[2024-01-24 13:46:25,562] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf8f2994-5a57-42c8-b7d1-ba43be66c782/dqc_reference
[2024-01-24 13:46:27,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,122] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg76a979ab-13d4-4a14-9fbb-d6f79e42f8b3/GCF_000010425.1_ASM1042v1_genomic.fna.gz | prodigal -d GCF_000010425.1_ASM1042v1_genomic.fna/cds.fna -a GCF_000010425.1_ASM1042v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:34,555] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:34,556] [INFO] Task started: HMMsearch
[2024-01-24 13:46:34,556] [INFO] Running command: hmmsearch --tblout GCF_000010425.1_ASM1042v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf8f2994-5a57-42c8-b7d1-ba43be66c782/dqc_reference/reference_markers.hmm GCF_000010425.1_ASM1042v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:34,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:34,816] [INFO] Found 6/6 markers.
[2024-01-24 13:46:34,837] [INFO] Query marker FASTA was written to GCF_000010425.1_ASM1042v1_genomic.fna/markers.fasta
[2024-01-24 13:46:34,838] [INFO] Task started: Blastn
[2024-01-24 13:46:34,838] [INFO] Running command: blastn -query GCF_000010425.1_ASM1042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf8f2994-5a57-42c8-b7d1-ba43be66c782/dqc_reference/reference_markers.fasta -out GCF_000010425.1_ASM1042v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:35,759] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:35,763] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:35,763] [INFO] Target genome list was writen to GCF_000010425.1_ASM1042v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:35,773] [INFO] Task started: fastANI
[2024-01-24 13:46:35,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg76a979ab-13d4-4a14-9fbb-d6f79e42f8b3/GCF_000010425.1_ASM1042v1_genomic.fna.gz --refList GCF_000010425.1_ASM1042v1_genomic.fna/target_genomes.txt --output GCF_000010425.1_ASM1042v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,454] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf8f2994-5a57-42c8-b7d1-ba43be66c782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf8f2994-5a57-42c8-b7d1-ba43be66c782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:42,465] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:42,465] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:42,466] [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 adolescentis	strain=ATCC 15703	GCA_000010425.1	1680	1680	type	True	100.0	696	696	95	conclusive
Bifidobacterium adolescentis	strain=NCTC11814	GCA_900445615.1	1680	1680	type	True	99.993	685	696	95	conclusive
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000687635.1	78346	78346	type	True	88.6481	512	696	95	below_threshold
Bifidobacterium ruminantium	strain=DSM 6489	GCA_000770925.1	78346	78346	type	True	88.637	526	696	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	84.9186	471	696	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000771025.1	1686	1686	type	True	84.8854	432	696	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	84.8316	495	696	95	below_threshold
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000771545.1	630129	1686	type	True	84.7874	474	696	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	84.7034	492	696	95	below_threshold
Bifidobacterium moukalabense	strain=DSM 27321	GCA_000522505.1	1333651	1333651	type	True	83.6241	474	696	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.4725	373	696	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.6018	252	696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:42,467] [INFO] DFAST Taxonomy check result was written to GCF_000010425.1_ASM1042v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:42,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:42,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:42,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf8f2994-5a57-42c8-b7d1-ba43be66c782/dqc_reference/checkm_data
[2024-01-24 13:46:42,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:42,496] [INFO] Task started: CheckM
[2024-01-24 13:46:42,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000010425.1_ASM1042v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000010425.1_ASM1042v1_genomic.fna/checkm_input GCF_000010425.1_ASM1042v1_genomic.fna/checkm_result
[2024-01-24 13:47:10,795] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:10,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:10,814] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:10,814] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:10,815] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000010425.1_ASM1042v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:10,815] [INFO] Task started: Blastn
[2024-01-24 13:47:10,816] [INFO] Running command: blastn -query GCF_000010425.1_ASM1042v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf8f2994-5a57-42c8-b7d1-ba43be66c782/dqc_reference/reference_markers_gtdb.fasta -out GCF_000010425.1_ASM1042v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:12,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:12,165] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:12,165] [INFO] Target genome list was writen to GCF_000010425.1_ASM1042v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:12,180] [INFO] Task started: fastANI
[2024-01-24 13:47:12,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg76a979ab-13d4-4a14-9fbb-d6f79e42f8b3/GCF_000010425.1_ASM1042v1_genomic.fna.gz --refList GCF_000010425.1_ASM1042v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000010425.1_ASM1042v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:17,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:17,675] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:17,675] [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_000010425.1	s__Bifidobacterium adolescentis	100.0	696	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	conclusive
GCF_000770925.1	s__Bifidobacterium ruminantium	88.637	526	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_001025195.1	s__Bifidobacterium catenulatum	85.0644	466	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	84.8564	495	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
GCF_001042615.1	s__Bifidobacterium kashiwanohense	84.8172	496	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_000800455.1	s__Bifidobacterium kashiwanohense_A	84.3678	471	696	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	84.3136	469	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCA_002451435.1	s__Bifidobacterium sp002451435	84.0888	416	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000522505.1	s__Bifidobacterium moukalabense	83.6642	476	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_001042595.1	s__Bifidobacterium dentium	83.3593	474	696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:17,679] [INFO] GTDB search result was written to GCF_000010425.1_ASM1042v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:17,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:17,683] [INFO] DFAST_QC result json was written to GCF_000010425.1_ASM1042v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:17,684] [INFO] DFAST_QC completed!
[2024-01-24 13:47:17,684] [INFO] Total running time: 0h0m52s