[2024-01-24 13:25:58,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,113] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,114] [INFO] DQC Reference Directory: /var/lib/cwl/stgf21e40fc-d8fc-4310-b0ca-6a6dd4cc98c1/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,377] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa279f25-6c52-43c4-b3d6-8bd0f6f4a668/GCF_000770945.1_DSM-6492_genomic.fna.gz | prodigal -d GCF_000770945.1_DSM-6492_genomic.fna/cds.fna -a GCF_000770945.1_DSM-6492_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:07,929] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:07,929] [INFO] Task started: HMMsearch
[2024-01-24 13:26:07,929] [INFO] Running command: hmmsearch --tblout GCF_000770945.1_DSM-6492_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf21e40fc-d8fc-4310-b0ca-6a6dd4cc98c1/dqc_reference/reference_markers.hmm GCF_000770945.1_DSM-6492_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:08,215] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:08,216] [INFO] Found 6/6 markers.
[2024-01-24 13:26:08,242] [INFO] Query marker FASTA was written to GCF_000770945.1_DSM-6492_genomic.fna/markers.fasta
[2024-01-24 13:26:08,242] [INFO] Task started: Blastn
[2024-01-24 13:26:08,242] [INFO] Running command: blastn -query GCF_000770945.1_DSM-6492_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21e40fc-d8fc-4310-b0ca-6a6dd4cc98c1/dqc_reference/reference_markers.fasta -out GCF_000770945.1_DSM-6492_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:09,150] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:09,160] [INFO] Selected 10 target genomes.
[2024-01-24 13:26:09,161] [INFO] Target genome list was writen to GCF_000770945.1_DSM-6492_genomic.fna/target_genomes.txt
[2024-01-24 13:26:09,170] [INFO] Task started: fastANI
[2024-01-24 13:26:09,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa279f25-6c52-43c4-b3d6-8bd0f6f4a668/GCF_000770945.1_DSM-6492_genomic.fna.gz --refList GCF_000770945.1_DSM-6492_genomic.fna/target_genomes.txt --output GCF_000770945.1_DSM-6492_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:15,259] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:15,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf21e40fc-d8fc-4310-b0ca-6a6dd4cc98c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:15,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf21e40fc-d8fc-4310-b0ca-6a6dd4cc98c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:15,271] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:26:15,271] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:15,272] [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 merycicum	strain=DSM 6492	GCA_000770945.1	78345	78345	type	True	100.0	736	739	95	conclusive
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	99.9908	737	739	95	conclusive
Bifidobacterium merycicum	strain=LMG 11341	GCA_000741615.1	78345	78345	type	True	99.9733	733	739	95	conclusive
Bifidobacterium pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	90.7386	572	739	95	below_threshold
Bifidobacterium angulatum	strain=LMG 11039	GCA_000741065.1	1683	1683	type	True	88.2751	529	739	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.8831	363	739	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.4054	58	739	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.0174	53	739	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	75.6995	68	739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:15,274] [INFO] DFAST Taxonomy check result was written to GCF_000770945.1_DSM-6492_genomic.fna/tc_result.tsv
[2024-01-24 13:26:15,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:15,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:15,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf21e40fc-d8fc-4310-b0ca-6a6dd4cc98c1/dqc_reference/checkm_data
[2024-01-24 13:26:15,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:15,303] [INFO] Task started: CheckM
[2024-01-24 13:26:15,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000770945.1_DSM-6492_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000770945.1_DSM-6492_genomic.fna/checkm_input GCF_000770945.1_DSM-6492_genomic.fna/checkm_result
[2024-01-24 13:26:43,392] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:43,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:43,415] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:43,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:43,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000770945.1_DSM-6492_genomic.fna/markers.fasta)
[2024-01-24 13:26:43,417] [INFO] Task started: Blastn
[2024-01-24 13:26:43,417] [INFO] Running command: blastn -query GCF_000770945.1_DSM-6492_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21e40fc-d8fc-4310-b0ca-6a6dd4cc98c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000770945.1_DSM-6492_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:44,680] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:44,685] [INFO] Selected 12 target genomes.
[2024-01-24 13:26:44,685] [INFO] Target genome list was writen to GCF_000770945.1_DSM-6492_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:44,711] [INFO] Task started: fastANI
[2024-01-24 13:26:44,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa279f25-6c52-43c4-b3d6-8bd0f6f4a668/GCF_000770945.1_DSM-6492_genomic.fna.gz --refList GCF_000770945.1_DSM-6492_genomic.fna/target_genomes_gtdb.txt --output GCF_000770945.1_DSM-6492_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:51,082] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:51,096] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:51,096] [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	99.9908	737	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	conclusive
GCF_001025155.1	s__Bifidobacterium angulatum	88.1708	544	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.71	95.22	0.93	0.74	7	-
GCF_012932675.1	s__Bifidobacterium sp012932675	86.869	561	739	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	81.8093	397	739	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	81.7454	360	739	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	81.697	337	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	81.5885	393	739	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	81.5813	374	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	81.3318	388	739	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	80.6521	307	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_012932445.1	s__Bifidobacterium sp012932445	80.6469	250	739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932425.1	s__Bifidobacterium sp012932425	80.4802	326	739	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 13:26:51,098] [INFO] GTDB search result was written to GCF_000770945.1_DSM-6492_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:51,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:51,102] [INFO] DFAST_QC result json was written to GCF_000770945.1_DSM-6492_genomic.fna/dqc_result.json
[2024-01-24 13:26:51,103] [INFO] DFAST_QC completed!
[2024-01-24 13:26:51,103] [INFO] Total running time: 0h0m53s