[2024-01-24 13:40:44,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg781033d0-8c88-437f-ade9-8cb8198d1135/dqc_reference
[2024-01-24 13:40:45,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,411] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg685b80ed-7e71-4f16-baf2-3488b966a8af/GCF_004404025.1_ASM440402v1_genomic.fna.gz | prodigal -d GCF_004404025.1_ASM440402v1_genomic.fna/cds.fna -a GCF_004404025.1_ASM440402v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:57,356] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:57,357] [INFO] Task started: HMMsearch
[2024-01-24 13:40:57,357] [INFO] Running command: hmmsearch --tblout GCF_004404025.1_ASM440402v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg781033d0-8c88-437f-ade9-8cb8198d1135/dqc_reference/reference_markers.hmm GCF_004404025.1_ASM440402v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:57,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:57,623] [INFO] Found 6/6 markers.
[2024-01-24 13:40:57,660] [INFO] Query marker FASTA was written to GCF_004404025.1_ASM440402v1_genomic.fna/markers.fasta
[2024-01-24 13:40:57,660] [INFO] Task started: Blastn
[2024-01-24 13:40:57,661] [INFO] Running command: blastn -query GCF_004404025.1_ASM440402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg781033d0-8c88-437f-ade9-8cb8198d1135/dqc_reference/reference_markers.fasta -out GCF_004404025.1_ASM440402v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:58,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:58,590] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:58,591] [INFO] Target genome list was writen to GCF_004404025.1_ASM440402v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:58,597] [INFO] Task started: fastANI
[2024-01-24 13:40:58,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg685b80ed-7e71-4f16-baf2-3488b966a8af/GCF_004404025.1_ASM440402v1_genomic.fna.gz --refList GCF_004404025.1_ASM440402v1_genomic.fna/target_genomes.txt --output GCF_004404025.1_ASM440402v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:08,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:08,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg781033d0-8c88-437f-ade9-8cb8198d1135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:08,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg781033d0-8c88-437f-ade9-8cb8198d1135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:08,764] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:08,764] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:08,764] [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	86.4619	894	1187	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	85.9265	896	1187	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	85.9083	897	1187	95	below_threshold
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	85.5078	833	1187	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	85.2561	837	1187	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	85.1927	846	1187	95	below_threshold
Cryobacterium levicorallinum	strain=Hh34	GCA_004402405.1	995038	995038	type	True	84.6888	821	1187	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	84.6584	832	1187	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	84.6509	823	1187	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	79.7659	436	1187	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.6911	273	1187	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.6097	242	1187	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.5613	268	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:08,766] [INFO] DFAST Taxonomy check result was written to GCF_004404025.1_ASM440402v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:08,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:08,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:08,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg781033d0-8c88-437f-ade9-8cb8198d1135/dqc_reference/checkm_data
[2024-01-24 13:41:08,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:08,804] [INFO] Task started: CheckM
[2024-01-24 13:41:08,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004404025.1_ASM440402v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004404025.1_ASM440402v1_genomic.fna/checkm_input GCF_004404025.1_ASM440402v1_genomic.fna/checkm_result
[2024-01-24 13:41:45,585] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:45,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,607] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:45,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:45,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004404025.1_ASM440402v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:45,608] [INFO] Task started: Blastn
[2024-01-24 13:41:45,608] [INFO] Running command: blastn -query GCF_004404025.1_ASM440402v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg781033d0-8c88-437f-ade9-8cb8198d1135/dqc_reference/reference_markers_gtdb.fasta -out GCF_004404025.1_ASM440402v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:47,007] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:47,010] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:47,010] [INFO] Target genome list was writen to GCF_004404025.1_ASM440402v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:47,016] [INFO] Task started: fastANI
[2024-01-24 13:41:47,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg685b80ed-7e71-4f16-baf2-3488b966a8af/GCF_004404025.1_ASM440402v1_genomic.fna.gz --refList GCF_004404025.1_ASM440402v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004404025.1_ASM440402v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:55,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:55,627] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:55,627] [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_002929495.1	s__Cryobacterium sp002929495	97.0851	1045	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.09	97.09	0.88	0.88	2	conclusive
GCF_004403185.1	s__Cryobacterium sp004403185	91.5016	913	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929825.1	s__Cryobacterium sp002929825	89.4262	890	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	95.15	95.07	0.83	0.81	4	-
GCF_002929505.1	s__Cryobacterium sp002929505	89.3471	902	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403985.1	s__Cryobacterium sp004403985	86.4935	826	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.96	97.96	0.88	0.88	2	-
GCF_900103805.1	s__Cryobacterium flavum	85.9418	894	1187	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	85.7856	831	1187	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	84.6727	823	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.20	96.46	0.88	0.78	9	-
GCF_002929805.1	s__Cryobacterium sp002929805	84.2797	798	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.19	99.19	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:55,631] [INFO] GTDB search result was written to GCF_004404025.1_ASM440402v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:55,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:55,637] [INFO] DFAST_QC result json was written to GCF_004404025.1_ASM440402v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:55,637] [INFO] DFAST_QC completed!
[2024-01-24 13:41:55,637] [INFO] Total running time: 0h1m11s