[2024-01-24 14:19:15,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,151] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,151] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8d154f3-0a94-4677-bd45-b78eaa1e9b14/dqc_reference
[2024-01-24 14:19:16,465] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:16,466] [INFO] Task started: Prodigal
[2024-01-24 14:19:16,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ec13f9c-ac55-4875-8537-19c6058d4245/GCF_007989085.1_ASM798908v1_genomic.fna.gz | prodigal -d GCF_007989085.1_ASM798908v1_genomic.fna/cds.fna -a GCF_007989085.1_ASM798908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:33,544] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:33,545] [INFO] Task started: HMMsearch
[2024-01-24 14:19:33,545] [INFO] Running command: hmmsearch --tblout GCF_007989085.1_ASM798908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8d154f3-0a94-4677-bd45-b78eaa1e9b14/dqc_reference/reference_markers.hmm GCF_007989085.1_ASM798908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:33,898] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:33,899] [INFO] Found 6/6 markers.
[2024-01-24 14:19:33,955] [INFO] Query marker FASTA was written to GCF_007989085.1_ASM798908v1_genomic.fna/markers.fasta
[2024-01-24 14:19:33,956] [INFO] Task started: Blastn
[2024-01-24 14:19:33,956] [INFO] Running command: blastn -query GCF_007989085.1_ASM798908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8d154f3-0a94-4677-bd45-b78eaa1e9b14/dqc_reference/reference_markers.fasta -out GCF_007989085.1_ASM798908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:35,450] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:35,457] [INFO] Selected 14 target genomes.
[2024-01-24 14:19:35,458] [INFO] Target genome list was writen to GCF_007989085.1_ASM798908v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:35,465] [INFO] Task started: fastANI
[2024-01-24 14:19:35,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec13f9c-ac55-4875-8537-19c6058d4245/GCF_007989085.1_ASM798908v1_genomic.fna.gz --refList GCF_007989085.1_ASM798908v1_genomic.fna/target_genomes.txt --output GCF_007989085.1_ASM798908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:02,701] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:02,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8d154f3-0a94-4677-bd45-b78eaa1e9b14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:02,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8d154f3-0a94-4677-bd45-b78eaa1e9b14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:02,717] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:02,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:02,718] [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 sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	100.0	2080	2095	95	conclusive
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	85.8529	1556	2095	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	80.3963	1020	2095	95	below_threshold
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	80.3714	907	2095	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	80.3631	1074	2095	95	below_threshold
Pseudonocardia terrae	strain=RS11V-5	GCA_021343995.1	2905831	2905831	type	True	80.1338	1100	2095	95	below_threshold
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	80.0856	1090	2095	95	below_threshold
Pseudonocardia asaccharolytica	strain=DSM 44247	GCA_000423625.1	54010	54010	type	True	79.9128	839	2095	95	below_threshold
Pseudonocardia asaccharolytica	strain=NBRC 16224	GCA_007989065.1	54010	54010	type	True	79.8719	823	2095	95	below_threshold
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	79.6664	953	2095	95	below_threshold
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	79.6618	903	2095	95	below_threshold
Pseudonocardia nigra	strain=DSM 104088	GCA_019396355.1	1921578	1921578	type	True	79.574	937	2095	95	below_threshold
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	79.5112	997	2095	95	below_threshold
Pseudonocardia alaniniphila	strain=Y-16303	GCA_022524485.1	75291	75291	type	True	79.0532	966	2095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:02,727] [INFO] DFAST Taxonomy check result was written to GCF_007989085.1_ASM798908v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:02,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:02,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:02,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8d154f3-0a94-4677-bd45-b78eaa1e9b14/dqc_reference/checkm_data
[2024-01-24 14:20:02,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:02,854] [INFO] Task started: CheckM
[2024-01-24 14:20:02,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989085.1_ASM798908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989085.1_ASM798908v1_genomic.fna/checkm_input GCF_007989085.1_ASM798908v1_genomic.fna/checkm_result
[2024-01-24 14:21:33,231] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:33,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:33,257] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:33,257] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:33,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989085.1_ASM798908v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:33,258] [INFO] Task started: Blastn
[2024-01-24 14:21:33,258] [INFO] Running command: blastn -query GCF_007989085.1_ASM798908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8d154f3-0a94-4677-bd45-b78eaa1e9b14/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989085.1_ASM798908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:35,454] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:35,459] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:35,460] [INFO] Target genome list was writen to GCF_007989085.1_ASM798908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:35,470] [INFO] Task started: fastANI
[2024-01-24 14:21:35,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ec13f9c-ac55-4875-8537-19c6058d4245/GCF_007989085.1_ASM798908v1_genomic.fna.gz --refList GCF_007989085.1_ASM798908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989085.1_ASM798908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:53,310] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:53,320] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:53,320] [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_007989085.1	s__Pseudonocardia sulfidoxydans	100.0	2080	2095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001725415.1	s__Pseudonocardia sp001725415	91.4535	1632	2095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	97.90	95.81	0.91	0.83	3	-
GCF_002583555.1	s__Pseudonocardia sp002583555	88.6395	1527	2095	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	85.8568	1554	2095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCF_012911875.1	s__Pseudonocardia bannensis	80.38	906	2095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911935.1	s__Pseudonocardia sp012911935	80.3505	1028	2095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531475.1	s__Pseudonocardia sp018531475	80.245	940	2095	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	80.188	1122	2095	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	79.6494	906	2095	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531445.1	s__Pseudonocardia sp018531445	79.4439	1000	2095	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 14:21:53,322] [INFO] GTDB search result was written to GCF_007989085.1_ASM798908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:53,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:53,326] [INFO] DFAST_QC result json was written to GCF_007989085.1_ASM798908v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:53,326] [INFO] DFAST_QC completed!
[2024-01-24 14:21:53,326] [INFO] Total running time: 0h2m38s