[2024-01-24 12:47:05,632] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg5532d621-8059-45ac-af6f-e42c61264ec4/dqc_reference
[2024-01-24 12:47:06,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,838] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c507c36-c416-4b0c-ad7a-a62442685247/GCF_009745985.1_ASM974598v1_genomic.fna.gz | prodigal -d GCF_009745985.1_ASM974598v1_genomic.fna/cds.fna -a GCF_009745985.1_ASM974598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:17,575] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:17,575] [INFO] Task started: HMMsearch
[2024-01-24 12:47:17,576] [INFO] Running command: hmmsearch --tblout GCF_009745985.1_ASM974598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5532d621-8059-45ac-af6f-e42c61264ec4/dqc_reference/reference_markers.hmm GCF_009745985.1_ASM974598v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:17,843] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:17,844] [INFO] Found 6/6 markers.
[2024-01-24 12:47:17,880] [INFO] Query marker FASTA was written to GCF_009745985.1_ASM974598v1_genomic.fna/markers.fasta
[2024-01-24 12:47:17,881] [INFO] Task started: Blastn
[2024-01-24 12:47:17,881] [INFO] Running command: blastn -query GCF_009745985.1_ASM974598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5532d621-8059-45ac-af6f-e42c61264ec4/dqc_reference/reference_markers.fasta -out GCF_009745985.1_ASM974598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:19,025] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:19,030] [INFO] Selected 19 target genomes.
[2024-01-24 12:47:19,031] [INFO] Target genome list was writen to GCF_009745985.1_ASM974598v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:19,040] [INFO] Task started: fastANI
[2024-01-24 12:47:19,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c507c36-c416-4b0c-ad7a-a62442685247/GCF_009745985.1_ASM974598v1_genomic.fna.gz --refList GCF_009745985.1_ASM974598v1_genomic.fna/target_genomes.txt --output GCF_009745985.1_ASM974598v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:33,620] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:33,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5532d621-8059-45ac-af6f-e42c61264ec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:33,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5532d621-8059-45ac-af6f-e42c61264ec4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:33,633] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:33,633] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:33,634] [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 suaedae	strain=YZYP 306	GCA_003254645.1	2067813	2067813	type	True	86.1268	852	1296	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	82.6194	619	1296	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	82.1337	593	1296	95	below_threshold
Microbacterium gubbeenense	strain=DSM 15944	GCA_000422745.1	159896	159896	type	True	82.0848	588	1296	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	81.5259	610	1296	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	81.5004	609	1296	95	below_threshold
Microbacterium faecale	strain=CGMCC 1.15152	GCA_014640975.1	1804630	1804630	type	True	81.2657	590	1296	95	below_threshold
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	81.1972	559	1296	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.3536	532	1296	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	79.2665	488	1296	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.2148	448	1296	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.1165	411	1296	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.8271	427	1296	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.3431	452	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:33,635] [INFO] DFAST Taxonomy check result was written to GCF_009745985.1_ASM974598v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:33,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:33,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:33,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5532d621-8059-45ac-af6f-e42c61264ec4/dqc_reference/checkm_data
[2024-01-24 12:47:33,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:33,678] [INFO] Task started: CheckM
[2024-01-24 12:47:33,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009745985.1_ASM974598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009745985.1_ASM974598v1_genomic.fna/checkm_input GCF_009745985.1_ASM974598v1_genomic.fna/checkm_result
[2024-01-24 12:48:28,553] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:28,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 23.19%
Strain heterogeneity: 4.55%
--------------------------------------------------------------------------------
[2024-01-24 12:48:28,588] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:28,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:28,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009745985.1_ASM974598v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:28,589] [INFO] Task started: Blastn
[2024-01-24 12:48:28,589] [INFO] Running command: blastn -query GCF_009745985.1_ASM974598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5532d621-8059-45ac-af6f-e42c61264ec4/dqc_reference/reference_markers_gtdb.fasta -out GCF_009745985.1_ASM974598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:30,385] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:30,389] [INFO] Selected 17 target genomes.
[2024-01-24 12:48:30,389] [INFO] Target genome list was writen to GCF_009745985.1_ASM974598v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:30,399] [INFO] Task started: fastANI
[2024-01-24 12:48:30,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c507c36-c416-4b0c-ad7a-a62442685247/GCF_009745985.1_ASM974598v1_genomic.fna.gz --refList GCF_009745985.1_ASM974598v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009745985.1_ASM974598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:42,048] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:42,059] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:42,059] [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_009745985.1	s__Microbacterium karelineae	100.0	1293	1296	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_003254645.1	s__Microbacterium suaedae	86.1134	853	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011326725.1	s__Microbacterium excoecariae	82.5707	624	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_000422745.1	s__Microbacterium gubbeenense	82.0872	588	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422385.1	s__Microbacterium indicum	82.08	597	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117025.1	s__Microbacterium stercoravium	81.9357	521	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003327285.1	s__Microbacterium sorbitolivorans	81.5216	611	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014640975.1	s__Microbacterium faecale	81.2692	589	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.13	95.13	0.92	0.92	2	-
GCF_014646015.1	s__Microbacterium nanhaiense	81.1921	559	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645325.1	s__Microbacterium sp903645325	79.5205	408	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002837415.1	s__Microbacterium sp002837415	79.2183	385	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268515.1	s__Microbacterium sp018268515	78.7068	429	1296	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268455.1	s__Microbacterium sp018268455	78.6779	399	1296	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 12:48:42,061] [INFO] GTDB search result was written to GCF_009745985.1_ASM974598v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:42,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:42,065] [INFO] DFAST_QC result json was written to GCF_009745985.1_ASM974598v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:42,065] [INFO] DFAST_QC completed!
[2024-01-24 12:48:42,065] [INFO] Total running time: 0h1m36s