[2024-01-24 13:47:10,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,457] [INFO] DQC Reference Directory: /var/lib/cwl/stgba312019-214a-4769-a9d1-68999c97451e/dqc_reference
[2024-01-24 13:47:11,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:11,866] [INFO] Task started: Prodigal
[2024-01-24 13:47:11,867] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e0fb03d-d916-4bd8-9277-6ee8cdfea08d/GCF_000308595.1_ASM30859v1_genomic.fna.gz | prodigal -d GCF_000308595.1_ASM30859v1_genomic.fna/cds.fna -a GCF_000308595.1_ASM30859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:34,381] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:34,381] [INFO] Task started: HMMsearch
[2024-01-24 13:47:34,382] [INFO] Running command: hmmsearch --tblout GCF_000308595.1_ASM30859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba312019-214a-4769-a9d1-68999c97451e/dqc_reference/reference_markers.hmm GCF_000308595.1_ASM30859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:34,691] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:34,693] [INFO] Found 6/6 markers.
[2024-01-24 13:47:34,747] [INFO] Query marker FASTA was written to GCF_000308595.1_ASM30859v1_genomic.fna/markers.fasta
[2024-01-24 13:47:34,747] [INFO] Task started: Blastn
[2024-01-24 13:47:34,748] [INFO] Running command: blastn -query GCF_000308595.1_ASM30859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba312019-214a-4769-a9d1-68999c97451e/dqc_reference/reference_markers.fasta -out GCF_000308595.1_ASM30859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:36,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:36,088] [INFO] Selected 7 target genomes.
[2024-01-24 13:47:36,089] [INFO] Target genome list was writen to GCF_000308595.1_ASM30859v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:36,093] [INFO] Task started: fastANI
[2024-01-24 13:47:36,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e0fb03d-d916-4bd8-9277-6ee8cdfea08d/GCF_000308595.1_ASM30859v1_genomic.fna.gz --refList GCF_000308595.1_ASM30859v1_genomic.fna/target_genomes.txt --output GCF_000308595.1_ASM30859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:47,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:47,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba312019-214a-4769-a9d1-68999c97451e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:47,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba312019-214a-4769-a9d1-68999c97451e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:47,694] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:47,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:47,695] [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 higoensis	strain=NBRC 100133	GCA_000308595.1	228599	228599	type	True	100.0	2232	2242	95	conclusive
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	89.5463	1627	2242	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	84.696	1260	2242	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	84.6729	1327	2242	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	84.6448	1313	2242	95	below_threshold
Nocardia arizonensis	strain=W9405	GCA_001310275.1	1141647	1141647	type	True	81.1336	1098	2242	95	below_threshold
Nocardia arizonensis	strain=NBRC 108935	GCA_001618405.1	1141647	1141647	type	True	81.0706	1099	2242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:47,696] [INFO] DFAST Taxonomy check result was written to GCF_000308595.1_ASM30859v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:47,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:47,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:47,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba312019-214a-4769-a9d1-68999c97451e/dqc_reference/checkm_data
[2024-01-24 13:47:47,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:47,759] [INFO] Task started: CheckM
[2024-01-24 13:47:47,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308595.1_ASM30859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308595.1_ASM30859v1_genomic.fna/checkm_input GCF_000308595.1_ASM30859v1_genomic.fna/checkm_result
[2024-01-24 13:48:57,721] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:57,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:57,749] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:57,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:57,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308595.1_ASM30859v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:57,751] [INFO] Task started: Blastn
[2024-01-24 13:48:57,751] [INFO] Running command: blastn -query GCF_000308595.1_ASM30859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba312019-214a-4769-a9d1-68999c97451e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308595.1_ASM30859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:59,836] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:59,841] [INFO] Selected 11 target genomes.
[2024-01-24 13:48:59,841] [INFO] Target genome list was writen to GCF_000308595.1_ASM30859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:59,852] [INFO] Task started: fastANI
[2024-01-24 13:48:59,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e0fb03d-d916-4bd8-9277-6ee8cdfea08d/GCF_000308595.1_ASM30859v1_genomic.fna.gz --refList GCF_000308595.1_ASM30859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000308595.1_ASM30859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:19,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:19,738] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:19,738] [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_000308595.1	s__Nocardia higoensis	100.0	2232	2242	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_001613125.1	s__Nocardia shimofusensis	89.5176	1630	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477835.1	s__Nocardia higoensis_A	88.9288	1554	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	84.7248	1320	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	82.3628	1195	2242	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	82.356	1172	2242	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	82.2137	1171	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612785.1	s__Nocardia beijingensis	81.4515	1138	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_009829325.1	s__Nocardia sp009829325	81.3144	1077	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_001612885.1	s__Nocardia harenae	81.1666	1108	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310275.1	s__Nocardia arizonensis	81.12	1101	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,739] [INFO] GTDB search result was written to GCF_000308595.1_ASM30859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:19,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:19,743] [INFO] DFAST_QC result json was written to GCF_000308595.1_ASM30859v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:19,743] [INFO] DFAST_QC completed!
[2024-01-24 13:49:19,743] [INFO] Total running time: 0h2m9s