[2024-01-24 14:28:08,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg38abb904-57a9-4921-9f23-7f5c3dc76b62/dqc_reference
[2024-01-24 14:28:10,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,416] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d09ec44-ee73-40e4-b0a4-cf13cf223347/GCF_012911935.1_ASM1291193v1_genomic.fna.gz | prodigal -d GCF_012911935.1_ASM1291193v1_genomic.fna/cds.fna -a GCF_012911935.1_ASM1291193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:30,941] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:30,942] [INFO] Task started: HMMsearch
[2024-01-24 14:28:30,942] [INFO] Running command: hmmsearch --tblout GCF_012911935.1_ASM1291193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38abb904-57a9-4921-9f23-7f5c3dc76b62/dqc_reference/reference_markers.hmm GCF_012911935.1_ASM1291193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:31,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:31,305] [INFO] Found 6/6 markers.
[2024-01-24 14:28:31,369] [INFO] Query marker FASTA was written to GCF_012911935.1_ASM1291193v1_genomic.fna/markers.fasta
[2024-01-24 14:28:31,369] [INFO] Task started: Blastn
[2024-01-24 14:28:31,369] [INFO] Running command: blastn -query GCF_012911935.1_ASM1291193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38abb904-57a9-4921-9f23-7f5c3dc76b62/dqc_reference/reference_markers.fasta -out GCF_012911935.1_ASM1291193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:32,741] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:32,745] [INFO] Selected 14 target genomes.
[2024-01-24 14:28:32,745] [INFO] Target genome list was writen to GCF_012911935.1_ASM1291193v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:32,764] [INFO] Task started: fastANI
[2024-01-24 14:28:32,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d09ec44-ee73-40e4-b0a4-cf13cf223347/GCF_012911935.1_ASM1291193v1_genomic.fna.gz --refList GCF_012911935.1_ASM1291193v1_genomic.fna/target_genomes.txt --output GCF_012911935.1_ASM1291193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:57,956] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:57,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38abb904-57a9-4921-9f23-7f5c3dc76b62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:57,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38abb904-57a9-4921-9f23-7f5c3dc76b62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:57,971] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:57,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:57,971] [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
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	100.0	2297	2306	95	conclusive
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	85.6301	1354	2306	95	below_threshold
Pseudonocardia asaccharolytica	strain=DSM 44247	GCA_000423625.1	54010	54010	type	True	81.5943	960	2306	95	below_threshold
Pseudonocardia asaccharolytica	strain=NBRC 16224	GCA_007989065.1	54010	54010	type	True	81.5148	944	2306	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	80.9742	1017	2306	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	80.7306	1131	2306	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	80.616	995	2306	95	below_threshold
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	80.5528	1155	2306	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	80.5216	1105	2306	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	80.3342	997	2306	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	79.8481	1061	2306	95	below_threshold
Pseudonocardia antarctica	strain=DSM 44749	GCA_013408715.1	237656	237656	type	True	79.8425	968	2306	95	below_threshold
Pseudonocardia ammonioxydans	strain=CGMCC 4.1877	GCA_900115005.1	260086	260086	type	True	79.769	1023	2306	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	79.6361	1028	2306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:57,975] [INFO] DFAST Taxonomy check result was written to GCF_012911935.1_ASM1291193v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:57,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:57,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:57,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38abb904-57a9-4921-9f23-7f5c3dc76b62/dqc_reference/checkm_data
[2024-01-24 14:28:57,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:58,051] [INFO] Task started: CheckM
[2024-01-24 14:28:58,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012911935.1_ASM1291193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012911935.1_ASM1291193v1_genomic.fna/checkm_input GCF_012911935.1_ASM1291193v1_genomic.fna/checkm_result
[2024-01-24 14:30:37,491] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:37,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:37,519] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:37,519] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:37,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012911935.1_ASM1291193v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:37,520] [INFO] Task started: Blastn
[2024-01-24 14:30:37,520] [INFO] Running command: blastn -query GCF_012911935.1_ASM1291193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38abb904-57a9-4921-9f23-7f5c3dc76b62/dqc_reference/reference_markers_gtdb.fasta -out GCF_012911935.1_ASM1291193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:39,481] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:39,485] [INFO] Selected 15 target genomes.
[2024-01-24 14:30:39,486] [INFO] Target genome list was writen to GCF_012911935.1_ASM1291193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:39,517] [INFO] Task started: fastANI
[2024-01-24 14:30:39,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d09ec44-ee73-40e4-b0a4-cf13cf223347/GCF_012911935.1_ASM1291193v1_genomic.fna.gz --refList GCF_012911935.1_ASM1291193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012911935.1_ASM1291193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:06,082] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:06,096] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:06,096] [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_012911935.1	s__Pseudonocardia sp012911935	100.0	2297	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018531475.1	s__Pseudonocardia sp018531475	85.6848	1426	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911875.1	s__Pseudonocardia bannensis	85.6185	1355	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423625.1	s__Pseudonocardia asaccharolytica	81.609	958	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006539565.1	s__Pseudonocardia hydrocarbonoxydans	80.9272	1024	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717175.1	s__Pseudonocardia autotrophica_A	80.7449	1144	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	80.7334	1129	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCF_007989085.1	s__Pseudonocardia sulfidoxydans	80.5695	1003	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725415.1	s__Pseudonocardia sp001725415	80.5246	1060	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
GCA_019263595.1	s__Pseudonocardia sp019263595	80.4235	932	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911925.1	s__Pseudonocardia xinjiangensis	80.3527	994	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717045.1	s__Pseudonocardia cypriaca	80.0042	1010	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994075.1	s__Pseudonocardia hierapolitana	79.8374	1062	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014267175.1	s__Pseudonocardia sp014267175	79.7895	938	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876315.1	s__Pseudonocardia parietis	79.6013	1034	2306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:06,098] [INFO] GTDB search result was written to GCF_012911935.1_ASM1291193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:06,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:06,102] [INFO] DFAST_QC result json was written to GCF_012911935.1_ASM1291193v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:06,102] [INFO] DFAST_QC completed!
[2024-01-24 14:31:06,102] [INFO] Total running time: 0h2m58s