[2024-01-24 14:31:30,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:30,170] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:30,170] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ad5e66f-9337-4305-acad-f881ab596486/dqc_reference
[2024-01-24 14:31:31,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:31,440] [INFO] Task started: Prodigal
[2024-01-24 14:31:31,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg5113490e-7523-4de3-a493-be571996a4b5/GCF_003999995.1_ASM399999v1_genomic.fna.gz | prodigal -d GCF_003999995.1_ASM399999v1_genomic.fna/cds.fna -a GCF_003999995.1_ASM399999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:42,772] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:42,773] [INFO] Task started: HMMsearch
[2024-01-24 14:31:42,773] [INFO] Running command: hmmsearch --tblout GCF_003999995.1_ASM399999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ad5e66f-9337-4305-acad-f881ab596486/dqc_reference/reference_markers.hmm GCF_003999995.1_ASM399999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:43,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:43,083] [INFO] Found 6/6 markers.
[2024-01-24 14:31:43,117] [INFO] Query marker FASTA was written to GCF_003999995.1_ASM399999v1_genomic.fna/markers.fasta
[2024-01-24 14:31:43,117] [INFO] Task started: Blastn
[2024-01-24 14:31:43,117] [INFO] Running command: blastn -query GCF_003999995.1_ASM399999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad5e66f-9337-4305-acad-f881ab596486/dqc_reference/reference_markers.fasta -out GCF_003999995.1_ASM399999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:44,541] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:44,544] [INFO] Selected 14 target genomes.
[2024-01-24 14:31:44,545] [INFO] Target genome list was writen to GCF_003999995.1_ASM399999v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:44,550] [INFO] Task started: fastANI
[2024-01-24 14:31:44,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg5113490e-7523-4de3-a493-be571996a4b5/GCF_003999995.1_ASM399999v1_genomic.fna.gz --refList GCF_003999995.1_ASM399999v1_genomic.fna/target_genomes.txt --output GCF_003999995.1_ASM399999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:57,335] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:57,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ad5e66f-9337-4305-acad-f881ab596486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:57,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ad5e66f-9337-4305-acad-f881ab596486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:57,348] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:57,348] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:57,348] [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 sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	100.0	1260	1260	95	conclusive
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	85.3567	837	1260	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	84.9803	855	1260	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	83.139	778	1260	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	83.0456	744	1260	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	83.0273	799	1260	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	82.6805	743	1260	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	82.6787	804	1260	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	82.5621	770	1260	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	82.4392	772	1260	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	82.3299	711	1260	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	81.8556	733	1260	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	81.3242	620	1260	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.0841	592	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:57,351] [INFO] DFAST Taxonomy check result was written to GCF_003999995.1_ASM399999v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:57,351] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:57,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:57,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ad5e66f-9337-4305-acad-f881ab596486/dqc_reference/checkm_data
[2024-01-24 14:31:57,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:57,398] [INFO] Task started: CheckM
[2024-01-24 14:31:57,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003999995.1_ASM399999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003999995.1_ASM399999v1_genomic.fna/checkm_input GCF_003999995.1_ASM399999v1_genomic.fna/checkm_result
[2024-01-24 14:32:54,541] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:54,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:54,569] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:54,569] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:54,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003999995.1_ASM399999v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:54,570] [INFO] Task started: Blastn
[2024-01-24 14:32:54,570] [INFO] Running command: blastn -query GCF_003999995.1_ASM399999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad5e66f-9337-4305-acad-f881ab596486/dqc_reference/reference_markers_gtdb.fasta -out GCF_003999995.1_ASM399999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:56,924] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:56,929] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:56,929] [INFO] Target genome list was writen to GCF_003999995.1_ASM399999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:56,940] [INFO] Task started: fastANI
[2024-01-24 14:32:56,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg5113490e-7523-4de3-a493-be571996a4b5/GCF_003999995.1_ASM399999v1_genomic.fna.gz --refList GCF_003999995.1_ASM399999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003999995.1_ASM399999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:09,526] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:09,540] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:09,541] [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_003999995.1	s__Microbacterium sp003999995	100.0	1260	1260	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_018588945.1	s__Microbacterium flavescens	85.3252	840	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837165.1	s__Microbacterium sp014837165	84.9803	855	1260	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	84.7165	808	1260	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	84.2262	814	1260	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	83.7469	809	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907635.1	s__Microbacterium insulae	83.3501	780	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	83.139	778	1260	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	83.0788	793	1260	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	82.8806	508	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000304335.1	s__Microbacterium yannicii_A	82.4658	727	1260	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	82.3492	720	1260	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	81.3137	621	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156455.1	s__Microbacterium sp900156455	80.4514	545	1260	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.72	96.66	0.88	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:09,542] [INFO] GTDB search result was written to GCF_003999995.1_ASM399999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:09,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:09,546] [INFO] DFAST_QC result json was written to GCF_003999995.1_ASM399999v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:09,547] [INFO] DFAST_QC completed!
[2024-01-24 14:33:09,547] [INFO] Total running time: 0h1m39s