[2024-01-24 15:18:18,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,614] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9da405d-5207-4c4e-b491-0f6108946c00/dqc_reference
[2024-01-24 15:18:19,869] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:19,870] [INFO] Task started: Prodigal
[2024-01-24 15:18:19,870] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1a2b625-eb3e-42e5-a7ef-a545b30c6304/GCF_001025195.1_ASM102519v1_genomic.fna.gz | prodigal -d GCF_001025195.1_ASM102519v1_genomic.fna/cds.fna -a GCF_001025195.1_ASM102519v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:27,092] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:27,093] [INFO] Task started: HMMsearch
[2024-01-24 15:18:27,093] [INFO] Running command: hmmsearch --tblout GCF_001025195.1_ASM102519v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9da405d-5207-4c4e-b491-0f6108946c00/dqc_reference/reference_markers.hmm GCF_001025195.1_ASM102519v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:27,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:27,311] [INFO] Found 6/6 markers.
[2024-01-24 15:18:27,343] [INFO] Query marker FASTA was written to GCF_001025195.1_ASM102519v1_genomic.fna/markers.fasta
[2024-01-24 15:18:27,343] [INFO] Task started: Blastn
[2024-01-24 15:18:27,343] [INFO] Running command: blastn -query GCF_001025195.1_ASM102519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9da405d-5207-4c4e-b491-0f6108946c00/dqc_reference/reference_markers.fasta -out GCF_001025195.1_ASM102519v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:28,114] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:28,118] [INFO] Selected 12 target genomes.
[2024-01-24 15:18:28,118] [INFO] Target genome list was writen to GCF_001025195.1_ASM102519v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:28,133] [INFO] Task started: fastANI
[2024-01-24 15:18:28,135] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1a2b625-eb3e-42e5-a7ef-a545b30c6304/GCF_001025195.1_ASM102519v1_genomic.fna.gz --refList GCF_001025195.1_ASM102519v1_genomic.fna/target_genomes.txt --output GCF_001025195.1_ASM102519v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:34,336] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:34,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9da405d-5207-4c4e-b491-0f6108946c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:34,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9da405d-5207-4c4e-b491-0f6108946c00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:34,351] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 15:18:34,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:34,351] [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 catenulatum	strain=JCM 1194	GCA_001025195.1	1686	1686	type	True	100.0	690	693	95	conclusive
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000173455.1	1686	1686	type	True	99.975	668	693	95	conclusive
Bifidobacterium catenulatum	strain=LMG 11043	GCA_000741565.1	1686	1686	type	True	99.9474	681	693	95	conclusive
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000771025.1	1686	1686	type	True	99.8811	636	693	95	conclusive
Bifidobacterium catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	96.3599	582	693	95	conclusive
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	96.2931	575	693	95	conclusive
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	92.5467	578	693	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.0233	279	693	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.9269	274	693	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	79.8472	285	693	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.7747	88	693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:34,352] [INFO] DFAST Taxonomy check result was written to GCF_001025195.1_ASM102519v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:34,354] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:34,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:34,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9da405d-5207-4c4e-b491-0f6108946c00/dqc_reference/checkm_data
[2024-01-24 15:18:34,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:34,386] [INFO] Task started: CheckM
[2024-01-24 15:18:34,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001025195.1_ASM102519v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001025195.1_ASM102519v1_genomic.fna/checkm_input GCF_001025195.1_ASM102519v1_genomic.fna/checkm_result
[2024-01-24 15:19:02,432] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:02,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:02,461] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:02,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:02,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001025195.1_ASM102519v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:02,463] [INFO] Task started: Blastn
[2024-01-24 15:19:02,463] [INFO] Running command: blastn -query GCF_001025195.1_ASM102519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9da405d-5207-4c4e-b491-0f6108946c00/dqc_reference/reference_markers_gtdb.fasta -out GCF_001025195.1_ASM102519v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:03,569] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:03,574] [INFO] Selected 5 target genomes.
[2024-01-24 15:19:03,574] [INFO] Target genome list was writen to GCF_001025195.1_ASM102519v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:03,579] [INFO] Task started: fastANI
[2024-01-24 15:19:03,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1a2b625-eb3e-42e5-a7ef-a545b30c6304/GCF_001025195.1_ASM102519v1_genomic.fna.gz --refList GCF_001025195.1_ASM102519v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001025195.1_ASM102519v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:06,344] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:06,352] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:06,353] [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_001025195.1	s__Bifidobacterium catenulatum	100.0	691	693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	conclusive
GCF_001042615.1	s__Bifidobacterium kashiwanohense	96.3606	582	693	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	94.7653	558	693	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	94.018	555	693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	92.5682	584	693	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:06,354] [INFO] GTDB search result was written to GCF_001025195.1_ASM102519v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:06,355] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:06,357] [INFO] DFAST_QC result json was written to GCF_001025195.1_ASM102519v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:06,358] [INFO] DFAST_QC completed!
[2024-01-24 15:19:06,358] [INFO] Total running time: 0h0m48s