[2024-01-24 10:47:24,122] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg84b85520-0029-414e-89bb-658d04c34d9e/dqc_reference
[2024-01-24 10:47:26,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,250] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg235631db-2023-45d1-a437-7dfc9d181936/GCF_016882605.1_ASM1688260v1_genomic.fna.gz | prodigal -d GCF_016882605.1_ASM1688260v1_genomic.fna/cds.fna -a GCF_016882605.1_ASM1688260v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:33,794] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:33,795] [INFO] Task started: HMMsearch
[2024-01-24 10:47:33,795] [INFO] Running command: hmmsearch --tblout GCF_016882605.1_ASM1688260v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84b85520-0029-414e-89bb-658d04c34d9e/dqc_reference/reference_markers.hmm GCF_016882605.1_ASM1688260v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:34,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:34,035] [INFO] Found 6/6 markers.
[2024-01-24 10:47:34,060] [INFO] Query marker FASTA was written to GCF_016882605.1_ASM1688260v1_genomic.fna/markers.fasta
[2024-01-24 10:47:34,060] [INFO] Task started: Blastn
[2024-01-24 10:47:34,061] [INFO] Running command: blastn -query GCF_016882605.1_ASM1688260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84b85520-0029-414e-89bb-658d04c34d9e/dqc_reference/reference_markers.fasta -out GCF_016882605.1_ASM1688260v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:35,045] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:35,049] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:35,050] [INFO] Target genome list was writen to GCF_016882605.1_ASM1688260v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:35,074] [INFO] Task started: fastANI
[2024-01-24 10:47:35,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg235631db-2023-45d1-a437-7dfc9d181936/GCF_016882605.1_ASM1688260v1_genomic.fna.gz --refList GCF_016882605.1_ASM1688260v1_genomic.fna/target_genomes.txt --output GCF_016882605.1_ASM1688260v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:42,261] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:42,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84b85520-0029-414e-89bb-658d04c34d9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:42,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84b85520-0029-414e-89bb-658d04c34d9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:42,273] [INFO] Found 13 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 10:47:42,273] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:42,273] [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 longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	100.0	742	744	95	conclusive
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	99.9984	742	744	95	conclusive
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	98.6657	653	744	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	96.5354	608	744	95	conclusive
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	96.5353	608	744	95	conclusive
Bifidobacterium longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	96.4453	612	744	95	conclusive
Bifidobacterium longum subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	95.9527	579	744	95	conclusive
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	95.9032	599	744	95	conclusive
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	84.2159	503	744	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.0481	142	744	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.3643	53	744	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.3166	60	744	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	75.9814	60	744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:42,275] [INFO] DFAST Taxonomy check result was written to GCF_016882605.1_ASM1688260v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:42,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:42,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:42,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84b85520-0029-414e-89bb-658d04c34d9e/dqc_reference/checkm_data
[2024-01-24 10:47:42,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:42,302] [INFO] Task started: CheckM
[2024-01-24 10:47:42,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016882605.1_ASM1688260v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016882605.1_ASM1688260v1_genomic.fna/checkm_input GCF_016882605.1_ASM1688260v1_genomic.fna/checkm_result
[2024-01-24 10:48:09,581] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:09,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,601] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:09,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:09,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016882605.1_ASM1688260v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:09,603] [INFO] Task started: Blastn
[2024-01-24 10:48:09,603] [INFO] Running command: blastn -query GCF_016882605.1_ASM1688260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84b85520-0029-414e-89bb-658d04c34d9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016882605.1_ASM1688260v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:11,006] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:11,010] [INFO] Selected 8 target genomes.
[2024-01-24 10:48:11,010] [INFO] Target genome list was writen to GCF_016882605.1_ASM1688260v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:11,017] [INFO] Task started: fastANI
[2024-01-24 10:48:11,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg235631db-2023-45d1-a437-7dfc9d181936/GCF_016882605.1_ASM1688260v1_genomic.fna.gz --refList GCF_016882605.1_ASM1688260v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016882605.1_ASM1688260v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:15,671] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:15,677] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 10:48:15,678] [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_000196555.1	s__Bifidobacterium longum	96.5354	608	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	inconclusive
GCF_000269965.1	s__Bifidobacterium infantis	95.9108	601	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	inconclusive
GCF_001025175.1	s__Bifidobacterium breve	87.2856	511	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_018555355.1	s__Bifidobacterium sp018555355	84.4205	497	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	84.0108	497	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259745.1	s__Bifidobacterium myosotis	83.5083	477	744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_012932425.1	s__Bifidobacterium sp012932425	81.3171	412	744	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 10:48:15,679] [INFO] GTDB search result was written to GCF_016882605.1_ASM1688260v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:15,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:15,683] [INFO] DFAST_QC result json was written to GCF_016882605.1_ASM1688260v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:15,683] [INFO] DFAST_QC completed!
[2024-01-24 10:48:15,683] [INFO] Total running time: 0h0m52s