[2024-01-24 13:40:30,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgadd0d141-631c-4207-a5a0-812b8831a28e/dqc_reference
[2024-01-24 13:40:31,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,560] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,561] [INFO] Running command: gunzip -c /var/lib/cwl/stga407dffb-6cad-49d6-9ee4-0953385349dc/GCF_004403345.1_ASM440334v1_genomic.fna.gz | prodigal -d GCF_004403345.1_ASM440334v1_genomic.fna/cds.fna -a GCF_004403345.1_ASM440334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:42,793] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:42,794] [INFO] Task started: HMMsearch
[2024-01-24 13:40:42,794] [INFO] Running command: hmmsearch --tblout GCF_004403345.1_ASM440334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadd0d141-631c-4207-a5a0-812b8831a28e/dqc_reference/reference_markers.hmm GCF_004403345.1_ASM440334v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:43,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:43,081] [INFO] Found 6/6 markers.
[2024-01-24 13:40:43,113] [INFO] Query marker FASTA was written to GCF_004403345.1_ASM440334v1_genomic.fna/markers.fasta
[2024-01-24 13:40:43,113] [INFO] Task started: Blastn
[2024-01-24 13:40:43,113] [INFO] Running command: blastn -query GCF_004403345.1_ASM440334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd0d141-631c-4207-a5a0-812b8831a28e/dqc_reference/reference_markers.fasta -out GCF_004403345.1_ASM440334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:44,071] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:44,074] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:44,074] [INFO] Target genome list was writen to GCF_004403345.1_ASM440334v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:44,075] [INFO] Task started: fastANI
[2024-01-24 13:40:44,076] [INFO] Running command: fastANI --query /var/lib/cwl/stga407dffb-6cad-49d6-9ee4-0953385349dc/GCF_004403345.1_ASM440334v1_genomic.fna.gz --refList GCF_004403345.1_ASM440334v1_genomic.fna/target_genomes.txt --output GCF_004403345.1_ASM440334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:54,311] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:54,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadd0d141-631c-4207-a5a0-812b8831a28e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:54,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadd0d141-631c-4207-a5a0-812b8831a28e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:54,323] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:40:54,324] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:40:54,324] [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
Cryobacterium aureum	strain=Hh31	GCA_002954245.1	995037	995037	type	True	86.1163	828	1168	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	85.9469	825	1168	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	85.9314	828	1168	95	below_threshold
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	85.5459	807	1168	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	84.9847	800	1168	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	84.9342	811	1168	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	84.6613	793	1168	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	84.6425	796	1168	95	below_threshold
Cryobacterium levicorallinum	strain=Hh34	GCA_004402405.1	995038	995038	type	True	84.5638	803	1168	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	79.7038	451	1168	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.9626	266	1168	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.5684	251	1168	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	77.3544	225	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:54,325] [INFO] DFAST Taxonomy check result was written to GCF_004403345.1_ASM440334v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:54,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:54,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:54,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadd0d141-631c-4207-a5a0-812b8831a28e/dqc_reference/checkm_data
[2024-01-24 13:40:54,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:54,373] [INFO] Task started: CheckM
[2024-01-24 13:40:54,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004403345.1_ASM440334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004403345.1_ASM440334v1_genomic.fna/checkm_input GCF_004403345.1_ASM440334v1_genomic.fna/checkm_result
[2024-01-24 13:41:31,171] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:31,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:31,190] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:31,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:31,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004403345.1_ASM440334v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:31,191] [INFO] Task started: Blastn
[2024-01-24 13:41:31,191] [INFO] Running command: blastn -query GCF_004403345.1_ASM440334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd0d141-631c-4207-a5a0-812b8831a28e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004403345.1_ASM440334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:32,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:32,635] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:32,636] [INFO] Target genome list was writen to GCF_004403345.1_ASM440334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:32,648] [INFO] Task started: fastANI
[2024-01-24 13:41:32,649] [INFO] Running command: fastANI --query /var/lib/cwl/stga407dffb-6cad-49d6-9ee4-0953385349dc/GCF_004403345.1_ASM440334v1_genomic.fna.gz --refList GCF_004403345.1_ASM440334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004403345.1_ASM440334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:42,068] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:42,078] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:42,078] [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_002929825.1	s__Cryobacterium sp002929825	95.0227	959	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	95.15	95.07	0.83	0.81	4	conclusive
GCF_002929505.1	s__Cryobacterium sp002929505	94.3191	977	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403185.1	s__Cryobacterium sp004403185	89.8294	853	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929495.1	s__Cryobacterium sp002929495	89.546	864	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.09	97.09	0.88	0.88	2	-
GCF_004403985.1	s__Cryobacterium sp004403985	86.7039	841	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.96	97.96	0.88	0.88	2	-
GCF_002954245.1	s__Cryobacterium aureum	86.0962	829	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103805.1	s__Cryobacterium flavum	85.9147	830	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.64	97.38	0.89	0.83	6	-
GCF_004402535.1	s__Cryobacterium sp004402535	85.6302	767	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004404055.1	s__Cryobacterium ruanii	85.5567	806	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402405.1	s__Cryobacterium levicorallinum	84.5638	803	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.20	96.46	0.88	0.78	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:42,081] [INFO] GTDB search result was written to GCF_004403345.1_ASM440334v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:42,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:42,087] [INFO] DFAST_QC result json was written to GCF_004403345.1_ASM440334v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:42,087] [INFO] DFAST_QC completed!
[2024-01-24 13:41:42,087] [INFO] Total running time: 0h1m12s