[2024-01-25 20:11:50,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:50,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:50,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg13f01bcc-64e5-486f-91d5-c245364d032c/dqc_reference
[2024-01-25 20:11:51,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:51,820] [INFO] Task started: Prodigal
[2024-01-25 20:11:51,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg15ea54df-2bed-4ff4-abd9-9616773bb57c/GCF_001042595.1_ASM104259v1_genomic.fna.gz | prodigal -d GCF_001042595.1_ASM104259v1_genomic.fna/cds.fna -a GCF_001042595.1_ASM104259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:59,765] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:59,765] [INFO] Task started: HMMsearch
[2024-01-25 20:11:59,765] [INFO] Running command: hmmsearch --tblout GCF_001042595.1_ASM104259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13f01bcc-64e5-486f-91d5-c245364d032c/dqc_reference/reference_markers.hmm GCF_001042595.1_ASM104259v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:59,953] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:59,954] [INFO] Found 6/6 markers.
[2024-01-25 20:11:59,976] [INFO] Query marker FASTA was written to GCF_001042595.1_ASM104259v1_genomic.fna/markers.fasta
[2024-01-25 20:11:59,977] [INFO] Task started: Blastn
[2024-01-25 20:11:59,977] [INFO] Running command: blastn -query GCF_001042595.1_ASM104259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f01bcc-64e5-486f-91d5-c245364d032c/dqc_reference/reference_markers.fasta -out GCF_001042595.1_ASM104259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:00,817] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:00,820] [INFO] Selected 10 target genomes.
[2024-01-25 20:12:00,820] [INFO] Target genome list was writen to GCF_001042595.1_ASM104259v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:00,828] [INFO] Task started: fastANI
[2024-01-25 20:12:00,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ea54df-2bed-4ff4-abd9-9616773bb57c/GCF_001042595.1_ASM104259v1_genomic.fna.gz --refList GCF_001042595.1_ASM104259v1_genomic.fna/target_genomes.txt --output GCF_001042595.1_ASM104259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:07,647] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:07,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13f01bcc-64e5-486f-91d5-c245364d032c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:07,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13f01bcc-64e5-486f-91d5-c245364d032c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:07,655] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 20:12:07,655] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:07,655] [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 dentium	strain=JCM 1195	GCA_001042595.1	1689	1689	type	True	100.0	877	878	95	conclusive
Bifidobacterium dentium	strain=NCTC11816	GCA_900637175.1	1689	1689	type	True	99.9993	877	878	95	conclusive
Bifidobacterium dentium	strain=DSM 20436	GCA_900105745.1	1689	1689	type	True	99.999	877	878	95	conclusive
Bifidobacterium dentium	strain=DSM 20436	GCA_000771725.1	1689	1689	type	True	99.9802	856	878	95	conclusive
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	89.477	694	878	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.46	365	878	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.0444	355	878	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.401	236	878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:07,656] [INFO] DFAST Taxonomy check result was written to GCF_001042595.1_ASM104259v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:07,657] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:07,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:07,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13f01bcc-64e5-486f-91d5-c245364d032c/dqc_reference/checkm_data
[2024-01-25 20:12:07,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:07,686] [INFO] Task started: CheckM
[2024-01-25 20:12:07,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001042595.1_ASM104259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001042595.1_ASM104259v1_genomic.fna/checkm_input GCF_001042595.1_ASM104259v1_genomic.fna/checkm_result
[2024-01-25 20:12:35,529] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:35,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:35,560] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:35,560] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:35,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001042595.1_ASM104259v1_genomic.fna/markers.fasta)
[2024-01-25 20:12:35,561] [INFO] Task started: Blastn
[2024-01-25 20:12:35,561] [INFO] Running command: blastn -query GCF_001042595.1_ASM104259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13f01bcc-64e5-486f-91d5-c245364d032c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001042595.1_ASM104259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:36,752] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:36,754] [INFO] Selected 10 target genomes.
[2024-01-25 20:12:36,755] [INFO] Target genome list was writen to GCF_001042595.1_ASM104259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:36,768] [INFO] Task started: fastANI
[2024-01-25 20:12:36,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ea54df-2bed-4ff4-abd9-9616773bb57c/GCF_001042595.1_ASM104259v1_genomic.fna.gz --refList GCF_001042595.1_ASM104259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001042595.1_ASM104259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:41,958] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:41,965] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:41,965] [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_001042595.1	s__Bifidobacterium dentium	100.0	876	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	conclusive
GCF_000522505.1	s__Bifidobacterium moukalabense	89.4801	694	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_000010425.1	s__Bifidobacterium adolescentis	83.4568	455	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	82.6746	443	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCA_002451435.1	s__Bifidobacterium sp002451435	82.507	387	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	82.5046	454	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_000770925.1	s__Bifidobacterium ruminantium	82.5019	447	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	82.2763	437	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	-
GCF_002742445.1	s__Bifidobacterium sp002742445	82.1611	440	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_012932425.1	s__Bifidobacterium sp012932425	79.8271	319	878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:41,968] [INFO] GTDB search result was written to GCF_001042595.1_ASM104259v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:41,968] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:41,971] [INFO] DFAST_QC result json was written to GCF_001042595.1_ASM104259v1_genomic.fna/dqc_result.json
[2024-01-25 20:12:41,971] [INFO] DFAST_QC completed!
[2024-01-25 20:12:41,971] [INFO] Total running time: 0h0m51s