[2024-01-24 13:57:29,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:29,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:29,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c70dd9b-f47c-4e6c-8ce7-3f88e31b232c/dqc_reference
[2024-01-24 13:57:30,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:30,632] [INFO] Task started: Prodigal
[2024-01-24 13:57:30,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg09c8e71c-5cd8-4d54-813d-001e483322d4/GCF_006540085.1_ASM654008v1_genomic.fna.gz | prodigal -d GCF_006540085.1_ASM654008v1_genomic.fna/cds.fna -a GCF_006540085.1_ASM654008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:42,663] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:42,664] [INFO] Task started: HMMsearch
[2024-01-24 13:57:42,664] [INFO] Running command: hmmsearch --tblout GCF_006540085.1_ASM654008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c70dd9b-f47c-4e6c-8ce7-3f88e31b232c/dqc_reference/reference_markers.hmm GCF_006540085.1_ASM654008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:43,001] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:43,002] [INFO] Found 6/6 markers.
[2024-01-24 13:57:43,046] [INFO] Query marker FASTA was written to GCF_006540085.1_ASM654008v1_genomic.fna/markers.fasta
[2024-01-24 13:57:43,046] [INFO] Task started: Blastn
[2024-01-24 13:57:43,046] [INFO] Running command: blastn -query GCF_006540085.1_ASM654008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c70dd9b-f47c-4e6c-8ce7-3f88e31b232c/dqc_reference/reference_markers.fasta -out GCF_006540085.1_ASM654008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:44,250] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:44,254] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:44,254] [INFO] Target genome list was writen to GCF_006540085.1_ASM654008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:44,257] [INFO] Task started: fastANI
[2024-01-24 13:57:44,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c8e71c-5cd8-4d54-813d-001e483322d4/GCF_006540085.1_ASM654008v1_genomic.fna.gz --refList GCF_006540085.1_ASM654008v1_genomic.fna/target_genomes.txt --output GCF_006540085.1_ASM654008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:53,232] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:53,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c70dd9b-f47c-4e6c-8ce7-3f88e31b232c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:53,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c70dd9b-f47c-4e6c-8ce7-3f88e31b232c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:53,242] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:53,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:53,242] [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 oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	100.0	1292	1292	95	conclusive
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	99.9996	1292	1292	95	conclusive
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	87.6104	876	1292	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	87.5461	880	1292	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	85.6234	930	1292	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	82.7647	740	1292	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.0282	583	1292	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.805	562	1292	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.6635	447	1292	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.5862	404	1292	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.3442	442	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:53,244] [INFO] DFAST Taxonomy check result was written to GCF_006540085.1_ASM654008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:53,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:53,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:53,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c70dd9b-f47c-4e6c-8ce7-3f88e31b232c/dqc_reference/checkm_data
[2024-01-24 13:57:53,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:53,286] [INFO] Task started: CheckM
[2024-01-24 13:57:53,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540085.1_ASM654008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540085.1_ASM654008v1_genomic.fna/checkm_input GCF_006540085.1_ASM654008v1_genomic.fna/checkm_result
[2024-01-24 13:58:57,400] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:57,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:57,422] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:57,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:57,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540085.1_ASM654008v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:57,423] [INFO] Task started: Blastn
[2024-01-24 13:58:57,423] [INFO] Running command: blastn -query GCF_006540085.1_ASM654008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c70dd9b-f47c-4e6c-8ce7-3f88e31b232c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540085.1_ASM654008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:59,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:59,465] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:59,466] [INFO] Target genome list was writen to GCF_006540085.1_ASM654008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:59,480] [INFO] Task started: fastANI
[2024-01-24 13:58:59,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c8e71c-5cd8-4d54-813d-001e483322d4/GCF_006540085.1_ASM654008v1_genomic.fna.gz --refList GCF_006540085.1_ASM654008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540085.1_ASM654008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:09,948] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:09,957] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:09,957] [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_006540085.1	s__Microbacterium oxydans	100.0	1292	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.85	98.27	0.91	0.87	12	conclusive
GCF_000956405.1	s__Microbacterium oxydans_C	92.0388	998	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455825.1	s__Microbacterium maritypicum_A	87.5921	1022	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.67	97.88	0.89	0.87	11	-
GCA_008868125.1	s__Microbacterium maritypicum	87.5509	987	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.89	96.90	0.89	0.86	8	-
GCF_002979475.1	s__Microbacterium sp002979475	86.6668	959	1292	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	85.8559	920	1292	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	85.8053	930	1292	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	85.5748	910	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.69	97.67	0.91	0.90	5	-
GCF_007954505.1	s__Microbacterium sp000800925	85.1865	921	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.26	97.84	0.89	0.86	5	-
GCF_904066215.1	s__Microbacterium sp002456035	83.7595	844	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	98.64	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,958] [INFO] GTDB search result was written to GCF_006540085.1_ASM654008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:09,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:09,961] [INFO] DFAST_QC result json was written to GCF_006540085.1_ASM654008v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:09,962] [INFO] DFAST_QC completed!
[2024-01-24 13:59:09,962] [INFO] Total running time: 0h1m41s