[2024-01-24 13:22:11,381] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,383] [INFO] DQC Reference Directory: /var/lib/cwl/stga67ce19f-8a39-4d65-bd9a-31a9f0a87eb7/dqc_reference
[2024-01-24 13:22:13,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,355] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f608b07-b26e-4ab7-9430-5cceed8f1754/GCF_017876695.1_ASM1787669v1_genomic.fna.gz | prodigal -d GCF_017876695.1_ASM1787669v1_genomic.fna/cds.fna -a GCF_017876695.1_ASM1787669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:20,574] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:20,574] [INFO] Task started: HMMsearch
[2024-01-24 13:22:20,574] [INFO] Running command: hmmsearch --tblout GCF_017876695.1_ASM1787669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga67ce19f-8a39-4d65-bd9a-31a9f0a87eb7/dqc_reference/reference_markers.hmm GCF_017876695.1_ASM1787669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:20,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:20,840] [INFO] Found 6/6 markers.
[2024-01-24 13:22:20,864] [INFO] Query marker FASTA was written to GCF_017876695.1_ASM1787669v1_genomic.fna/markers.fasta
[2024-01-24 13:22:20,865] [INFO] Task started: Blastn
[2024-01-24 13:22:20,865] [INFO] Running command: blastn -query GCF_017876695.1_ASM1787669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga67ce19f-8a39-4d65-bd9a-31a9f0a87eb7/dqc_reference/reference_markers.fasta -out GCF_017876695.1_ASM1787669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:21,785] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:21,788] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:21,788] [INFO] Target genome list was writen to GCF_017876695.1_ASM1787669v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:21,845] [INFO] Task started: fastANI
[2024-01-24 13:22:21,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f608b07-b26e-4ab7-9430-5cceed8f1754/GCF_017876695.1_ASM1787669v1_genomic.fna.gz --refList GCF_017876695.1_ASM1787669v1_genomic.fna/target_genomes.txt --output GCF_017876695.1_ASM1787669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:33,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:33,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga67ce19f-8a39-4d65-bd9a-31a9f0a87eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:33,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga67ce19f-8a39-4d65-bd9a-31a9f0a87eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:33,118] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:33,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:33,118] [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 amylolyticum	strain=DSM 24221	GCA_017876695.1	936337	936337	type	True	100.0	861	862	95	conclusive
Microbacterium amylolyticum	strain=DSM 24221	GCA_011046975.1	936337	936337	type	True	99.9949	861	862	95	conclusive
Microbacterium suaedae	strain=YZYP 306	GCA_003254645.1	2067813	2067813	type	True	79.3213	345	862	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	79.2488	309	862	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	79.1751	308	862	95	below_threshold
Microbacterium gubbeenense	strain=DSM 15944	GCA_000422745.1	159896	159896	type	True	79.156	322	862	95	below_threshold
Microbacterium faecale	strain=CGMCC 1.15152	GCA_014640975.1	1804630	1804630	type	True	79.1252	288	862	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	79.1013	338	862	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	79.0094	355	862	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	78.9899	280	862	95	below_threshold
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	78.9229	313	862	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	78.8102	270	862	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	78.7946	271	862	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	78.5827	285	862	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	78.2834	200	862	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	78.1475	210	862	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.0602	204	862	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	78.0469	196	862	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	77.4907	131	862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:33,119] [INFO] DFAST Taxonomy check result was written to GCF_017876695.1_ASM1787669v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:33,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:33,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:33,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga67ce19f-8a39-4d65-bd9a-31a9f0a87eb7/dqc_reference/checkm_data
[2024-01-24 13:22:33,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:33,146] [INFO] Task started: CheckM
[2024-01-24 13:22:33,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876695.1_ASM1787669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876695.1_ASM1787669v1_genomic.fna/checkm_input GCF_017876695.1_ASM1787669v1_genomic.fna/checkm_result
[2024-01-24 13:22:59,766] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:59,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:59,781] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:59,781] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:59,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876695.1_ASM1787669v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:59,781] [INFO] Task started: Blastn
[2024-01-24 13:22:59,781] [INFO] Running command: blastn -query GCF_017876695.1_ASM1787669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga67ce19f-8a39-4d65-bd9a-31a9f0a87eb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876695.1_ASM1787669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:01,168] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:01,171] [INFO] Selected 12 target genomes.
[2024-01-24 13:23:01,171] [INFO] Target genome list was writen to GCF_017876695.1_ASM1787669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:01,177] [INFO] Task started: fastANI
[2024-01-24 13:23:01,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f608b07-b26e-4ab7-9430-5cceed8f1754/GCF_017876695.1_ASM1787669v1_genomic.fna.gz --refList GCF_017876695.1_ASM1787669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876695.1_ASM1787669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:08,177] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:08,185] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:08,186] [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_011046975.1	s__Microbacterium amylolyticum	99.9949	861	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009745985.1	s__Microbacterium karelineae	79.4926	384	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254645.1	s__Microbacterium suaedae	79.29	348	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003327285.1	s__Microbacterium sorbitolivorans	79.2412	310	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011326725.1	s__Microbacterium excoecariae	79.2216	334	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_000422745.1	s__Microbacterium gubbeenense	79.1588	321	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640975.1	s__Microbacterium faecale	79.109	289	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.13	95.13	0.92	0.92	2	-
GCA_019117025.1	s__Microbacterium stercoravium	79.1071	259	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422385.1	s__Microbacterium indicum	79.0009	355	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564075.1	s__Microbacterium sediminis	78.9947	280	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_014646015.1	s__Microbacterium nanhaiense	78.9233	313	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105335.1	s__Microbacterium paraoxydans	78.2622	201	862	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	99.12	98.76	0.96	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:08,187] [INFO] GTDB search result was written to GCF_017876695.1_ASM1787669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:08,188] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:08,190] [INFO] DFAST_QC result json was written to GCF_017876695.1_ASM1787669v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:08,191] [INFO] DFAST_QC completed!
[2024-01-24 13:23:08,191] [INFO] Total running time: 0h0m57s