[2024-01-24 13:46:25,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg89b7be75-e156-4589-9646-c7509cb9bf6d/dqc_reference
[2024-01-24 13:46:28,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:28,614] [INFO] Task started: Prodigal
[2024-01-24 13:46:28,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg74e07e9b-1555-41dc-b864-377204425613/GCF_022691205.1_ASM2269120v1_genomic.fna.gz | prodigal -d GCF_022691205.1_ASM2269120v1_genomic.fna/cds.fna -a GCF_022691205.1_ASM2269120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:34,914] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:34,915] [INFO] Task started: HMMsearch
[2024-01-24 13:46:34,915] [INFO] Running command: hmmsearch --tblout GCF_022691205.1_ASM2269120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89b7be75-e156-4589-9646-c7509cb9bf6d/dqc_reference/reference_markers.hmm GCF_022691205.1_ASM2269120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:35,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:35,161] [INFO] Found 6/6 markers.
[2024-01-24 13:46:35,180] [INFO] Query marker FASTA was written to GCF_022691205.1_ASM2269120v1_genomic.fna/markers.fasta
[2024-01-24 13:46:35,181] [INFO] Task started: Blastn
[2024-01-24 13:46:35,181] [INFO] Running command: blastn -query GCF_022691205.1_ASM2269120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89b7be75-e156-4589-9646-c7509cb9bf6d/dqc_reference/reference_markers.fasta -out GCF_022691205.1_ASM2269120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:38,926] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:38,929] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:38,929] [INFO] Target genome list was writen to GCF_022691205.1_ASM2269120v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:38,968] [INFO] Task started: fastANI
[2024-01-24 13:46:38,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e07e9b-1555-41dc-b864-377204425613/GCF_022691205.1_ASM2269120v1_genomic.fna.gz --refList GCF_022691205.1_ASM2269120v1_genomic.fna/target_genomes.txt --output GCF_022691205.1_ASM2269120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:43,586] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:43,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89b7be75-e156-4589-9646-c7509cb9bf6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:43,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89b7be75-e156-4589-9646-c7509cb9bf6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:43,594] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:43,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:43,595] [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 pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	99.9889	625	663	95	conclusive
Bifidobacterium pseudolongum subsp. pseudolongum	strain=LMG 11571	GCA_000741325.1	31954	1694	type	True	99.969	619	663	95	conclusive
Bifidobacterium pseudolongum subsp. pseudolongum	strain=DSM 20099	GCA_000771225.1	31954	1694	type	True	99.9491	619	663	95	conclusive
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000771145.1	1690	1694	type	True	94.2357	552	663	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_002706665.1	1690	1694	type	True	94.1744	562	663	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.2608	327	663	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.4591	302	663	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.7197	83	663	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.3945	98	663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:43,596] [INFO] DFAST Taxonomy check result was written to GCF_022691205.1_ASM2269120v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:43,596] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:43,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:43,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89b7be75-e156-4589-9646-c7509cb9bf6d/dqc_reference/checkm_data
[2024-01-24 13:46:43,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:43,625] [INFO] Task started: CheckM
[2024-01-24 13:46:43,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022691205.1_ASM2269120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022691205.1_ASM2269120v1_genomic.fna/checkm_input GCF_022691205.1_ASM2269120v1_genomic.fna/checkm_result
[2024-01-24 13:47:14,645] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:14,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,659] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:14,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:14,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022691205.1_ASM2269120v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:14,660] [INFO] Task started: Blastn
[2024-01-24 13:47:14,660] [INFO] Running command: blastn -query GCF_022691205.1_ASM2269120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89b7be75-e156-4589-9646-c7509cb9bf6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_022691205.1_ASM2269120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:16,067] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:16,070] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:16,070] [INFO] Target genome list was writen to GCF_022691205.1_ASM2269120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:16,089] [INFO] Task started: fastANI
[2024-01-24 13:47:16,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e07e9b-1555-41dc-b864-377204425613/GCF_022691205.1_ASM2269120v1_genomic.fna.gz --refList GCF_022691205.1_ASM2269120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022691205.1_ASM2269120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:20,425] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:20,431] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:20,432] [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_000771225.1	s__Bifidobacterium pseudolongum	99.9491	619	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.10	98.38	0.94	0.92	10	conclusive
GCF_000741295.1	s__Bifidobacterium globosum	94.1989	562	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.22	96.02	0.90	0.78	79	-
GCF_004155535.1	s__Bifidobacterium pseudolongum_C	92.6909	554	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741135.1	s__Bifidobacterium choerinum	82.9816	461	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_003952025.1	s__Bifidobacterium castoris	82.9173	468	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286915.1	s__Bifidobacterium italicum	82.8697	458	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286935.1	s__Bifidobacterium criceti	82.5693	444	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.26	97.26	0.94	0.94	2	-
GCF_000741575.1	s__Bifidobacterium cuniculi	81.0384	383	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003952945.1	s__Bifidobacterium samirii	80.1748	335	663	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:20,433] [INFO] GTDB search result was written to GCF_022691205.1_ASM2269120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:20,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:20,436] [INFO] DFAST_QC result json was written to GCF_022691205.1_ASM2269120v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:20,436] [INFO] DFAST_QC completed!
[2024-01-24 13:47:20,437] [INFO] Total running time: 0h0m55s