[2024-01-25 17:45:05,760] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:05,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:05,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ccd1a34-9a9c-4743-94fd-12aeed6eb6cd/dqc_reference
[2024-01-25 17:45:06,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:06,988] [INFO] Task started: Prodigal
[2024-01-25 17:45:06,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg65e12c89-9523-4d98-b9ef-dd2f88fa8489/GCF_015278255.1_ASM1527825v1_genomic.fna.gz | prodigal -d GCF_015278255.1_ASM1527825v1_genomic.fna/cds.fna -a GCF_015278255.1_ASM1527825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:17,886] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:17,887] [INFO] Task started: HMMsearch
[2024-01-25 17:45:17,887] [INFO] Running command: hmmsearch --tblout GCF_015278255.1_ASM1527825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ccd1a34-9a9c-4743-94fd-12aeed6eb6cd/dqc_reference/reference_markers.hmm GCF_015278255.1_ASM1527825v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:18,094] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:18,095] [INFO] Found 6/6 markers.
[2024-01-25 17:45:18,134] [INFO] Query marker FASTA was written to GCF_015278255.1_ASM1527825v1_genomic.fna/markers.fasta
[2024-01-25 17:45:18,134] [INFO] Task started: Blastn
[2024-01-25 17:45:18,134] [INFO] Running command: blastn -query GCF_015278255.1_ASM1527825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ccd1a34-9a9c-4743-94fd-12aeed6eb6cd/dqc_reference/reference_markers.fasta -out GCF_015278255.1_ASM1527825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:19,400] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:19,402] [INFO] Selected 12 target genomes.
[2024-01-25 17:45:19,402] [INFO] Target genome list was writen to GCF_015278255.1_ASM1527825v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:19,409] [INFO] Task started: fastANI
[2024-01-25 17:45:19,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e12c89-9523-4d98-b9ef-dd2f88fa8489/GCF_015278255.1_ASM1527825v1_genomic.fna.gz --refList GCF_015278255.1_ASM1527825v1_genomic.fna/target_genomes.txt --output GCF_015278255.1_ASM1527825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:31,243] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:31,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ccd1a34-9a9c-4743-94fd-12aeed6eb6cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:31,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ccd1a34-9a9c-4743-94fd-12aeed6eb6cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:31,252] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:31,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:31,252] [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 hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	100.0	1312	1314	95	conclusive
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	89.0054	1048	1314	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	85.9579	948	1314	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	84.6739	908	1314	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	84.4566	810	1314	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	84.452	889	1314	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	84.2847	894	1314	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	84.077	851	1314	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	83.8383	806	1314	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	83.0643	744	1314	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	82.8442	752	1314	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.8909	591	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:31,254] [INFO] DFAST Taxonomy check result was written to GCF_015278255.1_ASM1527825v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:31,254] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:31,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:31,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ccd1a34-9a9c-4743-94fd-12aeed6eb6cd/dqc_reference/checkm_data
[2024-01-25 17:45:31,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:31,294] [INFO] Task started: CheckM
[2024-01-25 17:45:31,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015278255.1_ASM1527825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015278255.1_ASM1527825v1_genomic.fna/checkm_input GCF_015278255.1_ASM1527825v1_genomic.fna/checkm_result
[2024-01-25 17:46:32,934] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:32,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:32,957] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:32,957] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:32,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015278255.1_ASM1527825v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:32,959] [INFO] Task started: Blastn
[2024-01-25 17:46:32,959] [INFO] Running command: blastn -query GCF_015278255.1_ASM1527825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ccd1a34-9a9c-4743-94fd-12aeed6eb6cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_015278255.1_ASM1527825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:35,379] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:35,387] [INFO] Selected 10 target genomes.
[2024-01-25 17:46:35,388] [INFO] Target genome list was writen to GCF_015278255.1_ASM1527825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:35,410] [INFO] Task started: fastANI
[2024-01-25 17:46:35,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e12c89-9523-4d98-b9ef-dd2f88fa8489/GCF_015278255.1_ASM1527825v1_genomic.fna.gz --refList GCF_015278255.1_ASM1527825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015278255.1_ASM1527825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:47,026] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:47,034] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:47,034] [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_015278255.1	s__Microbacterium hibisci	100.0	1312	1314	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_015278315.1	s__Microbacterium ureisolvens	88.9938	1049	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	86.0086	930	1314	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	85.9592	990	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	85.9208	951	1314	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	85.7794	869	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858275.1	s__Microbacterium sp009858275	85.6116	874	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278355.1	s__Microbacterium yannicii_B	84.623	936	1314	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277815.1	s__Microbacterium sp015277815	84.4685	809	1314	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	84.3283	890	1314	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 17:46:47,036] [INFO] GTDB search result was written to GCF_015278255.1_ASM1527825v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:47,037] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:47,040] [INFO] DFAST_QC result json was written to GCF_015278255.1_ASM1527825v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:47,040] [INFO] DFAST_QC completed!
[2024-01-25 17:46:47,040] [INFO] Total running time: 0h1m41s