[2024-01-25 18:46:50,796] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:50,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:50,800] [INFO] DQC Reference Directory: /var/lib/cwl/stge2a95aa2-316b-401a-8282-5e1bbe78cc5b/dqc_reference
[2024-01-25 18:46:52,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:52,010] [INFO] Task started: Prodigal
[2024-01-25 18:46:52,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ae0a3ae-417c-4cd1-9860-39589d3d94ec/GCF_018717645.1_ASM1871764v1_genomic.fna.gz | prodigal -d GCF_018717645.1_ASM1871764v1_genomic.fna/cds.fna -a GCF_018717645.1_ASM1871764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:00,228] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:00,228] [INFO] Task started: HMMsearch
[2024-01-25 18:47:00,228] [INFO] Running command: hmmsearch --tblout GCF_018717645.1_ASM1871764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2a95aa2-316b-401a-8282-5e1bbe78cc5b/dqc_reference/reference_markers.hmm GCF_018717645.1_ASM1871764v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:00,473] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:00,474] [INFO] Found 6/6 markers.
[2024-01-25 18:47:00,501] [INFO] Query marker FASTA was written to GCF_018717645.1_ASM1871764v1_genomic.fna/markers.fasta
[2024-01-25 18:47:00,502] [INFO] Task started: Blastn
[2024-01-25 18:47:00,502] [INFO] Running command: blastn -query GCF_018717645.1_ASM1871764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a95aa2-316b-401a-8282-5e1bbe78cc5b/dqc_reference/reference_markers.fasta -out GCF_018717645.1_ASM1871764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:01,574] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:01,576] [INFO] Selected 16 target genomes.
[2024-01-25 18:47:01,577] [INFO] Target genome list was writen to GCF_018717645.1_ASM1871764v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:01,591] [INFO] Task started: fastANI
[2024-01-25 18:47:01,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae0a3ae-417c-4cd1-9860-39589d3d94ec/GCF_018717645.1_ASM1871764v1_genomic.fna.gz --refList GCF_018717645.1_ASM1871764v1_genomic.fna/target_genomes.txt --output GCF_018717645.1_ASM1871764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:13,092] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:13,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2a95aa2-316b-401a-8282-5e1bbe78cc5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:13,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2a95aa2-316b-401a-8282-5e1bbe78cc5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:13,103] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:13,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:13,103] [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 flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	100.0	1070	1072	95	conclusive
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	83.7247	636	1072	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	83.6179	637	1072	95	below_threshold
Microbacterium lacticum	strain=DSM 20427	GCA_006716815.1	33885	33885	type	True	83.5018	680	1072	95	below_threshold
Microbacterium paulum	strain=2C	GCA_015707995.1	2707006	2707006	type	True	83.2646	635	1072	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	82.9177	643	1072	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	82.8411	664	1072	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	82.6813	657	1072	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	82.5538	664	1072	95	below_threshold
Microbacterium laevaniformans	strain=DSM 20140	GCA_016907555.1	36807	36807	type	True	82.1121	611	1072	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.5296	549	1072	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.4919	538	1072	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	80.3495	545	1072	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.3201	523	1072	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.116	521	1072	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.9479	541	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:13,107] [INFO] DFAST Taxonomy check result was written to GCF_018717645.1_ASM1871764v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:13,107] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:13,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:13,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2a95aa2-316b-401a-8282-5e1bbe78cc5b/dqc_reference/checkm_data
[2024-01-25 18:47:13,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:13,160] [INFO] Task started: CheckM
[2024-01-25 18:47:13,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018717645.1_ASM1871764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018717645.1_ASM1871764v1_genomic.fna/checkm_input GCF_018717645.1_ASM1871764v1_genomic.fna/checkm_result
[2024-01-25 18:47:56,964] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:56,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:56,985] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:56,985] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:56,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018717645.1_ASM1871764v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:56,986] [INFO] Task started: Blastn
[2024-01-25 18:47:56,986] [INFO] Running command: blastn -query GCF_018717645.1_ASM1871764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a95aa2-316b-401a-8282-5e1bbe78cc5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_018717645.1_ASM1871764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:58,725] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:58,729] [INFO] Selected 14 target genomes.
[2024-01-25 18:47:58,729] [INFO] Target genome list was writen to GCF_018717645.1_ASM1871764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:58,737] [INFO] Task started: fastANI
[2024-01-25 18:47:58,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ae0a3ae-417c-4cd1-9860-39589d3d94ec/GCF_018717645.1_ASM1871764v1_genomic.fna.gz --refList GCF_018717645.1_ASM1871764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018717645.1_ASM1871764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:08,601] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:08,610] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:08,611] [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_018717645.1	s__Microbacterium flavum	100.0	1070	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017305435.1	s__Microbacterium sp017305435	84.2905	706	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716815.1	s__Microbacterium lacticum	83.5179	679	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	-
GCA_003248845.1	s__Microbacterium sp003248845	83.4491	453	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCF_015707995.1	s__Microbacterium sp015707995	83.2064	640	1072	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	82.9278	643	1072	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	82.8245	665	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	-
GCA_001898315.1	s__Microbacterium sp001898315	82.6589	647	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCA_003248655.1	s__Microbacterium sp003248655	82.6424	614	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724425.1	s__Microbacterium sp001724425	82.4924	604	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_016907555.1	s__Microbacterium laevaniformans	82.1645	607	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.33	96.04	0.85	0.81	5	-
GCF_000411455.1	s__Microbacterium sp000411455	81.8981	620	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.03	96.01	0.82	0.82	3	-
GCF_003999995.1	s__Microbacterium sp003999995	80.2809	527	1072	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	80.2398	367	1072	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 18:48:08,612] [INFO] GTDB search result was written to GCF_018717645.1_ASM1871764v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:08,612] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:08,615] [INFO] DFAST_QC result json was written to GCF_018717645.1_ASM1871764v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:08,616] [INFO] DFAST_QC completed!
[2024-01-25 18:48:08,616] [INFO] Total running time: 0h1m18s