[2024-01-25 18:41:20,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:20,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:20,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d6f2b10-8e56-4b8a-b0c0-325b4e013f3a/dqc_reference
[2024-01-25 18:41:21,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:21,826] [INFO] Task started: Prodigal
[2024-01-25 18:41:21,826] [INFO] Running command: gunzip -c /var/lib/cwl/stge19c24c2-916b-4de4-b688-faa105507c6a/GCF_002802865.1_ASM280286v1_genomic.fna.gz | prodigal -d GCF_002802865.1_ASM280286v1_genomic.fna/cds.fna -a GCF_002802865.1_ASM280286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:29,634] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:29,635] [INFO] Task started: HMMsearch
[2024-01-25 18:41:29,635] [INFO] Running command: hmmsearch --tblout GCF_002802865.1_ASM280286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d6f2b10-8e56-4b8a-b0c0-325b4e013f3a/dqc_reference/reference_markers.hmm GCF_002802865.1_ASM280286v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:29,825] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:29,826] [INFO] Found 6/6 markers.
[2024-01-25 18:41:29,862] [INFO] Query marker FASTA was written to GCF_002802865.1_ASM280286v1_genomic.fna/markers.fasta
[2024-01-25 18:41:29,863] [INFO] Task started: Blastn
[2024-01-25 18:41:29,863] [INFO] Running command: blastn -query GCF_002802865.1_ASM280286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6f2b10-8e56-4b8a-b0c0-325b4e013f3a/dqc_reference/reference_markers.fasta -out GCF_002802865.1_ASM280286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:30,642] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:30,645] [INFO] Selected 24 target genomes.
[2024-01-25 18:41:30,645] [INFO] Target genome list was writen to GCF_002802865.1_ASM280286v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:30,652] [INFO] Task started: fastANI
[2024-01-25 18:41:30,652] [INFO] Running command: fastANI --query /var/lib/cwl/stge19c24c2-916b-4de4-b688-faa105507c6a/GCF_002802865.1_ASM280286v1_genomic.fna.gz --refList GCF_002802865.1_ASM280286v1_genomic.fna/target_genomes.txt --output GCF_002802865.1_ASM280286v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:42,797] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:42,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d6f2b10-8e56-4b8a-b0c0-325b4e013f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:42,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d6f2b10-8e56-4b8a-b0c0-325b4e013f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:42,811] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:41:42,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:42,811] [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 scaligerum	strain=TRE D	GCA_002802865.1	2052656	2052656	type	True	100.0	875	875	95	conclusive
Bifidobacterium colobi	strain=LC6	GCA_018555455.1	2809026	2809026	type	True	84.6099	550	875	95	below_threshold
Bifidobacterium callitrichidarum	strain=TRI 5	GCA_003129905.1	2052941	2052941	type	True	84.327	577	875	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	84.225	556	875	95	below_threshold
Bifidobacterium myosotis	strain=DSM 100196	GCA_002259745.1	1630166	1630166	type	True	82.8996	521	875	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	82.5121	390	875	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	82.3867	439	875	95	below_threshold
Bifidobacterium longum subsp. longum	strain=KCTC 3128	GCA_017132775.1	1679	216816	type	True	82.3848	431	875	95	below_threshold
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	82.3592	440	875	95	below_threshold
Bifidobacterium longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	82.3405	441	875	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=ATCC 15697	GCA_000020425.1	1682	216816	type	True	82.3249	423	875	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	82.3017	423	875	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=JCM 1222	GCA_000269965.1	1682	216816	type	True	82.2871	424	875	95	below_threshold
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	82.2324	407	875	95	below_threshold
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	81.7436	377	875	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	81.5313	389	875	95	below_threshold
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000741175.1	762209	762209	type	True	81.48	390	875	95	below_threshold
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000771665.1	762209	762209	type	True	81.4152	387	875	95	below_threshold
Bifidobacterium adolescentis	strain=NCTC11814	GCA_900445615.1	1680	1680	type	True	80.3844	297	875	95	below_threshold
Bifidobacterium adolescentis	strain=ATCC 15703	GCA_000010425.1	1680	1680	type	True	80.3134	291	875	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=LMG 11569	GCA_000741295.1	1690	1694	type	True	78.8944	180	875	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_002706665.1	1690	1694	type	True	78.8766	189	875	95	below_threshold
Bifidobacterium pseudolongum subsp. globosum	strain=DSM 20092	GCA_000771145.1	1690	1694	type	True	78.7104	185	875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:42,813] [INFO] DFAST Taxonomy check result was written to GCF_002802865.1_ASM280286v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:42,813] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:42,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:42,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d6f2b10-8e56-4b8a-b0c0-325b4e013f3a/dqc_reference/checkm_data
[2024-01-25 18:41:42,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:42,841] [INFO] Task started: CheckM
[2024-01-25 18:41:42,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002802865.1_ASM280286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002802865.1_ASM280286v1_genomic.fna/checkm_input GCF_002802865.1_ASM280286v1_genomic.fna/checkm_result
[2024-01-25 18:42:09,593] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:09,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:09,612] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:09,613] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:09,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002802865.1_ASM280286v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:09,613] [INFO] Task started: Blastn
[2024-01-25 18:42:09,613] [INFO] Running command: blastn -query GCF_002802865.1_ASM280286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d6f2b10-8e56-4b8a-b0c0-325b4e013f3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002802865.1_ASM280286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:10,717] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:10,720] [INFO] Selected 13 target genomes.
[2024-01-25 18:42:10,720] [INFO] Target genome list was writen to GCF_002802865.1_ASM280286v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:10,728] [INFO] Task started: fastANI
[2024-01-25 18:42:10,729] [INFO] Running command: fastANI --query /var/lib/cwl/stge19c24c2-916b-4de4-b688-faa105507c6a/GCF_002802865.1_ASM280286v1_genomic.fna.gz --refList GCF_002802865.1_ASM280286v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002802865.1_ASM280286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:18,242] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:18,250] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:18,251] [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_002802865.1	s__Bifidobacterium scaligerum	100.0	875	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012932375.1	s__Bifidobacterium sp012932375	94.4568	781	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555455.1	s__Bifidobacterium sp018555455	84.6414	548	875	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	84.3299	576	875	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	83.9472	565	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_002802915.1	s__Bifidobacterium felsineum	83.554	507	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.66	98.66	0.97	0.97	2	-
GCF_002860405.1	s__Bifidobacterium imperatoris	83.5365	496	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000196555.1	s__Bifidobacterium longum	82.4079	439	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_000269965.1	s__Bifidobacterium infantis	82.2809	424	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	-
GCF_008698235.1	s__Bifidobacterium rousetti	81.7207	377	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_000741175.1	s__Bifidobacterium callitrichos	81.4626	391	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_012932425.1	s__Bifidobacterium sp012932425	81.0117	381	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:18,252] [INFO] GTDB search result was written to GCF_002802865.1_ASM280286v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:18,253] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:18,256] [INFO] DFAST_QC result json was written to GCF_002802865.1_ASM280286v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:18,256] [INFO] DFAST_QC completed!
[2024-01-25 18:42:18,256] [INFO] Total running time: 0h0m58s