[2024-01-25 18:52:50,572] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:50,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:50,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg5112f53b-5bda-4fa0-86f8-08a32dc486d3/dqc_reference
[2024-01-25 18:52:51,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:51,724] [INFO] Task started: Prodigal
[2024-01-25 18:52:51,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg97e589a7-4b11-47a8-8ee4-9c0a6fdb9363/GCF_014837165.1_ASM1483716v1_genomic.fna.gz | prodigal -d GCF_014837165.1_ASM1483716v1_genomic.fna/cds.fna -a GCF_014837165.1_ASM1483716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:00,215] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:00,216] [INFO] Task started: HMMsearch
[2024-01-25 18:53:00,216] [INFO] Running command: hmmsearch --tblout GCF_014837165.1_ASM1483716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5112f53b-5bda-4fa0-86f8-08a32dc486d3/dqc_reference/reference_markers.hmm GCF_014837165.1_ASM1483716v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:00,420] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:00,421] [INFO] Found 6/6 markers.
[2024-01-25 18:53:00,449] [INFO] Query marker FASTA was written to GCF_014837165.1_ASM1483716v1_genomic.fna/markers.fasta
[2024-01-25 18:53:00,449] [INFO] Task started: Blastn
[2024-01-25 18:53:00,449] [INFO] Running command: blastn -query GCF_014837165.1_ASM1483716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5112f53b-5bda-4fa0-86f8-08a32dc486d3/dqc_reference/reference_markers.fasta -out GCF_014837165.1_ASM1483716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:01,718] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:01,721] [INFO] Selected 12 target genomes.
[2024-01-25 18:53:01,721] [INFO] Target genome list was writen to GCF_014837165.1_ASM1483716v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:01,733] [INFO] Task started: fastANI
[2024-01-25 18:53:01,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e589a7-4b11-47a8-8ee4-9c0a6fdb9363/GCF_014837165.1_ASM1483716v1_genomic.fna.gz --refList GCF_014837165.1_ASM1483716v1_genomic.fna/target_genomes.txt --output GCF_014837165.1_ASM1483716v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:12,422] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:12,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5112f53b-5bda-4fa0-86f8-08a32dc486d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:12,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5112f53b-5bda-4fa0-86f8-08a32dc486d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:12,430] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:53:12,430] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:12,430] [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 gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	100.0	1108	1108	95	conclusive
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	87.6235	930	1108	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	84.8835	840	1108	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	83.2098	759	1108	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	83.1052	737	1108	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	83.0304	770	1108	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	82.831	722	1108	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	82.7702	744	1108	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	82.728	732	1108	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	82.5398	732	1108	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.2668	585	1108	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	80.344	565	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:12,432] [INFO] DFAST Taxonomy check result was written to GCF_014837165.1_ASM1483716v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:12,432] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:12,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:12,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5112f53b-5bda-4fa0-86f8-08a32dc486d3/dqc_reference/checkm_data
[2024-01-25 18:53:12,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:12,465] [INFO] Task started: CheckM
[2024-01-25 18:53:12,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837165.1_ASM1483716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837165.1_ASM1483716v1_genomic.fna/checkm_input GCF_014837165.1_ASM1483716v1_genomic.fna/checkm_result
[2024-01-25 18:54:04,078] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:04,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:04,101] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:04,101] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:04,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837165.1_ASM1483716v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:04,102] [INFO] Task started: Blastn
[2024-01-25 18:54:04,102] [INFO] Running command: blastn -query GCF_014837165.1_ASM1483716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5112f53b-5bda-4fa0-86f8-08a32dc486d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837165.1_ASM1483716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:06,491] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:06,495] [INFO] Selected 14 target genomes.
[2024-01-25 18:54:06,495] [INFO] Target genome list was writen to GCF_014837165.1_ASM1483716v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:06,515] [INFO] Task started: fastANI
[2024-01-25 18:54:06,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg97e589a7-4b11-47a8-8ee4-9c0a6fdb9363/GCF_014837165.1_ASM1483716v1_genomic.fna.gz --refList GCF_014837165.1_ASM1483716v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837165.1_ASM1483716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:18,837] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:18,847] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:18,847] [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_014837165.1	s__Microbacterium sp014837165	100.0	1108	1108	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_018588945.1	s__Microbacterium flavescens	87.6377	929	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999995.1	s__Microbacterium sp003999995	84.8742	841	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428485.1	s__Microbacterium sp001428485	84.1333	779	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	84.1298	757	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012847295.1	s__Microbacterium sp012847295	83.8643	789	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907635.1	s__Microbacterium insulae	83.4801	769	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	83.2558	763	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	83.2444	756	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873155.1	s__Microbacterium sp014873155	83.061	738	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	83.01	506	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	82.9222	752	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	82.8081	724	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	82.7481	746	1108	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 18:54:18,849] [INFO] GTDB search result was written to GCF_014837165.1_ASM1483716v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:18,849] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:18,852] [INFO] DFAST_QC result json was written to GCF_014837165.1_ASM1483716v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:18,852] [INFO] DFAST_QC completed!
[2024-01-25 18:54:18,852] [INFO] Total running time: 0h1m28s