[2024-01-24 13:18:33,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,402] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd9077d5-40d2-413c-9d87-56c062919325/dqc_reference
[2024-01-24 13:18:34,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,762] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,762] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e65215d-2d92-40be-97d5-1ba339352474/GCF_013408435.1_ASM1340843v1_genomic.fna.gz | prodigal -d GCF_013408435.1_ASM1340843v1_genomic.fna/cds.fna -a GCF_013408435.1_ASM1340843v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:40,216] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:40,217] [INFO] Task started: HMMsearch
[2024-01-24 13:18:40,217] [INFO] Running command: hmmsearch --tblout GCF_013408435.1_ASM1340843v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd9077d5-40d2-413c-9d87-56c062919325/dqc_reference/reference_markers.hmm GCF_013408435.1_ASM1340843v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:40,439] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:40,441] [INFO] Found 6/6 markers.
[2024-01-24 13:18:40,457] [INFO] Query marker FASTA was written to GCF_013408435.1_ASM1340843v1_genomic.fna/markers.fasta
[2024-01-24 13:18:40,457] [INFO] Task started: Blastn
[2024-01-24 13:18:40,458] [INFO] Running command: blastn -query GCF_013408435.1_ASM1340843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd9077d5-40d2-413c-9d87-56c062919325/dqc_reference/reference_markers.fasta -out GCF_013408435.1_ASM1340843v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:41,183] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:41,186] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:41,186] [INFO] Target genome list was writen to GCF_013408435.1_ASM1340843v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:41,203] [INFO] Task started: fastANI
[2024-01-24 13:18:41,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e65215d-2d92-40be-97d5-1ba339352474/GCF_013408435.1_ASM1340843v1_genomic.fna.gz --refList GCF_013408435.1_ASM1340843v1_genomic.fna/target_genomes.txt --output GCF_013408435.1_ASM1340843v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:51,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:51,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd9077d5-40d2-413c-9d87-56c062919325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:51,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd9077d5-40d2-413c-9d87-56c062919325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:51,068] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:51,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:51,068] [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
Aeriscardovia aeriphila	strain=DSM 22365	GCA_013408435.1	218139	218139	type	True	100.0	543	545	95	conclusive
Aeriscardovia aeriphila	strain=LMG 21773	GCA_002259595.1	218139	218139	type	True	99.9999	536	545	95	conclusive
Bifidobacterium breve	strain=JCM 1192	GCA_001025175.1	1685	1685	type	True	78.4112	53	545	95	below_threshold
Bifidobacterium breve	strain=NCTC11815	GCA_900637145.1	1685	1685	type	True	78.273	53	545	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	78.2366	56	545	95	below_threshold
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	78.1001	53	545	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	78.0968	53	545	95	below_threshold
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000741175.1	762209	762209	type	True	77.4439	50	545	95	below_threshold
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	77.2855	60	545	95	below_threshold
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	77.2332	57	545	95	below_threshold
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	76.9104	52	545	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	76.6279	66	545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:51,070] [INFO] DFAST Taxonomy check result was written to GCF_013408435.1_ASM1340843v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:51,071] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:51,071] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:51,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd9077d5-40d2-413c-9d87-56c062919325/dqc_reference/checkm_data
[2024-01-24 13:18:51,073] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:51,099] [INFO] Task started: CheckM
[2024-01-24 13:18:51,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408435.1_ASM1340843v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408435.1_ASM1340843v1_genomic.fna/checkm_input GCF_013408435.1_ASM1340843v1_genomic.fna/checkm_result
[2024-01-24 13:19:13,730] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:13,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:13,750] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:13,751] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:13,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408435.1_ASM1340843v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:13,752] [INFO] Task started: Blastn
[2024-01-24 13:19:13,752] [INFO] Running command: blastn -query GCF_013408435.1_ASM1340843v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd9077d5-40d2-413c-9d87-56c062919325/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408435.1_ASM1340843v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:14,731] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:14,735] [INFO] Selected 32 target genomes.
[2024-01-24 13:19:14,735] [INFO] Target genome list was writen to GCF_013408435.1_ASM1340843v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:14,772] [INFO] Task started: fastANI
[2024-01-24 13:19:14,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e65215d-2d92-40be-97d5-1ba339352474/GCF_013408435.1_ASM1340843v1_genomic.fna.gz --refList GCF_013408435.1_ASM1340843v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408435.1_ASM1340843v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:28,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:28,834] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:28,834] [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_002259595.1	s__Aeriscardovia aeriphila	99.9999	536	545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Aeriscardovia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001025175.1	s__Bifidobacterium breve	78.4721	54	545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_000269965.1	s__Bifidobacterium infantis	77.99	57	545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_000196555.1	s__Bifidobacterium longum	77.9682	53	545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_002234915.1	s__Galliscardovia vansinderenii	77.1607	60	545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903789535.1	s__Aeriscardovia sp903789535	76.7968	58	545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Aeriscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932675.1	s__Bifidobacterium sp012932675	76.6917	54	545	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	76.4732	64	545	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:28,836] [INFO] GTDB search result was written to GCF_013408435.1_ASM1340843v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:28,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:28,841] [INFO] DFAST_QC result json was written to GCF_013408435.1_ASM1340843v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:28,841] [INFO] DFAST_QC completed!
[2024-01-24 13:19:28,841] [INFO] Total running time: 0h0m55s