[2024-01-24 13:18:33,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg3534ae28-15ae-46c8-9b3a-e62a463afab0/dqc_reference
[2024-01-24 13:18:34,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,864] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,864] [INFO] Running command: gunzip -c /var/lib/cwl/stge78c6558-1ce1-44e6-bafc-ff41ea92b0f0/GCF_008698145.1_ASM869814v1_genomic.fna.gz | prodigal -d GCF_008698145.1_ASM869814v1_genomic.fna/cds.fna -a GCF_008698145.1_ASM869814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:44,972] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:44,973] [INFO] Task started: HMMsearch
[2024-01-24 13:18:44,973] [INFO] Running command: hmmsearch --tblout GCF_008698145.1_ASM869814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3534ae28-15ae-46c8-9b3a-e62a463afab0/dqc_reference/reference_markers.hmm GCF_008698145.1_ASM869814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:45,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:45,255] [INFO] Found 6/6 markers.
[2024-01-24 13:18:45,280] [INFO] Query marker FASTA was written to GCF_008698145.1_ASM869814v1_genomic.fna/markers.fasta
[2024-01-24 13:18:45,281] [INFO] Task started: Blastn
[2024-01-24 13:18:45,281] [INFO] Running command: blastn -query GCF_008698145.1_ASM869814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3534ae28-15ae-46c8-9b3a-e62a463afab0/dqc_reference/reference_markers.fasta -out GCF_008698145.1_ASM869814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:46,414] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:46,417] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:46,418] [INFO] Target genome list was writen to GCF_008698145.1_ASM869814v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:46,427] [INFO] Task started: fastANI
[2024-01-24 13:18:46,427] [INFO] Running command: fastANI --query /var/lib/cwl/stge78c6558-1ce1-44e6-bafc-ff41ea92b0f0/GCF_008698145.1_ASM869814v1_genomic.fna.gz --refList GCF_008698145.1_ASM869814v1_genomic.fna/target_genomes.txt --output GCF_008698145.1_ASM869814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:58,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:58,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3534ae28-15ae-46c8-9b3a-e62a463afab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:58,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3534ae28-15ae-46c8-9b3a-e62a463afab0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:58,379] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:58,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:58,379] [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 vespertilionis	strain=RST16	GCA_008698145.1	2562524	2562524	type	True	100.0	1007	1008	95	conclusive
Bifidobacterium avesanii	strain=TREC	GCA_010667745.1	1798157	1798157	type	True	86.8564	625	1008	95	below_threshold
Bifidobacterium avesanii	strain=DSM 100685	GCA_009299475.1	1798157	1798157	type	True	86.8292	624	1008	95	below_threshold
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000741175.1	762209	762209	type	True	83.8335	505	1008	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	83.3024	464	1008	95	below_threshold
Bifidobacterium callitrichidarum	strain=TRI 5	GCA_003129905.1	2052941	2052941	type	True	83.0823	446	1008	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	82.7318	459	1008	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	82.5238	453	1008	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.3564	494	1008	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	82.2945	438	1008	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	82.2659	448	1008	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	82.1705	460	1008	95	below_threshold
Bifidobacterium catulorum	strain=MRM 8.19	GCA_003129925.1	1630173	1630173	type	True	81.3109	355	1008	95	below_threshold
Bifidobacterium pluvialisilvae	strain=82T24	GCA_019331695.1	2834436	2834436	type	True	80.9844	402	1008	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.2418	280	1008	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.4947	114	1008	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.1062	122	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:58,381] [INFO] DFAST Taxonomy check result was written to GCF_008698145.1_ASM869814v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:58,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:58,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:58,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3534ae28-15ae-46c8-9b3a-e62a463afab0/dqc_reference/checkm_data
[2024-01-24 13:18:58,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:58,416] [INFO] Task started: CheckM
[2024-01-24 13:18:58,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008698145.1_ASM869814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008698145.1_ASM869814v1_genomic.fna/checkm_input GCF_008698145.1_ASM869814v1_genomic.fna/checkm_result
[2024-01-24 13:19:33,837] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:33,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,855] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:33,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:33,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008698145.1_ASM869814v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:33,856] [INFO] Task started: Blastn
[2024-01-24 13:19:33,857] [INFO] Running command: blastn -query GCF_008698145.1_ASM869814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3534ae28-15ae-46c8-9b3a-e62a463afab0/dqc_reference/reference_markers_gtdb.fasta -out GCF_008698145.1_ASM869814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:35,590] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:35,594] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:35,595] [INFO] Target genome list was writen to GCF_008698145.1_ASM869814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:35,642] [INFO] Task started: fastANI
[2024-01-24 13:19:35,643] [INFO] Running command: fastANI --query /var/lib/cwl/stge78c6558-1ce1-44e6-bafc-ff41ea92b0f0/GCF_008698145.1_ASM869814v1_genomic.fna.gz --refList GCF_008698145.1_ASM869814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008698145.1_ASM869814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:45,218] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:45,236] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:45,236] [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_008698145.1	s__Bifidobacterium vespertilionis	100.0	1007	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.94	97.88	0.96	0.92	3	conclusive
GCF_009299475.1	s__Bifidobacterium avesanii	86.824	624	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012932365.1	s__Bifidobacterium sp012932365	85.7024	615	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741175.1	s__Bifidobacterium callitrichos	83.8278	505	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_002860365.1	s__Bifidobacterium parmae	83.2948	465	1008	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	83.1408	443	1008	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	83.1163	492	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.5589	451	1008	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	82.5353	462	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	82.3306	436	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	82.074	466	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_003129925.1	s__Galliscardovia catulorum	81.3111	355	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298605.1	s__Bifidobacterium sp002298605	81.0939	360	1008	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.49	99.49	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:45,238] [INFO] GTDB search result was written to GCF_008698145.1_ASM869814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:45,238] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:45,244] [INFO] DFAST_QC result json was written to GCF_008698145.1_ASM869814v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:45,245] [INFO] DFAST_QC completed!
[2024-01-24 13:19:45,245] [INFO] Total running time: 0h1m12s