[2024-01-24 13:57:25,719] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:25,721] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:25,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg730ebbfe-740c-42b6-bc91-1f926cdffbca/dqc_reference
[2024-01-24 13:57:27,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:27,045] [INFO] Task started: Prodigal
[2024-01-24 13:57:27,046] [INFO] Running command: gunzip -c /var/lib/cwl/stg42442444-e4b5-4266-a697-617ef49d7b83/GCF_009299485.1_ASM929948v1_genomic.fna.gz | prodigal -d GCF_009299485.1_ASM929948v1_genomic.fna/cds.fna -a GCF_009299485.1_ASM929948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:35,403] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:35,404] [INFO] Task started: HMMsearch
[2024-01-24 13:57:35,404] [INFO] Running command: hmmsearch --tblout GCF_009299485.1_ASM929948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg730ebbfe-740c-42b6-bc91-1f926cdffbca/dqc_reference/reference_markers.hmm GCF_009299485.1_ASM929948v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:35,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:35,655] [INFO] Found 6/6 markers.
[2024-01-24 13:57:35,678] [INFO] Query marker FASTA was written to GCF_009299485.1_ASM929948v1_genomic.fna/markers.fasta
[2024-01-24 13:57:35,679] [INFO] Task started: Blastn
[2024-01-24 13:57:35,679] [INFO] Running command: blastn -query GCF_009299485.1_ASM929948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg730ebbfe-740c-42b6-bc91-1f926cdffbca/dqc_reference/reference_markers.fasta -out GCF_009299485.1_ASM929948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:36,508] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:36,512] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:36,513] [INFO] Target genome list was writen to GCF_009299485.1_ASM929948v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:36,522] [INFO] Task started: fastANI
[2024-01-24 13:57:36,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg42442444-e4b5-4266-a697-617ef49d7b83/GCF_009299485.1_ASM929948v1_genomic.fna.gz --refList GCF_009299485.1_ASM929948v1_genomic.fna/target_genomes.txt --output GCF_009299485.1_ASM929948v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:45,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:45,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg730ebbfe-740c-42b6-bc91-1f926cdffbca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:45,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg730ebbfe-740c-42b6-bc91-1f926cdffbca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:45,304] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:45,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:45,305] [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 apri	strain=DSM 100238	GCA_009299485.1	1769423	1769423	type	True	100.0	783	784	95	conclusive
Bifidobacterium porcinum	strain=DSM 17755	GCA_000771045.1	212365	212365	type	True	87.2787	576	784	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000771005.1	79262	246618	type	True	86.4991	587	784	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000426425.1	79262	246618	type	True	86.498	591	784	95	below_threshold
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=LMG 21395	GCA_000741455.1	79262	246618	type	True	86.3205	596	784	95	below_threshold
Bifidobacterium boum	strain=LMG 10736	GCA_000741535.1	78343	78343	type	True	86.2595	531	784	95	below_threshold
Bifidobacterium boum	strain=DSM 20432	GCA_000687615.1	78343	78343	type	True	86.2252	536	784	95	below_threshold
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	86.2121	538	784	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.0201	249	784	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	78.8851	210	784	95	below_threshold
Bifidobacterium hapali	strain=DSM 100202	GCA_002259755.1	1630172	1630172	type	True	78.842	143	784	95	below_threshold
Bifidobacterium choerinum	strain=LMG 10510	GCA_000741135.1	35760	35760	type	True	78.8398	207	784	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000771425.1	35760	35760	type	True	78.8369	196	784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:45,307] [INFO] DFAST Taxonomy check result was written to GCF_009299485.1_ASM929948v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:45,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:45,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:45,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg730ebbfe-740c-42b6-bc91-1f926cdffbca/dqc_reference/checkm_data
[2024-01-24 13:57:45,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:45,337] [INFO] Task started: CheckM
[2024-01-24 13:57:45,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009299485.1_ASM929948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009299485.1_ASM929948v1_genomic.fna/checkm_input GCF_009299485.1_ASM929948v1_genomic.fna/checkm_result
[2024-01-24 13:58:16,672] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:16,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:16,690] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:16,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:16,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009299485.1_ASM929948v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:16,691] [INFO] Task started: Blastn
[2024-01-24 13:58:16,692] [INFO] Running command: blastn -query GCF_009299485.1_ASM929948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg730ebbfe-740c-42b6-bc91-1f926cdffbca/dqc_reference/reference_markers_gtdb.fasta -out GCF_009299485.1_ASM929948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:17,877] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:17,881] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:17,882] [INFO] Target genome list was writen to GCF_009299485.1_ASM929948v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:17,897] [INFO] Task started: fastANI
[2024-01-24 13:58:17,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg42442444-e4b5-4266-a697-617ef49d7b83/GCF_009299485.1_ASM929948v1_genomic.fna.gz --refList GCF_009299485.1_ASM929948v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009299485.1_ASM929948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:24,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:24,138] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:24,138] [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_009299485.1	s__Bifidobacterium apri	100.0	783	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000771265.1	s__Bifidobacterium thermophilum	87.5721	608	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	-
GCF_000741535.1	s__Bifidobacterium boum	86.2595	531	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.80	97.54	0.95	0.91	9	-
GCA_000741495.1	s__Bifidobacterium thermophilum_A	85.0775	536	784	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	79.5678	256	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCA_002451435.1	s__Bifidobacterium sp002451435	79.2568	236	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.30	98.61	0.87	0.84	20	-
GCF_000771405.1	s__Bifidobacterium pullorum	79.1125	239	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_000522505.1	s__Bifidobacterium moukalabense	78.894	235	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_002860345.1	s__Bifidobacterium anseris	78.8914	198	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.21	99.21	0.95	0.95	2	-
GCF_000741135.1	s__Bifidobacterium choerinum	78.8398	207	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_002259755.1	s__Bifidobacterium hapali	78.8112	144	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286915.1	s__Bifidobacterium italicum	78.5118	206	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009371885.1	s__Bifidobacterium tibiigranuli	78.3907	219	784	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:24,140] [INFO] GTDB search result was written to GCF_009299485.1_ASM929948v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:24,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:24,144] [INFO] DFAST_QC result json was written to GCF_009299485.1_ASM929948v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:24,144] [INFO] DFAST_QC completed!
[2024-01-24 13:58:24,144] [INFO] Total running time: 0h0m58s