[2024-01-24 11:12:38,373] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:38,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:38,374] [INFO] DQC Reference Directory: /var/lib/cwl/stga1616078-e436-4fc2-806e-77ce90b11181/dqc_reference
[2024-01-24 11:12:39,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:39,738] [INFO] Task started: Prodigal
[2024-01-24 11:12:39,738] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc00664c-9e86-44fa-b108-f4a83ee71e2a/GCF_008727775.1_ASM872777v1_genomic.fna.gz | prodigal -d GCF_008727775.1_ASM872777v1_genomic.fna/cds.fna -a GCF_008727775.1_ASM872777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,747] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,747] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,747] [INFO] Running command: hmmsearch --tblout GCF_008727775.1_ASM872777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1616078-e436-4fc2-806e-77ce90b11181/dqc_reference/reference_markers.hmm GCF_008727775.1_ASM872777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:51,012] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:51,013] [INFO] Found 6/6 markers.
[2024-01-24 11:12:51,053] [INFO] Query marker FASTA was written to GCF_008727775.1_ASM872777v1_genomic.fna/markers.fasta
[2024-01-24 11:12:51,054] [INFO] Task started: Blastn
[2024-01-24 11:12:51,054] [INFO] Running command: blastn -query GCF_008727775.1_ASM872777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1616078-e436-4fc2-806e-77ce90b11181/dqc_reference/reference_markers.fasta -out GCF_008727775.1_ASM872777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:52,235] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:52,239] [INFO] Selected 20 target genomes.
[2024-01-24 11:12:52,240] [INFO] Target genome list was writen to GCF_008727775.1_ASM872777v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:52,246] [INFO] Task started: fastANI
[2024-01-24 11:12:52,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc00664c-9e86-44fa-b108-f4a83ee71e2a/GCF_008727775.1_ASM872777v1_genomic.fna.gz --refList GCF_008727775.1_ASM872777v1_genomic.fna/target_genomes.txt --output GCF_008727775.1_ASM872777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:07,108] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:07,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1616078-e436-4fc2-806e-77ce90b11181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:07,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1616078-e436-4fc2-806e-77ce90b11181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:07,124] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:07,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:07,125] [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 lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	100.0	1215	1216	95	conclusive
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	90.9421	1069	1216	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.0526	517	1216	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	80.7458	571	1216	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	80.7085	554	1216	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.6373	590	1216	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	80.6146	516	1216	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.6095	534	1216	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	80.5969	588	1216	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	80.5534	535	1216	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	80.533	535	1216	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.5107	545	1216	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.4595	557	1216	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.4343	578	1216	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.3667	576	1216	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.3616	566	1216	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	80.2312	483	1216	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.1934	492	1216	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	80.1835	481	1216	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.0309	576	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:07,126] [INFO] DFAST Taxonomy check result was written to GCF_008727775.1_ASM872777v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:07,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:07,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:07,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1616078-e436-4fc2-806e-77ce90b11181/dqc_reference/checkm_data
[2024-01-24 11:13:07,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:07,174] [INFO] Task started: CheckM
[2024-01-24 11:13:07,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008727775.1_ASM872777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008727775.1_ASM872777v1_genomic.fna/checkm_input GCF_008727775.1_ASM872777v1_genomic.fna/checkm_result
[2024-01-24 11:14:18,958] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:18,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:18,986] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:18,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:18,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008727775.1_ASM872777v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:18,987] [INFO] Task started: Blastn
[2024-01-24 11:14:18,988] [INFO] Running command: blastn -query GCF_008727775.1_ASM872777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1616078-e436-4fc2-806e-77ce90b11181/dqc_reference/reference_markers_gtdb.fasta -out GCF_008727775.1_ASM872777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:20,888] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:20,893] [INFO] Selected 16 target genomes.
[2024-01-24 11:14:20,893] [INFO] Target genome list was writen to GCF_008727775.1_ASM872777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:20,917] [INFO] Task started: fastANI
[2024-01-24 11:14:20,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc00664c-9e86-44fa-b108-f4a83ee71e2a/GCF_008727775.1_ASM872777v1_genomic.fna.gz --refList GCF_008727775.1_ASM872777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008727775.1_ASM872777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:32,985] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:33,004] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:33,004] [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_008727775.1	s__Microbacterium lushaniae	100.0	1215	1216	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_004564355.1	s__Microbacterium wangchenii	90.9421	1069	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.29	98.90	0.96	0.95	3	-
GCF_003931875.1	s__Microbacterium sp003931875	82.3285	676	1216	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	80.8411	559	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017415.1	s__Microbacterium hatanonis	80.7389	572	1216	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	80.64	518	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991875.1	s__Microbacterium lemovicicum	80.5843	588	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992455.1	s__Microbacterium saccharophilum	80.5769	533	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.54	98.03	0.93	0.90	5	-
GCF_015278315.1	s__Microbacterium ureisolvens	80.4614	589	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCA_900078385.1	s__Microbacterium sp900078385	80.4424	524	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	80.3695	567	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	80.3587	618	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409015.1	s__Microbacterium sp013409015	80.2977	550	1216	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	80.2479	518	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014197265.1	s__Microbacterium invictum	80.128	490	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410955.1	s__Microbacterium sp013410955	80.0087	539	1216	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 11:14:33,006] [INFO] GTDB search result was written to GCF_008727775.1_ASM872777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:33,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:33,013] [INFO] DFAST_QC result json was written to GCF_008727775.1_ASM872777v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:33,013] [INFO] DFAST_QC completed!
[2024-01-24 11:14:33,013] [INFO] Total running time: 0h1m55s