[2024-01-24 15:10:37,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:37,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:37,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg7eca9438-965f-4465-8a54-6b3e5adfaf61/dqc_reference
[2024-01-24 15:10:40,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,097] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,098] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3161b27-e85b-4e3b-9e02-02b4eb013441/GCF_013359885.1_ASM1335988v1_genomic.fna.gz | prodigal -d GCF_013359885.1_ASM1335988v1_genomic.fna/cds.fna -a GCF_013359885.1_ASM1335988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:50,385] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:50,385] [INFO] Task started: HMMsearch
[2024-01-24 15:10:50,385] [INFO] Running command: hmmsearch --tblout GCF_013359885.1_ASM1335988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7eca9438-965f-4465-8a54-6b3e5adfaf61/dqc_reference/reference_markers.hmm GCF_013359885.1_ASM1335988v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:50,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:50,706] [INFO] Found 6/6 markers.
[2024-01-24 15:10:50,741] [INFO] Query marker FASTA was written to GCF_013359885.1_ASM1335988v1_genomic.fna/markers.fasta
[2024-01-24 15:10:50,742] [INFO] Task started: Blastn
[2024-01-24 15:10:50,742] [INFO] Running command: blastn -query GCF_013359885.1_ASM1335988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eca9438-965f-4465-8a54-6b3e5adfaf61/dqc_reference/reference_markers.fasta -out GCF_013359885.1_ASM1335988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:52,059] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:52,061] [INFO] Selected 11 target genomes.
[2024-01-24 15:10:52,062] [INFO] Target genome list was writen to GCF_013359885.1_ASM1335988v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:52,068] [INFO] Task started: fastANI
[2024-01-24 15:10:52,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3161b27-e85b-4e3b-9e02-02b4eb013441/GCF_013359885.1_ASM1335988v1_genomic.fna.gz --refList GCF_013359885.1_ASM1335988v1_genomic.fna/target_genomes.txt --output GCF_013359885.1_ASM1335988v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:02,478] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:02,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7eca9438-965f-4465-8a54-6b3e5adfaf61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:02,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7eca9438-965f-4465-8a54-6b3e5adfaf61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:02,489] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:11:02,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:02,490] [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
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	100.0	1184	1209	95	conclusive
Curtobacterium luteum	strain=DSM 20542	GCA_016907595.1	33881	33881	type	True	99.9913	1178	1209	95	conclusive
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	99.979	1163	1209	95	conclusive
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	85.9555	894	1209	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	85.8817	902	1209	95	below_threshold
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	85.8534	874	1209	95	below_threshold
Curtobacterium pusillum	strain=ATCC 19096	GCA_013359865.1	69373	69373	suspected-type	True	85.7613	867	1209	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	85.1663	919	1209	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	85.1463	902	1209	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	84.1488	796	1209	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	84.1292	812	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:02,492] [INFO] DFAST Taxonomy check result was written to GCF_013359885.1_ASM1335988v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:02,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:02,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:02,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7eca9438-965f-4465-8a54-6b3e5adfaf61/dqc_reference/checkm_data
[2024-01-24 15:11:02,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:02,542] [INFO] Task started: CheckM
[2024-01-24 15:11:02,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013359885.1_ASM1335988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013359885.1_ASM1335988v1_genomic.fna/checkm_input GCF_013359885.1_ASM1335988v1_genomic.fna/checkm_result
[2024-01-24 15:11:58,367] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:58,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:58,388] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:58,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:58,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013359885.1_ASM1335988v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:58,389] [INFO] Task started: Blastn
[2024-01-24 15:11:58,389] [INFO] Running command: blastn -query GCF_013359885.1_ASM1335988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eca9438-965f-4465-8a54-6b3e5adfaf61/dqc_reference/reference_markers_gtdb.fasta -out GCF_013359885.1_ASM1335988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:00,403] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:00,407] [INFO] Selected 12 target genomes.
[2024-01-24 15:12:00,408] [INFO] Target genome list was writen to GCF_013359885.1_ASM1335988v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:00,418] [INFO] Task started: fastANI
[2024-01-24 15:12:00,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3161b27-e85b-4e3b-9e02-02b4eb013441/GCF_013359885.1_ASM1335988v1_genomic.fna.gz --refList GCF_013359885.1_ASM1335988v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013359885.1_ASM1335988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:12,186] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:12,196] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:12,196] [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_014646995.1	s__Curtobacterium luteum	99.979	1163	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	99.66	99.01	0.98	0.96	4	conclusive
GCF_001475545.1	s__Curtobacterium luteum_A	89.0357	932	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002412165.1	s__Curtobacterium sp002412165	87.4525	962	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806325.1	s__Curtobacterium sp001806325	86.1345	940	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.12	98.02	0.92	0.92	4	-
GCF_000333375.1	s__Curtobacterium sp000333375	86.0854	697	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025645.1	s__Curtobacterium pusillum_A	85.9242	916	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	95.99	95.99	0.91	0.91	2	-
GCF_006715175.1	s__Curtobacterium citreum	85.8678	922	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.94	96.06	0.93	0.88	10	-
GCF_001742745.1	s__Curtobacterium sp001742745	85.5679	836	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.38	97.38	0.89	0.89	2	-
GCF_003234185.1	s__Curtobacterium sp003234185	85.4314	805	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772085.1	s__Curtobacterium sp000772085	85.2866	858	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.95	98.95	0.96	0.96	2	-
GCF_003752025.1	s__Curtobacterium sp003752025	85.2337	897	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015350995.1	s__Curtobacterium sp015350995	85.0813	921	1209	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:12,198] [INFO] GTDB search result was written to GCF_013359885.1_ASM1335988v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:12,198] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:12,201] [INFO] DFAST_QC result json was written to GCF_013359885.1_ASM1335988v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:12,201] [INFO] DFAST_QC completed!
[2024-01-24 15:12:12,202] [INFO] Total running time: 0h1m34s