[2024-01-24 13:37:19,499] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:19,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:19,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg34f632bc-c1a7-4cf2-af5e-84a2e308d3b0/dqc_reference
[2024-01-24 13:37:20,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:20,823] [INFO] Task started: Prodigal
[2024-01-24 13:37:20,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg96f6a030-d6ff-4611-b281-1e89067869d8/GCF_013409785.1_ASM1340978v1_genomic.fna.gz | prodigal -d GCF_013409785.1_ASM1340978v1_genomic.fna/cds.fna -a GCF_013409785.1_ASM1340978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:32,891] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:32,891] [INFO] Task started: HMMsearch
[2024-01-24 13:37:32,891] [INFO] Running command: hmmsearch --tblout GCF_013409785.1_ASM1340978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34f632bc-c1a7-4cf2-af5e-84a2e308d3b0/dqc_reference/reference_markers.hmm GCF_013409785.1_ASM1340978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:33,218] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:33,219] [INFO] Found 6/6 markers.
[2024-01-24 13:37:33,256] [INFO] Query marker FASTA was written to GCF_013409785.1_ASM1340978v1_genomic.fna/markers.fasta
[2024-01-24 13:37:33,257] [INFO] Task started: Blastn
[2024-01-24 13:37:33,257] [INFO] Running command: blastn -query GCF_013409785.1_ASM1340978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f632bc-c1a7-4cf2-af5e-84a2e308d3b0/dqc_reference/reference_markers.fasta -out GCF_013409785.1_ASM1340978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:34,657] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:34,665] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:34,665] [INFO] Target genome list was writen to GCF_013409785.1_ASM1340978v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:34,678] [INFO] Task started: fastANI
[2024-01-24 13:37:34,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f6a030-d6ff-4611-b281-1e89067869d8/GCF_013409785.1_ASM1340978v1_genomic.fna.gz --refList GCF_013409785.1_ASM1340978v1_genomic.fna/target_genomes.txt --output GCF_013409785.1_ASM1340978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:49,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:49,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34f632bc-c1a7-4cf2-af5e-84a2e308d3b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:49,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34f632bc-c1a7-4cf2-af5e-84a2e308d3b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:49,366] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:49,366] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:49,366] [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 immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	100.0	1301	1302	95	conclusive
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	82.0806	718	1302	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	82.0451	668	1302	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	81.8935	710	1302	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	81.8679	694	1302	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	81.8185	680	1302	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	81.7565	698	1302	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	81.7387	719	1302	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	81.7109	698	1302	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	81.6985	711	1302	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	81.5441	691	1302	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	81.5127	636	1302	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	81.267	657	1302	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	81.0933	713	1302	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	80.984	566	1302	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	80.9324	560	1302	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.6284	542	1302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:49,368] [INFO] DFAST Taxonomy check result was written to GCF_013409785.1_ASM1340978v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:49,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:49,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:49,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34f632bc-c1a7-4cf2-af5e-84a2e308d3b0/dqc_reference/checkm_data
[2024-01-24 13:37:49,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:49,410] [INFO] Task started: CheckM
[2024-01-24 13:37:49,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409785.1_ASM1340978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409785.1_ASM1340978v1_genomic.fna/checkm_input GCF_013409785.1_ASM1340978v1_genomic.fna/checkm_result
[2024-01-24 13:38:59,389] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:59,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:59,413] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:59,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:59,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409785.1_ASM1340978v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:59,414] [INFO] Task started: Blastn
[2024-01-24 13:38:59,414] [INFO] Running command: blastn -query GCF_013409785.1_ASM1340978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f632bc-c1a7-4cf2-af5e-84a2e308d3b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409785.1_ASM1340978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:01,365] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:01,370] [INFO] Selected 20 target genomes.
[2024-01-24 13:39:01,370] [INFO] Target genome list was writen to GCF_013409785.1_ASM1340978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:01,403] [INFO] Task started: fastANI
[2024-01-24 13:39:01,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg96f6a030-d6ff-4611-b281-1e89067869d8/GCF_013409785.1_ASM1340978v1_genomic.fna.gz --refList GCF_013409785.1_ASM1340978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409785.1_ASM1340978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:18,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:18,336] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:18,337] [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_013409785.1	s__Microbacterium immunditiarum	100.0	1301	1302	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_011759705.1	s__Microbacterium ulmi	82.0836	668	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001422925.1	s__Microbacterium sp001422925	82.0557	712	1302	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	82.0237	701	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278315.1	s__Microbacterium ureisolvens	81.86	712	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_018588945.1	s__Microbacterium flavescens	81.829	679	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	81.8013	700	1302	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	81.7587	697	1302	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	81.756	718	1302	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	81.7559	695	1302	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	81.7069	609	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	81.6916	712	1302	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	81.56	689	1302	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	81.5125	660	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715675.1	s__Microbacterium sp006715675	81.5065	710	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907635.1	s__Microbacterium insulae	81.4447	662	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900292075.1	s__Microbacterium timonense	81.3127	656	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524205.1	s__Microbacterium sp012524205	81.2958	713	1302	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	80.9735	567	1302	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314225.1	s__Microbacterium sp001314225	80.8767	588	1302	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 13:39:18,338] [INFO] GTDB search result was written to GCF_013409785.1_ASM1340978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:18,339] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:18,343] [INFO] DFAST_QC result json was written to GCF_013409785.1_ASM1340978v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:18,343] [INFO] DFAST_QC completed!
[2024-01-24 13:39:18,343] [INFO] Total running time: 0h1m59s