[2024-01-24 11:59:35,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,660] [INFO] DQC Reference Directory: /var/lib/cwl/stgc56b7ceb-ccd1-4d10-8019-987bf1cad15f/dqc_reference
[2024-01-24 11:59:36,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,875] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg4be0b5ba-b823-4558-8425-8f958e00dbb9/GCF_020733705.1_ASM2073370v1_genomic.fna.gz | prodigal -d GCF_020733705.1_ASM2073370v1_genomic.fna/cds.fna -a GCF_020733705.1_ASM2073370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:01,402] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:01,403] [INFO] Task started: HMMsearch
[2024-01-24 12:00:01,403] [INFO] Running command: hmmsearch --tblout GCF_020733705.1_ASM2073370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc56b7ceb-ccd1-4d10-8019-987bf1cad15f/dqc_reference/reference_markers.hmm GCF_020733705.1_ASM2073370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:01,799] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:01,800] [INFO] Found 6/6 markers.
[2024-01-24 12:00:01,856] [INFO] Query marker FASTA was written to GCF_020733705.1_ASM2073370v1_genomic.fna/markers.fasta
[2024-01-24 12:00:01,857] [INFO] Task started: Blastn
[2024-01-24 12:00:01,857] [INFO] Running command: blastn -query GCF_020733705.1_ASM2073370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56b7ceb-ccd1-4d10-8019-987bf1cad15f/dqc_reference/reference_markers.fasta -out GCF_020733705.1_ASM2073370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:03,036] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:03,042] [INFO] Selected 18 target genomes.
[2024-01-24 12:00:03,043] [INFO] Target genome list was writen to GCF_020733705.1_ASM2073370v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:03,056] [INFO] Task started: fastANI
[2024-01-24 12:00:03,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg4be0b5ba-b823-4558-8425-8f958e00dbb9/GCF_020733705.1_ASM2073370v1_genomic.fna.gz --refList GCF_020733705.1_ASM2073370v1_genomic.fna/target_genomes.txt --output GCF_020733705.1_ASM2073370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:30,348] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:30,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc56b7ceb-ccd1-4d10-8019-987bf1cad15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:30,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc56b7ceb-ccd1-4d10-8019-987bf1cad15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:30,368] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:30,368] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:30,368] [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 anaemiae	strain=NBRC 100462	GCA_001612725.1	263910	263910	type	True	81.8232	1225	2283	95	below_threshold
Nocardia pseudovaccinii	strain=NBRC 100343	GCA_001613225.1	189540	189540	type	True	81.77	1175	2283	95	below_threshold
Nocardia vinacea	strain=NBRC 16497	GCA_000308835.1	96468	96468	type	True	81.7479	1251	2283	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	81.6605	1175	2283	95	below_threshold
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	81.5191	1157	2283	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	81.4197	1119	2283	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	81.4144	1108	2283	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	81.3981	1134	2283	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	81.364	1117	2283	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	81.2463	1122	2283	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	81.2021	1088	2283	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	81.0104	1031	2283	95	below_threshold
Nocardia gamkensis	strain=DSM 44956	GCA_012396055.1	352869	352869	type	True	80.9905	1090	2283	95	below_threshold
Nocardia gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	80.9543	1090	2283	95	below_threshold
Nocardia gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	80.9286	1077	2283	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	80.7636	1101	2283	95	below_threshold
Nocardia cyriacigeorgica	strain=NBRC 100375	GCA_000308555.1	135487	135487	type	True	80.6746	920	2283	95	below_threshold
Nocardia cyriacigeorgica	strain=DSM 44484	GCA_005863225.1	135487	135487	type	True	80.6185	964	2283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:30,370] [INFO] DFAST Taxonomy check result was written to GCF_020733705.1_ASM2073370v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:30,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:30,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:30,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc56b7ceb-ccd1-4d10-8019-987bf1cad15f/dqc_reference/checkm_data
[2024-01-24 12:00:30,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:30,439] [INFO] Task started: CheckM
[2024-01-24 12:00:30,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020733705.1_ASM2073370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020733705.1_ASM2073370v1_genomic.fna/checkm_input GCF_020733705.1_ASM2073370v1_genomic.fna/checkm_result
[2024-01-24 12:01:37,109] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:37,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:37,135] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:37,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:37,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020733705.1_ASM2073370v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:37,136] [INFO] Task started: Blastn
[2024-01-24 12:01:37,137] [INFO] Running command: blastn -query GCF_020733705.1_ASM2073370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc56b7ceb-ccd1-4d10-8019-987bf1cad15f/dqc_reference/reference_markers_gtdb.fasta -out GCF_020733705.1_ASM2073370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:38,823] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:38,828] [INFO] Selected 18 target genomes.
[2024-01-24 12:01:38,828] [INFO] Target genome list was writen to GCF_020733705.1_ASM2073370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:38,857] [INFO] Task started: fastANI
[2024-01-24 12:01:38,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg4be0b5ba-b823-4558-8425-8f958e00dbb9/GCF_020733705.1_ASM2073370v1_genomic.fna.gz --refList GCF_020733705.1_ASM2073370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020733705.1_ASM2073370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:06,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:06,162] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:02:06,162] [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_001612725.1	s__Nocardia anaemiae	81.8128	1227	2283	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	81.7854	1174	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308835.1	s__Nocardia vinacea	81.7533	1248	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019222765.1	s__Nocardia iowensis	81.6584	1176	2283	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	81.5286	1157	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_007990755.1	s__Nocardia ninae	81.4452	1126	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.51	95.51	0.86	0.86	2	-
GCF_001612615.1	s__Nocardia amikacinitolerans	81.4215	1108	2283	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	81.3792	1116	2283	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	81.1972	1088	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612745.1	s__Nocardia amamiensis	81.0237	1029	2283	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	80.9817	1087	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308435.1	s__Nocardia araoensis	80.9303	1028	2283	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	80.7998	995	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_005863245.1	s__Nocardia cyriacigeorgica_C	80.673	990	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.66	96.66	0.89	0.89	2	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	80.6561	983	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_011801145.1	s__Nocardia arthritidis_A	80.6523	1065	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308555.1	s__Nocardia cyriacigeorgica	80.6415	925	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.94	96.19	0.91	0.88	19	-
GCF_010868145.1	s__Nocardia cyriacigeorgica_D	80.3992	961	2283	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.70	99.66	0.98	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:06,164] [INFO] GTDB search result was written to GCF_020733705.1_ASM2073370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:06,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:06,169] [INFO] DFAST_QC result json was written to GCF_020733705.1_ASM2073370v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:06,169] [INFO] DFAST_QC completed!
[2024-01-24 12:02:06,169] [INFO] Total running time: 0h2m31s