[2024-01-24 11:26:38,315] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:38,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:38,317] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dc7f045-3226-461e-a42c-527cc89e63e0/dqc_reference
[2024-01-24 11:26:39,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,779] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,779] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbe086c2-82d5-4764-85f5-2fe4370d9ab6/GCF_000771665.1_DSM-23973_genomic.fna.gz | prodigal -d GCF_000771665.1_DSM-23973_genomic.fna/cds.fna -a GCF_000771665.1_DSM-23973_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:48,411] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:48,411] [INFO] Task started: HMMsearch
[2024-01-24 11:26:48,411] [INFO] Running command: hmmsearch --tblout GCF_000771665.1_DSM-23973_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dc7f045-3226-461e-a42c-527cc89e63e0/dqc_reference/reference_markers.hmm GCF_000771665.1_DSM-23973_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:48,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:48,656] [INFO] Found 6/6 markers.
[2024-01-24 11:26:48,681] [INFO] Query marker FASTA was written to GCF_000771665.1_DSM-23973_genomic.fna/markers.fasta
[2024-01-24 11:26:48,682] [INFO] Task started: Blastn
[2024-01-24 11:26:48,682] [INFO] Running command: blastn -query GCF_000771665.1_DSM-23973_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc7f045-3226-461e-a42c-527cc89e63e0/dqc_reference/reference_markers.fasta -out GCF_000771665.1_DSM-23973_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:49,772] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:49,775] [INFO] Selected 12 target genomes.
[2024-01-24 11:26:49,776] [INFO] Target genome list was writen to GCF_000771665.1_DSM-23973_genomic.fna/target_genomes.txt
[2024-01-24 11:26:49,779] [INFO] Task started: fastANI
[2024-01-24 11:26:49,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe086c2-82d5-4764-85f5-2fe4370d9ab6/GCF_000771665.1_DSM-23973_genomic.fna.gz --refList GCF_000771665.1_DSM-23973_genomic.fna/target_genomes.txt --output GCF_000771665.1_DSM-23973_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:57,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:57,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dc7f045-3226-461e-a42c-527cc89e63e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:57,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dc7f045-3226-461e-a42c-527cc89e63e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:57,339] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:57,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:57,339] [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_000771665.1	762209	762209	type	True	100.0	917	920	95	conclusive
Bifidobacterium callitrichos	strain=DSM 23973	GCA_000741175.1	762209	762209	type	True	99.9771	908	920	95	conclusive
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	91.4803	714	920	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	88.5896	669	920	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	86.6359	579	920	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	85.9857	570	920	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	85.8963	553	920	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	83.8036	552	920	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.6229	504	920	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.6969	298	920	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.6521	125	920	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.3942	140	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:57,341] [INFO] DFAST Taxonomy check result was written to GCF_000771665.1_DSM-23973_genomic.fna/tc_result.tsv
[2024-01-24 11:26:57,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:57,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:57,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dc7f045-3226-461e-a42c-527cc89e63e0/dqc_reference/checkm_data
[2024-01-24 11:26:57,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:57,373] [INFO] Task started: CheckM
[2024-01-24 11:26:57,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771665.1_DSM-23973_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771665.1_DSM-23973_genomic.fna/checkm_input GCF_000771665.1_DSM-23973_genomic.fna/checkm_result
[2024-01-24 11:27:27,428] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:27,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:27,452] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:27,453] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:27,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771665.1_DSM-23973_genomic.fna/markers.fasta)
[2024-01-24 11:27:27,454] [INFO] Task started: Blastn
[2024-01-24 11:27:27,454] [INFO] Running command: blastn -query GCF_000771665.1_DSM-23973_genomic.fna/markers.fasta -db /var/lib/cwl/stg2dc7f045-3226-461e-a42c-527cc89e63e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771665.1_DSM-23973_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:29,077] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:29,080] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:29,081] [INFO] Target genome list was writen to GCF_000771665.1_DSM-23973_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:29,090] [INFO] Task started: fastANI
[2024-01-24 11:27:29,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbe086c2-82d5-4764-85f5-2fe4370d9ab6/GCF_000771665.1_DSM-23973_genomic.fna.gz --refList GCF_000771665.1_DSM-23973_genomic.fna/target_genomes_gtdb.txt --output GCF_000771665.1_DSM-23973_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:35,015] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:35,023] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:35,024] [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	99.9771	908	920	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	91.4803	714	920	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	88.5932	669	920	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	86.6359	579	920	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	86.1811	575	920	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	86.0337	577	920	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	85.987	569	920	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	85.9389	560	920	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	82.8236	454	920	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 11:27:35,025] [INFO] GTDB search result was written to GCF_000771665.1_DSM-23973_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:35,026] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:35,029] [INFO] DFAST_QC result json was written to GCF_000771665.1_DSM-23973_genomic.fna/dqc_result.json
[2024-01-24 11:27:35,029] [INFO] DFAST_QC completed!
[2024-01-24 11:27:35,029] [INFO] Total running time: 0h0m57s