[2024-01-25 19:38:35,690] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:35,693] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:35,693] [INFO] DQC Reference Directory: /var/lib/cwl/stgd51ea3c8-fa30-47f3-b430-e279c0d1aa16/dqc_reference
[2024-01-25 19:38:36,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:36,843] [INFO] Task started: Prodigal
[2024-01-25 19:38:36,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg465f99dc-f00a-4e44-a84c-753578f6b8df/GCF_002802915.1_ASM280291v1_genomic.fna.gz | prodigal -d GCF_002802915.1_ASM280291v1_genomic.fna/cds.fna -a GCF_002802915.1_ASM280291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:44,241] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:44,241] [INFO] Task started: HMMsearch
[2024-01-25 19:38:44,241] [INFO] Running command: hmmsearch --tblout GCF_002802915.1_ASM280291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd51ea3c8-fa30-47f3-b430-e279c0d1aa16/dqc_reference/reference_markers.hmm GCF_002802915.1_ASM280291v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:44,441] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:44,442] [INFO] Found 6/6 markers.
[2024-01-25 19:38:44,462] [INFO] Query marker FASTA was written to GCF_002802915.1_ASM280291v1_genomic.fna/markers.fasta
[2024-01-25 19:38:44,462] [INFO] Task started: Blastn
[2024-01-25 19:38:44,462] [INFO] Running command: blastn -query GCF_002802915.1_ASM280291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd51ea3c8-fa30-47f3-b430-e279c0d1aa16/dqc_reference/reference_markers.fasta -out GCF_002802915.1_ASM280291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:45,232] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:45,235] [INFO] Selected 12 target genomes.
[2024-01-25 19:38:45,235] [INFO] Target genome list was writen to GCF_002802915.1_ASM280291v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:45,241] [INFO] Task started: fastANI
[2024-01-25 19:38:45,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg465f99dc-f00a-4e44-a84c-753578f6b8df/GCF_002802915.1_ASM280291v1_genomic.fna.gz --refList GCF_002802915.1_ASM280291v1_genomic.fna/target_genomes.txt --output GCF_002802915.1_ASM280291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:51,809] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:51,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd51ea3c8-fa30-47f3-b430-e279c0d1aa16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:51,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd51ea3c8-fa30-47f3-b430-e279c0d1aa16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:51,817] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:51,817] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:51,817] [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 felsineum	strain=TRE H	GCA_002802915.1	2045440	2045440	type	True	100.0	787	788	95	conclusive
Bifidobacterium cebidarum	strain=LMG 31469	GCA_009193305.1	2650773	2650773	type	True	88.1899	661	788	95	below_threshold
Bifidobacterium saguini	strain=DSM 23967	GCA_000771625.1	762210	762210	type	True	86.8365	606	788	95	below_threshold
Bifidobacterium saguini	strain=DSMZ 23967	GCA_017378515.1	762210	762210	type	True	86.8094	618	788	95	below_threshold
Bifidobacterium saguini	strain=DSM 23967	GCA_000741715.1	762210	762210	type	True	86.7193	603	788	95	below_threshold
Bifidobacterium imperatoris	strain=Tam1G	GCA_002860405.1	2020965	2020965	type	True	86.5151	593	788	95	below_threshold
Bifidobacterium colobi	strain=LC6	GCA_018555455.1	2809026	2809026	type	True	86.0396	606	788	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.6096	533	788	95	below_threshold
Bifidobacterium pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	81.0246	300	788	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.6836	181	788	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:51,818] [INFO] DFAST Taxonomy check result was written to GCF_002802915.1_ASM280291v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:51,819] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:51,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:51,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd51ea3c8-fa30-47f3-b430-e279c0d1aa16/dqc_reference/checkm_data
[2024-01-25 19:38:51,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:51,846] [INFO] Task started: CheckM
[2024-01-25 19:38:51,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002802915.1_ASM280291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002802915.1_ASM280291v1_genomic.fna/checkm_input GCF_002802915.1_ASM280291v1_genomic.fna/checkm_result
[2024-01-25 19:39:17,630] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:17,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:17,647] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:17,647] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:17,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002802915.1_ASM280291v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:17,648] [INFO] Task started: Blastn
[2024-01-25 19:39:17,648] [INFO] Running command: blastn -query GCF_002802915.1_ASM280291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd51ea3c8-fa30-47f3-b430-e279c0d1aa16/dqc_reference/reference_markers_gtdb.fasta -out GCF_002802915.1_ASM280291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:18,774] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:18,777] [INFO] Selected 10 target genomes.
[2024-01-25 19:39:18,777] [INFO] Target genome list was writen to GCF_002802915.1_ASM280291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:18,782] [INFO] Task started: fastANI
[2024-01-25 19:39:18,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg465f99dc-f00a-4e44-a84c-753578f6b8df/GCF_002802915.1_ASM280291v1_genomic.fna.gz --refList GCF_002802915.1_ASM280291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002802915.1_ASM280291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:23,983] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:23,989] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:23,989] [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_002802915.1	s__Bifidobacterium felsineum	100.0	787	788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	conclusive
GCF_009193305.1	s__Bifidobacterium cebidarum	88.2027	660	788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741715.1	s__Bifidobacterium saguini	86.7397	602	788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.97	3	-
GCF_002860405.1	s__Bifidobacterium imperatoris	86.5061	594	788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018555455.1	s__Bifidobacterium sp018555455	86.0396	606	788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802865.1	s__Bifidobacterium scaligerum	83.4087	521	788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741695.1	s__Bifidobacterium reuteri	83.0948	508	788	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:23,990] [INFO] GTDB search result was written to GCF_002802915.1_ASM280291v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:23,991] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:23,993] [INFO] DFAST_QC result json was written to GCF_002802915.1_ASM280291v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:23,993] [INFO] DFAST_QC completed!
[2024-01-25 19:39:23,993] [INFO] Total running time: 0h0m48s