[2024-01-24 13:22:25,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:25,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:25,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg547e3f9f-bc5b-4186-b979-1d1fe408a790/dqc_reference
[2024-01-24 13:22:26,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:26,625] [INFO] Task started: Prodigal
[2024-01-24 13:22:26,625] [INFO] Running command: gunzip -c /var/lib/cwl/stge134dcd4-899f-4679-976c-70943a5c019d/GCF_003696265.1_ASM369626v1_genomic.fna.gz | prodigal -d GCF_003696265.1_ASM369626v1_genomic.fna/cds.fna -a GCF_003696265.1_ASM369626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:57,207] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:57,207] [INFO] Task started: HMMsearch
[2024-01-24 13:22:57,207] [INFO] Running command: hmmsearch --tblout GCF_003696265.1_ASM369626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg547e3f9f-bc5b-4186-b979-1d1fe408a790/dqc_reference/reference_markers.hmm GCF_003696265.1_ASM369626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:57,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:57,472] [INFO] Found 6/6 markers.
[2024-01-24 13:22:57,528] [INFO] Query marker FASTA was written to GCF_003696265.1_ASM369626v1_genomic.fna/markers.fasta
[2024-01-24 13:22:57,529] [INFO] Task started: Blastn
[2024-01-24 13:22:57,529] [INFO] Running command: blastn -query GCF_003696265.1_ASM369626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg547e3f9f-bc5b-4186-b979-1d1fe408a790/dqc_reference/reference_markers.fasta -out GCF_003696265.1_ASM369626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:58,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:58,728] [INFO] Selected 24 target genomes.
[2024-01-24 13:22:58,728] [INFO] Target genome list was writen to GCF_003696265.1_ASM369626v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:58,735] [INFO] Task started: fastANI
[2024-01-24 13:22:58,735] [INFO] Running command: fastANI --query /var/lib/cwl/stge134dcd4-899f-4679-976c-70943a5c019d/GCF_003696265.1_ASM369626v1_genomic.fna.gz --refList GCF_003696265.1_ASM369626v1_genomic.fna/target_genomes.txt --output GCF_003696265.1_ASM369626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:36,282] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:36,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg547e3f9f-bc5b-4186-b979-1d1fe408a790/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:36,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg547e3f9f-bc5b-4186-b979-1d1fe408a790/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:36,295] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:36,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:36,296] [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 stercoris	strain=NEAU-LL90	GCA_003696265.1	2483361	2483361	type	True	100.0	2487	2489	95	conclusive
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	80.5739	1084	2489	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	80.2065	1105	2489	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	80.1618	1034	2489	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	80.1606	1044	2489	95	below_threshold
Nocardia aobensis	strain=NBRC 100429	GCA_000308375.1	257277	257277	type	True	80.1256	1024	2489	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	80.0782	953	2489	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	80.0755	926	2489	95	below_threshold
Nocardia mexicana	strain=DSM 44952	GCA_003350525.1	279262	279262	type	True	80.0526	1129	2489	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	80.0133	957	2489	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	79.9961	1097	2489	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	79.9873	1059	2489	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	79.9605	1033	2489	95	below_threshold
Nocardia mikamii	strain=NBRC 108933	GCA_001613505.1	508464	508464	type	True	79.9592	1045	2489	95	below_threshold
Nocardia nova	strain=NBRC 15556	GCA_001613005.1	37330	37330	type	True	79.9549	1040	2489	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	79.9481	1051	2489	95	below_threshold
Nocardia veterana	strain=NBRC 100344	GCA_000308855.1	132249	132249	type	True	79.8718	976	2489	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	79.7824	983	2489	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	79.7816	1034	2489	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	79.7527	1009	2489	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	79.7004	1015	2489	95	below_threshold
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	79.6685	1072	2489	95	below_threshold
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	79.6042	1077	2489	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	79.2917	1012	2489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:36,297] [INFO] DFAST Taxonomy check result was written to GCF_003696265.1_ASM369626v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:36,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:36,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:36,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg547e3f9f-bc5b-4186-b979-1d1fe408a790/dqc_reference/checkm_data
[2024-01-24 13:23:36,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:36,364] [INFO] Task started: CheckM
[2024-01-24 13:23:36,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003696265.1_ASM369626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003696265.1_ASM369626v1_genomic.fna/checkm_input GCF_003696265.1_ASM369626v1_genomic.fna/checkm_result
[2024-01-24 13:25:07,494] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:07,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:07,511] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:07,511] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:07,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003696265.1_ASM369626v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:07,512] [INFO] Task started: Blastn
[2024-01-24 13:25:07,512] [INFO] Running command: blastn -query GCF_003696265.1_ASM369626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg547e3f9f-bc5b-4186-b979-1d1fe408a790/dqc_reference/reference_markers_gtdb.fasta -out GCF_003696265.1_ASM369626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:09,283] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:09,286] [INFO] Selected 23 target genomes.
[2024-01-24 13:25:09,286] [INFO] Target genome list was writen to GCF_003696265.1_ASM369626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:09,297] [INFO] Task started: fastANI
[2024-01-24 13:25:09,297] [INFO] Running command: fastANI --query /var/lib/cwl/stge134dcd4-899f-4679-976c-70943a5c019d/GCF_003696265.1_ASM369626v1_genomic.fna.gz --refList GCF_003696265.1_ASM369626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003696265.1_ASM369626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:45,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:45,622] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:45,622] [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_003696265.1	s__Nocardia stercoris	100.0	2487	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015477355.1	s__Nocardia blacklockiae	80.6681	1112	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013186535.1	s__Nocardia terpenica	80.6117	1078	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.12	95.64	0.89	0.79	9	-
GCF_900637185.1	s__Nocardia asteroides	80.2294	1045	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_000308875.1	s__Nocardia transvalensis	80.1703	1111	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000308375.1	s__Nocardia aobensis	80.114	1022	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	98.11	97.03	0.89	0.86	3	-
GCF_001182745.1	s__Nocardia farcinica	80.0255	959	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_001613005.1	s__Nocardia nova	79.9688	1041	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	98.75	97.55	0.88	0.84	13	-
GCF_001612635.1	s__Nocardia africana	79.9671	1047	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001613505.1	s__Nocardia mikamii	79.9494	1050	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	79.9379	1035	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612845.1	s__Nocardia elegans	79.9194	1037	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9334	99.79	99.59	0.97	0.94	3	-
GCF_000381925.1	s__Nocardia sp000381925	79.8931	1135	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308595.1	s__Nocardia higoensis	79.8804	849	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	79.8712	924	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_000308855.1	s__Nocardia veterana	79.8586	978	2489	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	79.7623	989	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	79.7583	1038	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612615.1	s__Nocardia amikacinitolerans	79.7451	1010	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_015354405.1	s__Nocardia sp015354405	79.722	1009	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308615.1	s__Nocardia jiangxiensis	79.6778	1069	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	79.6764	891	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_011801125.1	s__Nocardia brasiliensis_C	79.5165	995	2489	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:45,623] [INFO] GTDB search result was written to GCF_003696265.1_ASM369626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:45,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:45,628] [INFO] DFAST_QC result json was written to GCF_003696265.1_ASM369626v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:45,628] [INFO] DFAST_QC completed!
[2024-01-24 13:25:45,628] [INFO] Total running time: 0h3m20s