[2024-01-25 18:42:50,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:50,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:50,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg8549ff39-4794-4c17-9878-381f51a1986a/dqc_reference
[2024-01-25 18:42:51,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:51,836] [INFO] Task started: Prodigal
[2024-01-25 18:42:51,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg25bfc54e-b747-4cc4-aae4-c3d3583f7b45/GCF_001025155.1_ASM102515v1_genomic.fna.gz | prodigal -d GCF_001025155.1_ASM102515v1_genomic.fna/cds.fna -a GCF_001025155.1_ASM102515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:57,998] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:57,998] [INFO] Task started: HMMsearch
[2024-01-25 18:42:57,998] [INFO] Running command: hmmsearch --tblout GCF_001025155.1_ASM102515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8549ff39-4794-4c17-9878-381f51a1986a/dqc_reference/reference_markers.hmm GCF_001025155.1_ASM102515v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:58,199] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:58,200] [INFO] Found 6/6 markers.
[2024-01-25 18:42:58,218] [INFO] Query marker FASTA was written to GCF_001025155.1_ASM102515v1_genomic.fna/markers.fasta
[2024-01-25 18:42:58,219] [INFO] Task started: Blastn
[2024-01-25 18:42:58,219] [INFO] Running command: blastn -query GCF_001025155.1_ASM102515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8549ff39-4794-4c17-9878-381f51a1986a/dqc_reference/reference_markers.fasta -out GCF_001025155.1_ASM102515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:58,969] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:58,972] [INFO] Selected 11 target genomes.
[2024-01-25 18:42:58,972] [INFO] Target genome list was writen to GCF_001025155.1_ASM102515v1_genomic.fna/target_genomes.txt
[2024-01-25 18:42:58,979] [INFO] Task started: fastANI
[2024-01-25 18:42:58,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg25bfc54e-b747-4cc4-aae4-c3d3583f7b45/GCF_001025155.1_ASM102515v1_genomic.fna.gz --refList GCF_001025155.1_ASM102515v1_genomic.fna/target_genomes.txt --output GCF_001025155.1_ASM102515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:05,998] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:05,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8549ff39-4794-4c17-9878-381f51a1986a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:05,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8549ff39-4794-4c17-9878-381f51a1986a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:06,005] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:43:06,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:06,005] [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
Bifidobacterium angulatum	strain=JCM 7096	GCA_001025155.1	1683	1683	type	True	100.0	672	673	95	conclusive
Bifidobacterium angulatum	strain=LMG 11039	GCA_000741065.1	1683	1683	type	True	99.9859	662	673	95	conclusive
Bifidobacterium angulatum	strain=DSM 20098	GCA_000156635.1	1683	1683	type	True	99.9789	666	673	95	conclusive
Bifidobacterium angulatum	strain=DSM 20098	GCA_000771205.1	1683	1683	type	True	99.9687	649	673	95	conclusive
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	88.2522	544	673	95	below_threshold
Bifidobacterium pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	86.0736	512	673	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.1503	322	673	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	75.4952	54	673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:06,008] [INFO] DFAST Taxonomy check result was written to GCF_001025155.1_ASM102515v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:06,008] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:06,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:06,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8549ff39-4794-4c17-9878-381f51a1986a/dqc_reference/checkm_data
[2024-01-25 18:43:06,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:06,036] [INFO] Task started: CheckM
[2024-01-25 18:43:06,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001025155.1_ASM102515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001025155.1_ASM102515v1_genomic.fna/checkm_input GCF_001025155.1_ASM102515v1_genomic.fna/checkm_result
[2024-01-25 18:43:28,206] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:28,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:28,222] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:28,222] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:28,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001025155.1_ASM102515v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:28,223] [INFO] Task started: Blastn
[2024-01-25 18:43:28,223] [INFO] Running command: blastn -query GCF_001025155.1_ASM102515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8549ff39-4794-4c17-9878-381f51a1986a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001025155.1_ASM102515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:29,284] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:29,286] [INFO] Selected 13 target genomes.
[2024-01-25 18:43:29,286] [INFO] Target genome list was writen to GCF_001025155.1_ASM102515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:29,294] [INFO] Task started: fastANI
[2024-01-25 18:43:29,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg25bfc54e-b747-4cc4-aae4-c3d3583f7b45/GCF_001025155.1_ASM102515v1_genomic.fna.gz --refList GCF_001025155.1_ASM102515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001025155.1_ASM102515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:35,590] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:35,598] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:35,599] [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_001025155.1	s__Bifidobacterium angulatum	100.0	672	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.71	95.22	0.93	0.74	7	conclusive
GCF_900129045.1	s__Bifidobacterium merycicum	88.2774	543	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	-
GCF_012932675.1	s__Bifidobacterium sp012932675	87.7943	562	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	81.0788	329	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.0314	310	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741175.1	s__Bifidobacterium callitrichos	80.9858	333	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_002860365.1	s__Bifidobacterium parmae	80.941	344	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	80.8199	354	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	80.8199	328	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	80.7317	331	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932445.1	s__Bifidobacterium sp012932445	80.7225	251	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932375.1	s__Bifidobacterium sp012932375	80.6018	287	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771405.1	s__Bifidobacterium pullorum	80.4856	282	673	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:35,601] [INFO] GTDB search result was written to GCF_001025155.1_ASM102515v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:35,601] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:35,604] [INFO] DFAST_QC result json was written to GCF_001025155.1_ASM102515v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:35,604] [INFO] DFAST_QC completed!
[2024-01-25 18:43:35,604] [INFO] Total running time: 0h0m45s