[2024-01-24 14:14:21,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:21,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:21,259] [INFO] DQC Reference Directory: /var/lib/cwl/stgda8b9237-93b1-486f-ade9-b778d483010d/dqc_reference
[2024-01-24 14:14:24,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:24,208] [INFO] Task started: Prodigal
[2024-01-24 14:14:24,209] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dc5d67a-3c6c-4336-b947-ccaaecc7bd63/GCF_001613185.1_ASM161318v1_genomic.fna.gz | prodigal -d GCF_001613185.1_ASM161318v1_genomic.fna/cds.fna -a GCF_001613185.1_ASM161318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:57,149] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:57,149] [INFO] Task started: HMMsearch
[2024-01-24 14:14:57,149] [INFO] Running command: hmmsearch --tblout GCF_001613185.1_ASM161318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda8b9237-93b1-486f-ade9-b778d483010d/dqc_reference/reference_markers.hmm GCF_001613185.1_ASM161318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:57,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:57,503] [INFO] Found 6/6 markers.
[2024-01-24 14:14:57,574] [INFO] Query marker FASTA was written to GCF_001613185.1_ASM161318v1_genomic.fna/markers.fasta
[2024-01-24 14:14:57,574] [INFO] Task started: Blastn
[2024-01-24 14:14:57,575] [INFO] Running command: blastn -query GCF_001613185.1_ASM161318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda8b9237-93b1-486f-ade9-b778d483010d/dqc_reference/reference_markers.fasta -out GCF_001613185.1_ASM161318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:59,018] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:59,022] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:59,022] [INFO] Target genome list was writen to GCF_001613185.1_ASM161318v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:59,029] [INFO] Task started: fastANI
[2024-01-24 14:14:59,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc5d67a-3c6c-4336-b947-ccaaecc7bd63/GCF_001613185.1_ASM161318v1_genomic.fna.gz --refList GCF_001613185.1_ASM161318v1_genomic.fna/target_genomes.txt --output GCF_001613185.1_ASM161318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:29,854] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:29,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda8b9237-93b1-486f-ade9-b778d483010d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:29,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda8b9237-93b1-486f-ade9-b778d483010d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:29,870] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:29,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:29,871] [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 puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	99.9893	2459	2470	95	conclusive
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	83.8531	1492	2470	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	83.8056	1407	2470	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	83.7491	1496	2470	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	83.7068	1516	2470	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	83.691	1447	2470	95	below_threshold
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	82.5765	1228	2470	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	82.459	1272	2470	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	81.993	1279	2470	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	81.985	1275	2470	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	81.9746	1268	2470	95	below_threshold
Nocardia niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	81.9413	1234	2470	95	below_threshold
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	81.9215	1301	2470	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	81.8326	1122	2470	95	below_threshold
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	81.6841	1326	2470	95	below_threshold
Nocardia terpenica	strain=IFM 0706	GCA_013186535.1	455432	455432	type	True	80.8122	1131	2470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:29,872] [INFO] DFAST Taxonomy check result was written to GCF_001613185.1_ASM161318v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:29,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:29,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:29,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda8b9237-93b1-486f-ade9-b778d483010d/dqc_reference/checkm_data
[2024-01-24 14:15:29,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:29,948] [INFO] Task started: CheckM
[2024-01-24 14:15:29,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613185.1_ASM161318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613185.1_ASM161318v1_genomic.fna/checkm_input GCF_001613185.1_ASM161318v1_genomic.fna/checkm_result
[2024-01-24 14:17:11,781] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:11,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:11,814] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:11,815] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:11,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613185.1_ASM161318v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:11,815] [INFO] Task started: Blastn
[2024-01-24 14:17:11,815] [INFO] Running command: blastn -query GCF_001613185.1_ASM161318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda8b9237-93b1-486f-ade9-b778d483010d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613185.1_ASM161318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:15,633] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:15,636] [INFO] Selected 18 target genomes.
[2024-01-24 14:17:15,637] [INFO] Target genome list was writen to GCF_001613185.1_ASM161318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:15,651] [INFO] Task started: fastANI
[2024-01-24 14:17:15,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc5d67a-3c6c-4336-b947-ccaaecc7bd63/GCF_001613185.1_ASM161318v1_genomic.fna.gz --refList GCF_001613185.1_ASM161318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613185.1_ASM161318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:51,416] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:51,431] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:51,432] [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_003315035.1	s__Nocardia puris	99.9893	2459	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	conclusive
GCF_006716565.1	s__Nocardia bhagyanarayanae	83.8453	1495	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613365.1	s__Nocardia xishanensis	83.7937	1410	2470	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	83.7388	1499	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_001613045.1	s__Nocardia lijiangensis	83.7042	1445	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308415.1	s__Nocardia asiatica	82.5687	1231	2470	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	82.0578	1244	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_900637185.1	s__Nocardia asteroides	81.9834	1288	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_001613465.1	s__Nocardia niwae	81.9079	1240	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477605.1	s__Nocardia amamiensis_A	81.8479	1213	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801125.1	s__Nocardia brasiliensis_C	81.8346	1286	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829325.1	s__Nocardia sp009829325	81.8213	1242	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_001612745.1	s__Nocardia amamiensis	81.7983	1127	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704205.1	s__Nocardia colli	81.716	1322	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250675.2	s__Nocardia brasiliensis_B	81.5407	1301	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
GCF_001886715.1	s__Nocardia mangyaensis	81.215	1199	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011801145.1	s__Nocardia arthritidis_A	81.0979	1250	2470	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	80.7803	1136	2470	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.12	95.64	0.89	0.79	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:51,434] [INFO] GTDB search result was written to GCF_001613185.1_ASM161318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:51,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:51,438] [INFO] DFAST_QC result json was written to GCF_001613185.1_ASM161318v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:51,438] [INFO] DFAST_QC completed!
[2024-01-24 14:17:51,439] [INFO] Total running time: 0h3m30s