[2024-01-24 12:30:52,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,596] [INFO] DQC Reference Directory: /var/lib/cwl/stge54b4d98-9e59-4340-af96-58151a409418/dqc_reference
[2024-01-24 12:30:53,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,822] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,822] [INFO] Running command: gunzip -c /var/lib/cwl/stgf28e15e7-4649-4f95-93eb-8fb29af4e7d8/GCF_008017415.1_ASM801741v1_genomic.fna.gz | prodigal -d GCF_008017415.1_ASM801741v1_genomic.fna/cds.fna -a GCF_008017415.1_ASM801741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:03,699] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:03,700] [INFO] Task started: HMMsearch
[2024-01-24 12:31:03,700] [INFO] Running command: hmmsearch --tblout GCF_008017415.1_ASM801741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge54b4d98-9e59-4340-af96-58151a409418/dqc_reference/reference_markers.hmm GCF_008017415.1_ASM801741v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:03,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:03,979] [INFO] Found 6/6 markers.
[2024-01-24 12:31:04,017] [INFO] Query marker FASTA was written to GCF_008017415.1_ASM801741v1_genomic.fna/markers.fasta
[2024-01-24 12:31:04,017] [INFO] Task started: Blastn
[2024-01-24 12:31:04,017] [INFO] Running command: blastn -query GCF_008017415.1_ASM801741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge54b4d98-9e59-4340-af96-58151a409418/dqc_reference/reference_markers.fasta -out GCF_008017415.1_ASM801741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:05,214] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:05,218] [INFO] Selected 23 target genomes.
[2024-01-24 12:31:05,219] [INFO] Target genome list was writen to GCF_008017415.1_ASM801741v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:05,234] [INFO] Task started: fastANI
[2024-01-24 12:31:05,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28e15e7-4649-4f95-93eb-8fb29af4e7d8/GCF_008017415.1_ASM801741v1_genomic.fna.gz --refList GCF_008017415.1_ASM801741v1_genomic.fna/target_genomes.txt --output GCF_008017415.1_ASM801741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:21,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:21,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge54b4d98-9e59-4340-af96-58151a409418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:21,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge54b4d98-9e59-4340-af96-58151a409418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:21,798] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:21,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:21,799] [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 hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	100.0	1180	1181	95	conclusive
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	81.0606	583	1181	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.8341	538	1181	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	80.8169	576	1181	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.7961	534	1181	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	80.7734	611	1181	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	80.7579	565	1181	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.7096	560	1181	95	below_threshold
Microbacterium proteolyticum	strain=CECT 8356	GCA_014192415.1	1572644	1572644	type	True	80.6754	572	1181	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	80.608	575	1181	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	80.5864	574	1181	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.5826	544	1181	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.5185	586	1181	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.4593	572	1181	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.4541	538	1181	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.3671	521	1181	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	80.3656	514	1181	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	80.3136	526	1181	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	80.2429	509	1181	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.226	579	1181	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	80.195	513	1181	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	80.1379	477	1181	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	79.3988	502	1181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:21,800] [INFO] DFAST Taxonomy check result was written to GCF_008017415.1_ASM801741v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:21,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:21,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:21,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge54b4d98-9e59-4340-af96-58151a409418/dqc_reference/checkm_data
[2024-01-24 12:31:21,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:21,844] [INFO] Task started: CheckM
[2024-01-24 12:31:21,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008017415.1_ASM801741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008017415.1_ASM801741v1_genomic.fna/checkm_input GCF_008017415.1_ASM801741v1_genomic.fna/checkm_result
[2024-01-24 12:32:11,557] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:11,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:11,583] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:11,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:11,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008017415.1_ASM801741v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:11,584] [INFO] Task started: Blastn
[2024-01-24 12:32:11,584] [INFO] Running command: blastn -query GCF_008017415.1_ASM801741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge54b4d98-9e59-4340-af96-58151a409418/dqc_reference/reference_markers_gtdb.fasta -out GCF_008017415.1_ASM801741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:13,406] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:13,411] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:13,411] [INFO] Target genome list was writen to GCF_008017415.1_ASM801741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:13,427] [INFO] Task started: fastANI
[2024-01-24 12:32:13,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28e15e7-4649-4f95-93eb-8fb29af4e7d8/GCF_008017415.1_ASM801741v1_genomic.fna.gz --refList GCF_008017415.1_ASM801741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008017415.1_ASM801741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:25,701] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:25,717] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:25,717] [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_008017415.1	s__Microbacterium hatanonis	100.0	1180	1181	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_003095395.1	s__Microbacterium sp003095395	91.8288	927	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635115.1	s__Microbacterium sp003635115	91.8232	947	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679045.1	s__Microbacterium sp007679045	81.0084	623	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.00	99.00	0.94	0.94	2	-
GCA_016870695.1	s__Microbacterium sp016870695	80.9343	407	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005774735.1	s__Microbacterium sp005774735	80.9278	561	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.07	96.07	0.82	0.82	2	-
GCF_001476285.1	s__Microbacterium testaceum_B	80.8656	580	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
GCF_004564355.1	s__Microbacterium wangchenii	80.8124	576	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.29	98.90	0.96	0.95	3	-
GCF_003991875.1	s__Microbacterium lemovicicum	80.7814	611	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000202635.1	s__Microbacterium testaceum_F	80.781	619	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727775.1	s__Microbacterium lushaniae	80.7363	565	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	80.7309	556	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015278315.1	s__Microbacterium ureisolvens	80.5782	579	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_006715565.1	s__Microbacterium sp006715565	80.1408	525	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003850245.1	s__Microbacterium sp003850245	80.068	496	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506375.1	s__Microbacterium sp902506375	79.5649	463	1181	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:25,719] [INFO] GTDB search result was written to GCF_008017415.1_ASM801741v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:25,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:25,724] [INFO] DFAST_QC result json was written to GCF_008017415.1_ASM801741v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:25,724] [INFO] DFAST_QC completed!
[2024-01-24 12:32:25,724] [INFO] Total running time: 0h1m33s