[2024-01-25 19:35:50,772] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:50,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:50,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgbff1cadf-8b9a-4dae-9da6-67485a841803/dqc_reference
[2024-01-25 19:35:52,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,010] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg79811256-97d0-46c8-a846-dbc2cd323c8d/GCF_015707995.1_ASM1570799v1_genomic.fna.gz | prodigal -d GCF_015707995.1_ASM1570799v1_genomic.fna/cds.fna -a GCF_015707995.1_ASM1570799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:59,793] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:59,794] [INFO] Task started: HMMsearch
[2024-01-25 19:35:59,794] [INFO] Running command: hmmsearch --tblout GCF_015707995.1_ASM1570799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbff1cadf-8b9a-4dae-9da6-67485a841803/dqc_reference/reference_markers.hmm GCF_015707995.1_ASM1570799v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:00,050] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:00,051] [INFO] Found 6/6 markers.
[2024-01-25 19:36:00,098] [INFO] Query marker FASTA was written to GCF_015707995.1_ASM1570799v1_genomic.fna/markers.fasta
[2024-01-25 19:36:00,098] [INFO] Task started: Blastn
[2024-01-25 19:36:00,098] [INFO] Running command: blastn -query GCF_015707995.1_ASM1570799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff1cadf-8b9a-4dae-9da6-67485a841803/dqc_reference/reference_markers.fasta -out GCF_015707995.1_ASM1570799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:01,256] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:01,259] [INFO] Selected 12 target genomes.
[2024-01-25 19:36:01,259] [INFO] Target genome list was writen to GCF_015707995.1_ASM1570799v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:01,265] [INFO] Task started: fastANI
[2024-01-25 19:36:01,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg79811256-97d0-46c8-a846-dbc2cd323c8d/GCF_015707995.1_ASM1570799v1_genomic.fna.gz --refList GCF_015707995.1_ASM1570799v1_genomic.fna/target_genomes.txt --output GCF_015707995.1_ASM1570799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:10,235] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:10,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbff1cadf-8b9a-4dae-9da6-67485a841803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:10,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbff1cadf-8b9a-4dae-9da6-67485a841803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:10,244] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:10,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:10,245] [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 paulum	strain=2C	GCA_015707995.1	2707006	2707006	type	True	100.0	1000	1005	95	conclusive
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	88.6963	668	1005	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	88.6453	672	1005	95	below_threshold
Microbacterium lacticum	strain=DSM 20427	GCA_006716815.1	33885	33885	type	True	88.4032	711	1005	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	83.7045	620	1005	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	83.3969	638	1005	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	83.0498	624	1005	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	82.4792	604	1005	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.1439	533	1005	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.1292	528	1005	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.7127	519	1005	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.531	526	1005	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:10,246] [INFO] DFAST Taxonomy check result was written to GCF_015707995.1_ASM1570799v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:10,246] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:10,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:10,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbff1cadf-8b9a-4dae-9da6-67485a841803/dqc_reference/checkm_data
[2024-01-25 19:36:10,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:10,282] [INFO] Task started: CheckM
[2024-01-25 19:36:10,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015707995.1_ASM1570799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015707995.1_ASM1570799v1_genomic.fna/checkm_input GCF_015707995.1_ASM1570799v1_genomic.fna/checkm_result
[2024-01-25 19:36:48,038] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:48,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:48,057] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:48,057] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:48,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015707995.1_ASM1570799v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:48,058] [INFO] Task started: Blastn
[2024-01-25 19:36:48,058] [INFO] Running command: blastn -query GCF_015707995.1_ASM1570799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbff1cadf-8b9a-4dae-9da6-67485a841803/dqc_reference/reference_markers_gtdb.fasta -out GCF_015707995.1_ASM1570799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:49,922] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:49,925] [INFO] Selected 11 target genomes.
[2024-01-25 19:36:49,925] [INFO] Target genome list was writen to GCF_015707995.1_ASM1570799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:49,933] [INFO] Task started: fastANI
[2024-01-25 19:36:49,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg79811256-97d0-46c8-a846-dbc2cd323c8d/GCF_015707995.1_ASM1570799v1_genomic.fna.gz --refList GCF_015707995.1_ASM1570799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015707995.1_ASM1570799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:57,574] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:57,582] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:57,582] [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_015707995.1	s__Microbacterium sp015707995	100.0	1000	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006716815.1	s__Microbacterium lacticum	88.3914	712	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCA_001898315.1	s__Microbacterium sp001898315	83.9675	632	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCA_017305435.1	s__Microbacterium sp017305435	83.9208	669	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907815.1	s__Microbacterium aurum	83.7271	648	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	-
GCA_003248655.1	s__Microbacterium sp003248655	83.672	599	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907295.1	s__Microbacterium dextranolyticum	83.6666	622	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018717645.1	s__Microbacterium flavum	83.39	639	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248845.1	s__Microbacterium sp003248845	83.2447	432	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCF_016807485.1	s__Microbacterium sp016807485	82.8366	407	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651225.1	s__Microbacterium telephonicum	82.5243	600	1005	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:57,584] [INFO] GTDB search result was written to GCF_015707995.1_ASM1570799v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:57,584] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:57,590] [INFO] DFAST_QC result json was written to GCF_015707995.1_ASM1570799v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:57,590] [INFO] DFAST_QC completed!
[2024-01-25 19:36:57,590] [INFO] Total running time: 0h1m7s