[2023-06-27 20:32:16,228] [INFO] DFAST_QC pipeline started.
[2023-06-27 20:32:16,230] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 20:32:16,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg76f37d9c-0d5d-4bc3-9b1f-c4cc0a9f98ee/dqc_reference
[2023-06-27 20:32:18,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 20:32:18,444] [INFO] Task started: Prodigal
[2023-06-27 20:32:18,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg0dc08038-f05b-47da-9e4e-0aaa7aa756f7/GCA_002354175.1_ASM235417v1_genomic.fna.gz | prodigal -d GCA_002354175.1_ASM235417v1_genomic.fna/cds.fna -a GCA_002354175.1_ASM235417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 20:32:25,767] [INFO] Task succeeded: Prodigal
[2023-06-27 20:32:25,767] [INFO] Task started: HMMsearch
[2023-06-27 20:32:25,767] [INFO] Running command: hmmsearch --tblout GCA_002354175.1_ASM235417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76f37d9c-0d5d-4bc3-9b1f-c4cc0a9f98ee/dqc_reference/reference_markers.hmm GCA_002354175.1_ASM235417v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 20:32:26,018] [INFO] Task succeeded: HMMsearch
[2023-06-27 20:32:26,020] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0dc08038-f05b-47da-9e4e-0aaa7aa756f7/GCA_002354175.1_ASM235417v1_genomic.fna.gz]
[2023-06-27 20:32:26,053] [INFO] Query marker FASTA was written to GCA_002354175.1_ASM235417v1_genomic.fna/markers.fasta
[2023-06-27 20:32:26,054] [INFO] Task started: Blastn
[2023-06-27 20:32:26,054] [INFO] Running command: blastn -query GCA_002354175.1_ASM235417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f37d9c-0d5d-4bc3-9b1f-c4cc0a9f98ee/dqc_reference/reference_markers.fasta -out GCA_002354175.1_ASM235417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:32:27,190] [INFO] Task succeeded: Blastn
[2023-06-27 20:32:27,196] [INFO] Selected 15 target genomes.
[2023-06-27 20:32:27,196] [INFO] Target genome list was writen to GCA_002354175.1_ASM235417v1_genomic.fna/target_genomes.txt
[2023-06-27 20:32:27,199] [INFO] Task started: fastANI
[2023-06-27 20:32:27,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc08038-f05b-47da-9e4e-0aaa7aa756f7/GCA_002354175.1_ASM235417v1_genomic.fna.gz --refList GCA_002354175.1_ASM235417v1_genomic.fna/target_genomes.txt --output GCA_002354175.1_ASM235417v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 20:32:37,567] [INFO] Task succeeded: fastANI
[2023-06-27 20:32:37,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76f37d9c-0d5d-4bc3-9b1f-c4cc0a9f98ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 20:32:37,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76f37d9c-0d5d-4bc3-9b1f-c4cc0a9f98ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 20:32:37,584] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2023-06-27 20:32:37,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 20:32:37,584] [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 paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	95.1908	783	878	95	conclusive
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	95.0742	729	878	95	conclusive
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	85.0926	716	878	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	83.8325	678	878	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	83.8032	674	878	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	83.8031	605	878	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	83.6918	609	878	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	83.0402	577	878	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	83.0159	602	878	95	below_threshold
Microbacterium phyllosphaerae	strain=DSM 13468	GCA_017876435.1	124798	124798	type	True	82.7592	598	878	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.3794	485	878	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.2086	475	878	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.9548	373	878	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.8722	381	878	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.8552	393	878	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 20:32:37,586] [INFO] DFAST Taxonomy check result was written to GCA_002354175.1_ASM235417v1_genomic.fna/tc_result.tsv
[2023-06-27 20:32:37,588] [INFO] ===== Taxonomy check completed =====
[2023-06-27 20:32:37,588] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 20:32:37,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76f37d9c-0d5d-4bc3-9b1f-c4cc0a9f98ee/dqc_reference/checkm_data
[2023-06-27 20:32:37,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 20:32:37,624] [INFO] Task started: CheckM
[2023-06-27 20:32:37,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002354175.1_ASM235417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002354175.1_ASM235417v1_genomic.fna/checkm_input GCA_002354175.1_ASM235417v1_genomic.fna/checkm_result
[2023-06-27 20:33:15,353] [INFO] Task succeeded: CheckM
[2023-06-27 20:33:15,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.48%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 20:33:15,379] [INFO] ===== Completeness check finished =====
[2023-06-27 20:33:15,379] [INFO] ===== Start GTDB Search =====
[2023-06-27 20:33:15,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002354175.1_ASM235417v1_genomic.fna/markers.fasta)
[2023-06-27 20:33:15,380] [INFO] Task started: Blastn
[2023-06-27 20:33:15,381] [INFO] Running command: blastn -query GCA_002354175.1_ASM235417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f37d9c-0d5d-4bc3-9b1f-c4cc0a9f98ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_002354175.1_ASM235417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:33:17,262] [INFO] Task succeeded: Blastn
[2023-06-27 20:33:17,267] [INFO] Selected 7 target genomes.
[2023-06-27 20:33:17,267] [INFO] Target genome list was writen to GCA_002354175.1_ASM235417v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 20:33:17,275] [INFO] Task started: fastANI
[2023-06-27 20:33:17,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc08038-f05b-47da-9e4e-0aaa7aa756f7/GCA_002354175.1_ASM235417v1_genomic.fna.gz --refList GCA_002354175.1_ASM235417v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002354175.1_ASM235417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 20:33:22,884] [INFO] Task succeeded: fastANI
[2023-06-27 20:33:22,895] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 20:33:22,896] [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_019056515.1	s__Microbacterium sp001595495	96.9872	800	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	98.29	96.93	0.91	0.85	10	conclusive
GCF_900105335.1	s__Microbacterium paraoxydans	95.1701	785	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	99.12	98.76	0.96	0.92	5	-
GCF_001866135.1	s__Microbacterium sp001866135	94.3323	781	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.261	97.41	95.65	0.93	0.91	3	-
GCF_904066215.1	s__Microbacterium sp002456035	92.8939	780	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	98.64	0.94	0.94	3	-
GCF_002848265.1	s__Microbacterium sp002848265	92.2966	803	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271365.1	s__Microbacterium sp008271365	90.0903	771	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939615.1	s__Microbacterium sp017939615	89.9772	735	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 20:33:22,898] [INFO] GTDB search result was written to GCA_002354175.1_ASM235417v1_genomic.fna/result_gtdb.tsv
[2023-06-27 20:33:22,899] [INFO] ===== GTDB Search completed =====
[2023-06-27 20:33:22,903] [INFO] DFAST_QC result json was written to GCA_002354175.1_ASM235417v1_genomic.fna/dqc_result.json
[2023-06-27 20:33:22,903] [INFO] DFAST_QC completed!
[2023-06-27 20:33:22,903] [INFO] Total running time: 0h1m7s