[2023-06-30 19:32:20,477] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:32:20,550] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:32:20,551] [INFO] DQC Reference Directory: /var/lib/cwl/stga2e7c9d0-7fec-4159-8e88-c5c98ebfdf0b/dqc_reference
[2023-06-30 19:32:21,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:32:21,907] [INFO] Task started: Prodigal
[2023-06-30 19:32:21,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cd43d91-c82a-40da-83f9-cad2648e5364/GCA_025698925.1_ASM2569892v1_genomic.fna.gz | prodigal -d GCA_025698925.1_ASM2569892v1_genomic.fna/cds.fna -a GCA_025698925.1_ASM2569892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:32:33,363] [INFO] Task succeeded: Prodigal
[2023-06-30 19:32:33,363] [INFO] Task started: HMMsearch
[2023-06-30 19:32:33,363] [INFO] Running command: hmmsearch --tblout GCA_025698925.1_ASM2569892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2e7c9d0-7fec-4159-8e88-c5c98ebfdf0b/dqc_reference/reference_markers.hmm GCA_025698925.1_ASM2569892v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:32:33,624] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:32:33,625] [INFO] Found 6/6 markers.
[2023-06-30 19:32:33,659] [INFO] Query marker FASTA was written to GCA_025698925.1_ASM2569892v1_genomic.fna/markers.fasta
[2023-06-30 19:32:33,660] [INFO] Task started: Blastn
[2023-06-30 19:32:33,660] [INFO] Running command: blastn -query GCA_025698925.1_ASM2569892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e7c9d0-7fec-4159-8e88-c5c98ebfdf0b/dqc_reference/reference_markers.fasta -out GCA_025698925.1_ASM2569892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:32:34,811] [INFO] Task succeeded: Blastn
[2023-06-30 19:32:34,815] [INFO] Selected 12 target genomes.
[2023-06-30 19:32:34,816] [INFO] Target genome list was writen to GCA_025698925.1_ASM2569892v1_genomic.fna/target_genomes.txt
[2023-06-30 19:32:34,818] [INFO] Task started: fastANI
[2023-06-30 19:32:34,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd43d91-c82a-40da-83f9-cad2648e5364/GCA_025698925.1_ASM2569892v1_genomic.fna.gz --refList GCA_025698925.1_ASM2569892v1_genomic.fna/target_genomes.txt --output GCA_025698925.1_ASM2569892v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:32:45,239] [INFO] Task succeeded: fastANI
[2023-06-30 19:32:45,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2e7c9d0-7fec-4159-8e88-c5c98ebfdf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:32:45,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2e7c9d0-7fec-4159-8e88-c5c98ebfdf0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:32:45,255] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:32:45,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:32:45,255] [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
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	88.8564	900	1257	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	88.8014	907	1257	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	87.5986	1079	1257	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	87.5951	1079	1257	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	85.3607	928	1257	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	83.5257	857	1257	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	82.9419	753	1257	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.9438	564	1257	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.9255	600	1257	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.5521	494	1257	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.2525	438	1257	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	79.0388	458	1257	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:32:45,258] [INFO] DFAST Taxonomy check result was written to GCA_025698925.1_ASM2569892v1_genomic.fna/tc_result.tsv
[2023-06-30 19:32:45,258] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:32:45,258] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:32:45,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2e7c9d0-7fec-4159-8e88-c5c98ebfdf0b/dqc_reference/checkm_data
[2023-06-30 19:32:45,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:32:45,299] [INFO] Task started: CheckM
[2023-06-30 19:32:45,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025698925.1_ASM2569892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025698925.1_ASM2569892v1_genomic.fna/checkm_input GCA_025698925.1_ASM2569892v1_genomic.fna/checkm_result
[2023-06-30 19:33:43,925] [INFO] Task succeeded: CheckM
[2023-06-30 19:33:43,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:33:43,955] [INFO] ===== Completeness check finished =====
[2023-06-30 19:33:43,956] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:33:43,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025698925.1_ASM2569892v1_genomic.fna/markers.fasta)
[2023-06-30 19:33:43,957] [INFO] Task started: Blastn
[2023-06-30 19:33:43,957] [INFO] Running command: blastn -query GCA_025698925.1_ASM2569892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2e7c9d0-7fec-4159-8e88-c5c98ebfdf0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_025698925.1_ASM2569892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:33:45,794] [INFO] Task succeeded: Blastn
[2023-06-30 19:33:45,798] [INFO] Selected 10 target genomes.
[2023-06-30 19:33:45,798] [INFO] Target genome list was writen to GCA_025698925.1_ASM2569892v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:33:45,805] [INFO] Task started: fastANI
[2023-06-30 19:33:45,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd43d91-c82a-40da-83f9-cad2648e5364/GCA_025698925.1_ASM2569892v1_genomic.fna.gz --refList GCA_025698925.1_ASM2569892v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025698925.1_ASM2569892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:33:56,183] [INFO] Task succeeded: fastANI
[2023-06-30 19:33:56,197] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 19:33:56,197] [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_000455825.1	s__Microbacterium maritypicum_A	98.6118	1136	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.67	97.88	0.89	0.87	11	conclusive
GCA_008868125.1	s__Microbacterium maritypicum	89.1532	1045	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.89	96.90	0.89	0.86	8	-
GCF_000425985.1	s__Microbacterium sp000425985	87.9146	1064	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.44	96.40	0.87	0.86	7	-
GCF_002979475.1	s__Microbacterium sp002979475	87.6798	992	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006540085.1	s__Microbacterium oxydans	87.5951	1079	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.85	98.27	0.91	0.87	12	-
GCF_000956405.1	s__Microbacterium oxydans_C	87.2468	972	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979435.1	s__Microbacterium sp002979435	86.7497	919	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794515.1	s__Microbacterium sp004794515	86.3807	954	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002979655.1	s__Microbacterium sp002979655	86.3744	947	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.69	97.67	0.91	0.90	5	-
GCF_900095745.1	s__Microbacterium oxydans_B	86.2289	927	1257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.33	97.96	0.92	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-30 19:33:56,199] [INFO] GTDB search result was written to GCA_025698925.1_ASM2569892v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:33:56,200] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:33:56,204] [INFO] DFAST_QC result json was written to GCA_025698925.1_ASM2569892v1_genomic.fna/dqc_result.json
[2023-06-30 19:33:56,204] [INFO] DFAST_QC completed!
[2023-06-30 19:33:56,204] [INFO] Total running time: 0h1m36s