[2024-01-24 11:43:53,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg77e0f921-0c1f-44c8-8590-0f74a8c14a43/dqc_reference
[2024-01-24 11:43:54,432] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,433] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg43794185-9f28-46ec-b196-85ba274fd4c4/GCF_000741175.1_Bifcal_genomic.fna.gz | prodigal -d GCF_000741175.1_Bifcal_genomic.fna/cds.fna -a GCF_000741175.1_Bifcal_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:03,011] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:03,011] [INFO] Task started: HMMsearch
[2024-01-24 11:44:03,011] [INFO] Running command: hmmsearch --tblout GCF_000741175.1_Bifcal_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77e0f921-0c1f-44c8-8590-0f74a8c14a43/dqc_reference/reference_markers.hmm GCF_000741175.1_Bifcal_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:03,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:03,211] [INFO] Found 6/6 markers.
[2024-01-24 11:44:03,234] [INFO] Query marker FASTA was written to GCF_000741175.1_Bifcal_genomic.fna/markers.fasta
[2024-01-24 11:44:03,234] [INFO] Task started: Blastn
[2024-01-24 11:44:03,234] [INFO] Running command: blastn -query GCF_000741175.1_Bifcal_genomic.fna/markers.fasta -db /var/lib/cwl/stg77e0f921-0c1f-44c8-8590-0f74a8c14a43/dqc_reference/reference_markers.fasta -out GCF_000741175.1_Bifcal_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:04,287] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:04,290] [INFO] Selected 12 target genomes.
[2024-01-24 11:44:04,291] [INFO] Target genome list was writen to GCF_000741175.1_Bifcal_genomic.fna/target_genomes.txt
[2024-01-24 11:44:04,295] [INFO] Task started: fastANI
[2024-01-24 11:44:04,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg43794185-9f28-46ec-b196-85ba274fd4c4/GCF_000741175.1_Bifcal_genomic.fna.gz --refList GCF_000741175.1_Bifcal_genomic.fna/target_genomes.txt --output GCF_000741175.1_Bifcal_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:12,129] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:12,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77e0f921-0c1f-44c8-8590-0f74a8c14a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:12,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77e0f921-0c1f-44c8-8590-0f74a8c14a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:12,140] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:12,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:12,141] [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 callitrichos	strain=DSM 23973	GCA_000741175.1	762209	762209	type	True	100.0	942	945	95	conclusive
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000771665.1	762209	762209	type	True	99.956	901	945	95	conclusive
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	91.3941	719	945	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	88.6791	677	945	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	86.6356	567	945	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	86.0937	568	945	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	85.6735	552	945	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	83.8846	545	945	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.5768	517	945	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.1079	285	945	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.5739	136	945	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.4686	135	945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:12,142] [INFO] DFAST Taxonomy check result was written to GCF_000741175.1_Bifcal_genomic.fna/tc_result.tsv
[2024-01-24 11:44:12,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:12,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:12,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77e0f921-0c1f-44c8-8590-0f74a8c14a43/dqc_reference/checkm_data
[2024-01-24 11:44:12,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:12,175] [INFO] Task started: CheckM
[2024-01-24 11:44:12,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741175.1_Bifcal_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741175.1_Bifcal_genomic.fna/checkm_input GCF_000741175.1_Bifcal_genomic.fna/checkm_result
[2024-01-24 11:44:41,285] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:41,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,304] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:41,304] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:41,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741175.1_Bifcal_genomic.fna/markers.fasta)
[2024-01-24 11:44:41,305] [INFO] Task started: Blastn
[2024-01-24 11:44:41,305] [INFO] Running command: blastn -query GCF_000741175.1_Bifcal_genomic.fna/markers.fasta -db /var/lib/cwl/stg77e0f921-0c1f-44c8-8590-0f74a8c14a43/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741175.1_Bifcal_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:42,881] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:42,884] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:42,885] [INFO] Target genome list was writen to GCF_000741175.1_Bifcal_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:42,891] [INFO] Task started: fastANI
[2024-01-24 11:44:42,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg43794185-9f28-46ec-b196-85ba274fd4c4/GCF_000741175.1_Bifcal_genomic.fna.gz --refList GCF_000741175.1_Bifcal_genomic.fna/target_genomes_gtdb.txt --output GCF_000741175.1_Bifcal_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:48,859] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:48,867] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:48,867] [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_000741175.1	s__Bifidobacterium callitrichos	100.0	942	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	conclusive
GCF_008698235.1	s__Bifidobacterium rousetti	91.3705	720	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.97	96.97	0.86	0.86	2	-
GCF_018555385.1	s__Bifidobacterium sp018555385	88.693	676	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860365.1	s__Bifidobacterium parmae	86.6344	567	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555635.1	s__Bifidobacterium sp018555635	86.1668	566	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	86.1583	578	945	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	86.1067	568	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741785.1	s__Bifidobacterium stellenboschense	86.0286	559	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299475.1	s__Bifidobacterium avesanii	82.9666	442	945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:48,870] [INFO] GTDB search result was written to GCF_000741175.1_Bifcal_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:48,871] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:48,874] [INFO] DFAST_QC result json was written to GCF_000741175.1_Bifcal_genomic.fna/dqc_result.json
[2024-01-24 11:44:48,874] [INFO] DFAST_QC completed!
[2024-01-24 11:44:48,874] [INFO] Total running time: 0h0m56s