[2024-01-24 12:21:57,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg925c0806-c9d2-4640-b01b-45377fe5ed3a/dqc_reference
[2024-01-24 12:21:59,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:59,007] [INFO] Task started: Prodigal
[2024-01-24 12:21:59,007] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa2759e8-7035-451e-bb40-eb78d9b75381/GCF_000308435.1_ASM30843v1_genomic.fna.gz | prodigal -d GCF_000308435.1_ASM30843v1_genomic.fna/cds.fna -a GCF_000308435.1_ASM30843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:31,767] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:31,767] [INFO] Task started: HMMsearch
[2024-01-24 12:22:31,767] [INFO] Running command: hmmsearch --tblout GCF_000308435.1_ASM30843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg925c0806-c9d2-4640-b01b-45377fe5ed3a/dqc_reference/reference_markers.hmm GCF_000308435.1_ASM30843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:32,111] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:32,112] [INFO] Found 6/6 markers.
[2024-01-24 12:22:32,172] [INFO] Query marker FASTA was written to GCF_000308435.1_ASM30843v1_genomic.fna/markers.fasta
[2024-01-24 12:22:32,173] [INFO] Task started: Blastn
[2024-01-24 12:22:32,173] [INFO] Running command: blastn -query GCF_000308435.1_ASM30843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg925c0806-c9d2-4640-b01b-45377fe5ed3a/dqc_reference/reference_markers.fasta -out GCF_000308435.1_ASM30843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:33,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:33,510] [INFO] Selected 13 target genomes.
[2024-01-24 12:22:33,510] [INFO] Target genome list was writen to GCF_000308435.1_ASM30843v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:33,516] [INFO] Task started: fastANI
[2024-01-24 12:22:33,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa2759e8-7035-451e-bb40-eb78d9b75381/GCF_000308435.1_ASM30843v1_genomic.fna.gz --refList GCF_000308435.1_ASM30843v1_genomic.fna/target_genomes.txt --output GCF_000308435.1_ASM30843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:57,460] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:57,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg925c0806-c9d2-4640-b01b-45377fe5ed3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:57,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg925c0806-c9d2-4640-b01b-45377fe5ed3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:57,472] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:57,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:57,472] [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 araoensis	strain=NBRC 100135	GCA_000308435.1	228600	228600	type	True	100.0	2406	2416	95	conclusive
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	91.7349	1948	2416	95	below_threshold
Nocardia exalbida	strain=NBRC 100660	GCA_000308575.1	290231	290231	type	True	89.7024	1809	2416	95	below_threshold
Nocardia gamkensis	strain=DSM 44956	GCA_012396055.1	352869	352869	type	True	89.6857	1875	2416	95	below_threshold
Nocardia gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	89.6574	1858	2416	95	below_threshold
Nocardia gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	89.6289	1849	2416	95	below_threshold
Nocardia niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	89.5844	1873	2416	95	below_threshold
Nocardia arthritidis	strain=NBRC 100137	GCA_001612765.1	228602	228602	type	True	89.5415	1805	2416	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	88.5613	1760	2416	95	below_threshold
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	88.2895	1721	2416	95	below_threshold
Nocardia amamiensis	strain=NBRC 102102	GCA_001612745.1	404578	404578	type	True	85.9772	1568	2416	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	82.1281	1195	2416	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	82.1271	1172	2416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:57,475] [INFO] DFAST Taxonomy check result was written to GCF_000308435.1_ASM30843v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:57,476] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:57,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:57,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg925c0806-c9d2-4640-b01b-45377fe5ed3a/dqc_reference/checkm_data
[2024-01-24 12:22:57,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:57,551] [INFO] Task started: CheckM
[2024-01-24 12:22:57,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308435.1_ASM30843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308435.1_ASM30843v1_genomic.fna/checkm_input GCF_000308435.1_ASM30843v1_genomic.fna/checkm_result
[2024-01-24 12:24:23,467] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:23,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:23,494] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:23,495] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:23,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308435.1_ASM30843v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:23,495] [INFO] Task started: Blastn
[2024-01-24 12:24:23,495] [INFO] Running command: blastn -query GCF_000308435.1_ASM30843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg925c0806-c9d2-4640-b01b-45377fe5ed3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308435.1_ASM30843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:25,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:25,339] [INFO] Selected 12 target genomes.
[2024-01-24 12:24:25,340] [INFO] Target genome list was writen to GCF_000308435.1_ASM30843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:25,347] [INFO] Task started: fastANI
[2024-01-24 12:24:25,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa2759e8-7035-451e-bb40-eb78d9b75381/GCF_000308435.1_ASM30843v1_genomic.fna.gz --refList GCF_000308435.1_ASM30843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000308435.1_ASM30843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:47,156] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:47,166] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:47,166] [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_000308435.1	s__Nocardia araoensis	100.0	2406	2416	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_001612785.1	s__Nocardia beijingensis	91.7291	1949	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_000308575.1	s__Nocardia exalbida	89.7012	1809	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_001612985.1	s__Nocardia gamkensis	89.6303	1849	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_001613465.1	s__Nocardia niwae	89.5789	1874	2416	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	89.5693	1904	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_001612765.1	s__Nocardia arthritidis	89.5162	1808	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_015477775.1	s__Nocardia abscessus_A	88.8849	1901	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013315795.1	s__Nocardia barduliensis	88.565	1760	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829295.1	s__Nocardia sp009829295	88.4154	1740	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.64	99.39	0.96	0.94	4	-
GCF_000308415.1	s__Nocardia asiatica	88.2997	1719	2416	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	82.0922	1202	2416	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:47,168] [INFO] GTDB search result was written to GCF_000308435.1_ASM30843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:47,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:47,172] [INFO] DFAST_QC result json was written to GCF_000308435.1_ASM30843v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:47,172] [INFO] DFAST_QC completed!
[2024-01-24 12:24:47,172] [INFO] Total running time: 0h2m50s