers.
[2024-01-24 15:11:03,252] [INFO] Query marker FASTA was written to GCF_013186535.1_ASM1318653v1_genomic.fna/markers.fasta
[2024-01-24 15:11:03,254] [INFO] Task started: Blastn
[2024-01-24 15:11:03,254] [INFO] Running command: blastn -query GCF_013186535.1_ASM1318653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f7070d4-a113-4224-92c2-50b455e9256f/dqc_reference/reference_markers.fasta -out GCF_013186535.1_ASM1318653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:04,622] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:04,625] [INFO] Selected 24 target genomes.
[2024-01-24 15:11:04,625] [INFO] Target genome list was writen to GCF_013186535.1_ASM1318653v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:04,634] [INFO] Task started: fastANI
[2024-01-24 15:11:04,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f90be0-ba15-494e-8a8e-c32e0ca12e09/GCF_013186535.1_ASM1318653v1_genomic.fna.gz --refList GCF_013186535.1_ASM1318653v1_genomic.fna/target_genomes.txt --output GCF_013186535.1_ASM1318653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:47,230] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:47,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f7070d4-a113-4224-92c2-50b455e9256f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:47,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f7070d4-a113-4224-92c2-50b455e9256f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:47,249] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:47,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:47,250] [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
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	100.0	3088	3088	95	conclusive
Nocardia transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	82.8695	1456	3088	95	below_threshold
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	82.8324	1489	3088	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	82.8012	1447	3088	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	82.7033	1438	3088	95	below_threshold
Nocardia pseudobrasiliensis	strain=DSM 44290	GCA_003350585.1	45979	45979	type	True	82.533	1536	3088	95	below_threshold
Nocardia pseudobrasiliensis	strain=NBRC 108224	GCA_001613105.1	45979	45979	type	True	82.5254	1517	3088	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	81.9573	1361	3088	95	below_threshold
Nocardia cerradoensis	strain=NBRC 101014	GCA_000308535.1	85688	85688	type	True	81.5534	1150	3088	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	81.47	1191	3088	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	81.4466	1180	3088	95	below_threshold
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	81.307	1320	3088	95	below_threshold
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	81.2949	1206	3088	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	81.2388	1231	3088	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	81.2183	1340	3088	95	below_threshold
Nocardia veterana	strain=NBRC 100344	GCA_000308855.1	132249	132249	type	True	81.1743	1151	3088	95	below_threshold
Nocardia veterana	strain=DSM 44445	GCA_012396305.1	132249	132249	type	True	81.1563	1157	3088	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	80.9332	1152	3088	95	below_threshold
Nocardia inohanensis	strain=NBRC 100128	GCA_001612945.1	209246	209246	type	True	80.3485	1250	3088	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	76.1597	462	3088	95	below_threshold
Streptomyces spirodelae	strain=DW4-2	GCA_017676385.1	2812904	2812904	type	True	76.1242	422	3088	95	below_threshold
Streptomyces prasinopilosus	strain=NRRL B-2711	GCA_001419695.1	67344	67344	type	True	75.9764	361	3088	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	75.8624	662	3088	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	75.8102	640	3088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:47,252] [INFO] DFAST Taxonomy check result was written to GCF_013186535.1_ASM1318653v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:47,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:47,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:47,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f7070d4-a113-4224-92c2-50b455e9256f/dqc_reference/checkm_data
[2024-01-24 15:11:47,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:47,343] [INFO] Task started: CheckM
[2024-01-24 15:11:47,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013186535.1_ASM1318653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013186535.1_ASM1318653v1_genomic.fna/checkm_input GCF_013186535.1_ASM1318653v1_genomic.fna/checkm_result
[2024-01-24 15:13:42,044] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:42,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 28.57%
--------------------------------------------------------------------------------
[2024-01-24 15:13:42,077] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:42,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:42,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013186535.1_ASM1318653v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:42,078] [INFO] Task started: Blastn
[2024-01-24 15:13:42,078] [INFO] Running command: blastn -query GCF_013186535.1_ASM1318653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f7070d4-a113-4224-92c2-50b455e9256f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013186535.1_ASM1318653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:44,041] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:44,045] [INFO] Selected 22 target genomes.
[2024-01-24 15:13:44,045] [INFO] Target genome list was writen to GCF_013186535.1_ASM1318653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:44,060] [INFO] Task started: fastANI
[2024-01-24 15:13:44,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4f90be0-ba15-494e-8a8e-c32e0ca12e09/GCF_013186535.1_ASM1318653v1_genomic.fna.gz --refList GCF_013186535.1_ASM1318653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013186535.1_ASM1318653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:14:24,305] [INFO] Task succeeded: fastANI
[2024-01-24 15:14:24,328] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:14:24,329] [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_013186535.1	s__Nocardia terpenica	100.0	3087	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.12	95.64	0.89	0.79	9	conclusive
GCF_015477355.1	s__Nocardia blacklockiae	83.2188	1432	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477765.1	s__Nocardia transvalensis_A	83.1964	1521	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308875.1	s__Nocardia transvalensis	82.7887	1448	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014466955.1	s__Nocardia wallacei	82.6633	1394	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613105.1	s__Nocardia pseudobrasiliensis	82.5455	1512	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018860155.1	s__Nocardia sp018860155	81.946	1365	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308535.1	s__Nocardia cerradoensis	81.5203	1155	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	-
GCF_001613005.1	s__Nocardia nova	81.4319	1182	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_001612845.1	s__Nocardia elegans	81.3893	1188	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	99.79	99.59	0.97	0.94	3	-
GCF_000308615.1	s__Nocardia jiangxiensis	81.3213	1316	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604425.1	s__Nocardia sp009604425	81.3036	1264	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308375.1	s__Nocardia aobensis	81.2997	1206	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_001613065.1	s__Nocardia miyunensis	81.2795	1286	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613505.1	s__Nocardia mikamii	81.2572	1228	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308855.1	s__Nocardia veterana	81.1518	1153	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003315035.1	s__Nocardia puris	80.9333	1151	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_001612945.1	s__Nocardia inohanensis	80.3515	1249	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010868145.1	s__Nocardia cyriacigeorgica_D	79.8753	946	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.70	99.66	0.98	0.98	4	-
GCF_017114865.1	s__Streptomyces verrucosisporus	76.1596	462	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.1585	N/A	N/A	N/A	N/A	1	-
GCF_000720635.1	s__Kitasatospora sp000720635	75.927	635	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655295.1	s__Streptomyces fumanus	75.8062	644	3088	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:14:24,331] [INFO] GTDB search result was written to GCF_013186535.1_ASM1318653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:14:24,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:14:24,337] [INFO] DFAST_QC result json was written to GCF_013186535.1_ASM1318653v1_genomic.fna/dqc_result.json
[2024-01-24 15:14:24,337] [INFO] DFAST_QC completed!
[2024-01-24 15:14:24,337] [INFO] Total running time: 0h4m4s