[2024-01-24 14:12:47,334] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f5d3a49-6e8a-4767-8dd1-2e8b3b4a76c5/dqc_reference
[2024-01-24 14:12:48,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,576] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg8662cce3-c88a-441a-81fd-7239eccb7691/GCF_019331805.1_ASM1933180v1_genomic.fna.gz | prodigal -d GCF_019331805.1_ASM1933180v1_genomic.fna/cds.fna -a GCF_019331805.1_ASM1933180v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:56,357] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:56,358] [INFO] Task started: HMMsearch
[2024-01-24 14:12:56,358] [INFO] Running command: hmmsearch --tblout GCF_019331805.1_ASM1933180v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f5d3a49-6e8a-4767-8dd1-2e8b3b4a76c5/dqc_reference/reference_markers.hmm GCF_019331805.1_ASM1933180v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:56,587] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:56,589] [INFO] Found 6/6 markers.
[2024-01-24 14:12:56,611] [INFO] Query marker FASTA was written to GCF_019331805.1_ASM1933180v1_genomic.fna/markers.fasta
[2024-01-24 14:12:56,611] [INFO] Task started: Blastn
[2024-01-24 14:12:56,612] [INFO] Running command: blastn -query GCF_019331805.1_ASM1933180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f5d3a49-6e8a-4767-8dd1-2e8b3b4a76c5/dqc_reference/reference_markers.fasta -out GCF_019331805.1_ASM1933180v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:57,627] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:57,631] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:57,631] [INFO] Target genome list was writen to GCF_019331805.1_ASM1933180v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:57,649] [INFO] Task started: fastANI
[2024-01-24 14:12:57,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg8662cce3-c88a-441a-81fd-7239eccb7691/GCF_019331805.1_ASM1933180v1_genomic.fna.gz --refList GCF_019331805.1_ASM1933180v1_genomic.fna/target_genomes.txt --output GCF_019331805.1_ASM1933180v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:03,121] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:03,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f5d3a49-6e8a-4767-8dd1-2e8b3b4a76c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:03,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f5d3a49-6e8a-4767-8dd1-2e8b3b4a76c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:03,135] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:03,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:03,135] [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 pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	100.0	760	783	95	conclusive
Bifidobacterium merycicum	strain=DSM 6492	GCA_000770945.1	78345	78345	type	True	90.7383	578	783	95	below_threshold
Bifidobacterium merycicum	strain=LMG 11341	GCA_000741615.1	78345	78345	type	True	90.6862	593	783	95	below_threshold
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	90.6658	586	783	95	below_threshold
Bifidobacterium angulatum	strain=LMG 11039	GCA_000741065.1	1683	1683	type	True	86.0617	513	783	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.8305	400	783	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.4554	367	783	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.1057	280	783	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.1231	65	783	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.0559	63	783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:03,137] [INFO] DFAST Taxonomy check result was written to GCF_019331805.1_ASM1933180v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:03,138] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:03,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:03,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f5d3a49-6e8a-4767-8dd1-2e8b3b4a76c5/dqc_reference/checkm_data
[2024-01-24 14:13:03,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:03,167] [INFO] Task started: CheckM
[2024-01-24 14:13:03,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019331805.1_ASM1933180v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019331805.1_ASM1933180v1_genomic.fna/checkm_input GCF_019331805.1_ASM1933180v1_genomic.fna/checkm_result
[2024-01-24 14:13:32,344] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:32,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 25.00%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:32,375] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:32,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:32,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019331805.1_ASM1933180v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:32,376] [INFO] Task started: Blastn
[2024-01-24 14:13:32,376] [INFO] Running command: blastn -query GCF_019331805.1_ASM1933180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f5d3a49-6e8a-4767-8dd1-2e8b3b4a76c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019331805.1_ASM1933180v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:33,830] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:33,835] [INFO] Selected 13 target genomes.
[2024-01-24 14:13:33,835] [INFO] Target genome list was writen to GCF_019331805.1_ASM1933180v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:33,846] [INFO] Task started: fastANI
[2024-01-24 14:13:33,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg8662cce3-c88a-441a-81fd-7239eccb7691/GCF_019331805.1_ASM1933180v1_genomic.fna.gz --refList GCF_019331805.1_ASM1933180v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019331805.1_ASM1933180v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:40,798] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:40,814] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:13:40,815] [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_900129045.1	s__Bifidobacterium merycicum	90.6894	585	783	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	86.993	576	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001025155.1	s__Bifidobacterium angulatum	85.9066	518	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.71	95.22	0.93	0.74	7	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	82.1677	399	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555355.1	s__Bifidobacterium sp018555355	82.0878	390	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.029	412	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	82.0208	393	783	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	81.9336	370	783	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	81.8588	382	783	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	81.7162	383	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_001417815.1	s__Bifidobacterium aesculapii	81.6642	386	783	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	81.5249	405	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	80.7929	324	783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:40,816] [INFO] GTDB search result was written to GCF_019331805.1_ASM1933180v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:40,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:40,820] [INFO] DFAST_QC result json was written to GCF_019331805.1_ASM1933180v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:40,820] [INFO] DFAST_QC completed!
[2024-01-24 14:13:40,820] [INFO] Total running time: 0h0m53s