[2024-01-24 12:29:37,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:37,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:37,431] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeb6a96d-b302-458f-9628-66f99ec729a0/dqc_reference
[2024-01-24 12:29:38,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:38,709] [INFO] Task started: Prodigal
[2024-01-24 12:29:38,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg5530794d-9e7e-4c2a-a1d8-bee8a94406fb/GCF_019038455.1_ASM1903845v1_genomic.fna.gz | prodigal -d GCF_019038455.1_ASM1903845v1_genomic.fna/cds.fna -a GCF_019038455.1_ASM1903845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:06,195] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:06,195] [INFO] Task started: HMMsearch
[2024-01-24 12:30:06,195] [INFO] Running command: hmmsearch --tblout GCF_019038455.1_ASM1903845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeb6a96d-b302-458f-9628-66f99ec729a0/dqc_reference/reference_markers.hmm GCF_019038455.1_ASM1903845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:06,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:06,559] [INFO] Found 6/6 markers.
[2024-01-24 12:30:06,634] [INFO] Query marker FASTA was written to GCF_019038455.1_ASM1903845v1_genomic.fna/markers.fasta
[2024-01-24 12:30:06,635] [INFO] Task started: Blastn
[2024-01-24 12:30:06,635] [INFO] Running command: blastn -query GCF_019038455.1_ASM1903845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb6a96d-b302-458f-9628-66f99ec729a0/dqc_reference/reference_markers.fasta -out GCF_019038455.1_ASM1903845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:07,787] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:07,792] [INFO] Selected 17 target genomes.
[2024-01-24 12:30:07,793] [INFO] Target genome list was writen to GCF_019038455.1_ASM1903845v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:07,809] [INFO] Task started: fastANI
[2024-01-24 12:30:07,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg5530794d-9e7e-4c2a-a1d8-bee8a94406fb/GCF_019038455.1_ASM1903845v1_genomic.fna.gz --refList GCF_019038455.1_ASM1903845v1_genomic.fna/target_genomes.txt --output GCF_019038455.1_ASM1903845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:38,558] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:38,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeb6a96d-b302-458f-9628-66f99ec729a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:38,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeb6a96d-b302-458f-9628-66f99ec729a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:38,572] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:38,573] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:30:38,573] [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 noduli	strain=ncl1	GCA_019038455.1	2815722	2815722	type	True	100.0	2815	2834	95	inconclusive
Nocardia aurea	strain=SYSU K10002	GCA_003123685.1	2144174	2144174	type	True	95.1538	2142	2834	95	inconclusive
Nocardia arizonensis	strain=NBRC 108935	GCA_001618405.1	1141647	1141647	type	True	82.7677	1385	2834	95	below_threshold
Nocardia arizonensis	strain=W9405	GCA_001310275.1	1141647	1141647	type	True	82.7458	1367	2834	95	below_threshold
Nocardia bovistercoris	strain=NEAU-351	GCA_015674855.1	2785916	2785916	type	True	82.6688	1538	2834	95	below_threshold
Nocardia takedensis	strain=NBRC 100417	GCA_000308695.1	259390	259390	type	True	82.4864	1492	2834	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	81.7142	1291	2834	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	81.6919	1315	2834	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	81.6638	1266	2834	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	81.6443	1302	2834	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	81.5969	1327	2834	95	below_threshold
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	80.9487	1234	2834	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	80.924	1223	2834	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	80.8926	1248	2834	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	80.8521	1204	2834	95	below_threshold
Nocardia pseudovaccinii	strain=NBRC 100343	GCA_001613225.1	189540	189540	type	True	80.5947	1227	2834	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	80.5092	1147	2834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:38,575] [INFO] DFAST Taxonomy check result was written to GCF_019038455.1_ASM1903845v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:38,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:38,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:38,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeb6a96d-b302-458f-9628-66f99ec729a0/dqc_reference/checkm_data
[2024-01-24 12:30:38,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:38,662] [INFO] Task started: CheckM
[2024-01-24 12:30:38,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019038455.1_ASM1903845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019038455.1_ASM1903845v1_genomic.fna/checkm_input GCF_019038455.1_ASM1903845v1_genomic.fna/checkm_result
[2024-01-24 12:32:02,294] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:02,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:02,320] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:02,320] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:02,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019038455.1_ASM1903845v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:02,321] [INFO] Task started: Blastn
[2024-01-24 12:32:02,322] [INFO] Running command: blastn -query GCF_019038455.1_ASM1903845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb6a96d-b302-458f-9628-66f99ec729a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_019038455.1_ASM1903845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:03,999] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:04,005] [INFO] Selected 20 target genomes.
[2024-01-24 12:32:04,005] [INFO] Target genome list was writen to GCF_019038455.1_ASM1903845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:04,030] [INFO] Task started: fastANI
[2024-01-24 12:32:04,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg5530794d-9e7e-4c2a-a1d8-bee8a94406fb/GCF_019038455.1_ASM1903845v1_genomic.fna.gz --refList GCF_019038455.1_ASM1903845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019038455.1_ASM1903845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:35,560] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:35,578] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:35,579] [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_003123685.1	s__Nocardia aurea	95.1476	2143	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.19	95.19	0.76	0.76	2	conclusive
GCF_001310275.1	s__Nocardia arizonensis	82.761	1365	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_015674855.1	s__Nocardia bovistercoris	82.6499	1541	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308695.1	s__Nocardia takedensis	82.5111	1487	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	81.7076	1292	2834	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	81.6529	1268	2834	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	81.6255	1307	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	81.5817	1330	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900269665.1	s__Nocardia suismassiliense	80.9694	1230	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_000308475.2	s__Nocardia brasiliensis	80.9255	1206	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	80.9141	1050	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_000308715.1	s__Nocardia tenerifensis	80.8821	1133	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001613425.1	s__Nocardia vulneris	80.8777	1251	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_019222765.1	s__Nocardia iowensis	80.8575	1203	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613225.1	s__Nocardia pseudovaccinii	80.5923	1226	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637185.1	s__Nocardia asteroides	80.5667	1123	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_010868145.1	s__Nocardia cyriacigeorgica_D	80.5175	997	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.70	99.66	0.98	0.98	4	-
GCF_017168335.1	s__Rhodococcus_B sp017168335	77.4256	398	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620545.1	s__Terrabacter sp000620545	76.1999	197	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001046875.1	s__Tetrasphaera_A jenkinsii	76.0201	142	2834	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Tetrasphaera_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:35,581] [INFO] GTDB search result was written to GCF_019038455.1_ASM1903845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:35,581] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:35,588] [INFO] DFAST_QC result json was written to GCF_019038455.1_ASM1903845v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:35,588] [INFO] DFAST_QC completed!
[2024-01-24 12:32:35,588] [INFO] Total running time: 0h2m58s