[2024-01-24 12:54:22,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,062] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg29c51236-51a6-477b-8d91-c3725d9aaf24/dqc_reference
[2024-01-24 12:54:23,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:23,881] [INFO] Task started: Prodigal
[2024-01-24 12:54:23,881] [INFO] Running command: gunzip -c /var/lib/cwl/stga45e8982-ee4c-4bd9-be30-ed2f9877ea07/GCF_000771045.1_DSM-17755_genomic.fna.gz | prodigal -d GCF_000771045.1_DSM-17755_genomic.fna/cds.fna -a GCF_000771045.1_DSM-17755_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:30,994] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:30,995] [INFO] Task started: HMMsearch
[2024-01-24 12:54:30,995] [INFO] Running command: hmmsearch --tblout GCF_000771045.1_DSM-17755_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29c51236-51a6-477b-8d91-c3725d9aaf24/dqc_reference/reference_markers.hmm GCF_000771045.1_DSM-17755_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:31,226] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:31,227] [INFO] Found 6/6 markers.
[2024-01-24 12:54:31,251] [INFO] Query marker FASTA was written to GCF_000771045.1_DSM-17755_genomic.fna/markers.fasta
[2024-01-24 12:54:31,251] [INFO] Task started: Blastn
[2024-01-24 12:54:31,251] [INFO] Running command: blastn -query GCF_000771045.1_DSM-17755_genomic.fna/markers.fasta -db /var/lib/cwl/stg29c51236-51a6-477b-8d91-c3725d9aaf24/dqc_reference/reference_markers.fasta -out GCF_000771045.1_DSM-17755_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:32,126] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:32,133] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:32,134] [INFO] Target genome list was writen to GCF_000771045.1_DSM-17755_genomic.fna/target_genomes.txt
[2024-01-24 12:54:32,139] [INFO] Task started: fastANI
[2024-01-24 12:54:32,139] [INFO] Running command: fastANI --query /var/lib/cwl/stga45e8982-ee4c-4bd9-be30-ed2f9877ea07/GCF_000771045.1_DSM-17755_genomic.fna.gz --refList GCF_000771045.1_DSM-17755_genomic.fna/target_genomes.txt --output GCF_000771045.1_DSM-17755_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:37,652] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:37,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29c51236-51a6-477b-8d91-c3725d9aaf24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:37,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29c51236-51a6-477b-8d91-c3725d9aaf24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:37,663] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:54:37,663] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:54:37,663] [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 porcinum	strain=DSM 17755	GCA_000771045.1	212365	212365	type	True	100.0	671	674	95	inconclusive
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000771005.1	79262	246618	type	True	95.7945	606	674	95	inconclusive
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=DSM 15837	GCA_000426425.1	79262	246618	type	True	95.7533	606	674	95	inconclusive
Bifidobacterium thermacidophilum subsp. thermacidophilum	strain=LMG 21395	GCA_000741455.1	79262	246618	type	True	95.7292	613	674	95	inconclusive
Bifidobacterium apri	strain=DSM 100238	GCA_009299485.1	1769423	1769423	type	True	87.3326	570	674	95	below_threshold
Bifidobacterium boum	strain=DSM 20432	GCA_000771385.1	78343	78343	type	True	86.5313	511	674	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	79.6711	296	674	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	79.4207	273	674	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.3736	217	674	95	below_threshold
Bifidobacterium commune	strain=DSM 28792	GCA_014191315.1	1505727	1505727	type	True	77.7959	78	674	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.1568	64	674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:37,665] [INFO] DFAST Taxonomy check result was written to GCF_000771045.1_DSM-17755_genomic.fna/tc_result.tsv
[2024-01-24 12:54:37,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:37,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:37,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29c51236-51a6-477b-8d91-c3725d9aaf24/dqc_reference/checkm_data
[2024-01-24 12:54:37,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:37,693] [INFO] Task started: CheckM
[2024-01-24 12:54:37,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000771045.1_DSM-17755_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000771045.1_DSM-17755_genomic.fna/checkm_input GCF_000771045.1_DSM-17755_genomic.fna/checkm_result
[2024-01-24 12:55:03,883] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:03,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:03,908] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:03,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:03,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000771045.1_DSM-17755_genomic.fna/markers.fasta)
[2024-01-24 12:55:03,909] [INFO] Task started: Blastn
[2024-01-24 12:55:03,909] [INFO] Running command: blastn -query GCF_000771045.1_DSM-17755_genomic.fna/markers.fasta -db /var/lib/cwl/stg29c51236-51a6-477b-8d91-c3725d9aaf24/dqc_reference/reference_markers_gtdb.fasta -out GCF_000771045.1_DSM-17755_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:05,140] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:05,144] [INFO] Selected 14 target genomes.
[2024-01-24 12:55:05,144] [INFO] Target genome list was writen to GCF_000771045.1_DSM-17755_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:05,159] [INFO] Task started: fastANI
[2024-01-24 12:55:05,159] [INFO] Running command: fastANI --query /var/lib/cwl/stga45e8982-ee4c-4bd9-be30-ed2f9877ea07/GCF_000771045.1_DSM-17755_genomic.fna.gz --refList GCF_000771045.1_DSM-17755_genomic.fna/target_genomes_gtdb.txt --output GCF_000771045.1_DSM-17755_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:11,928] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:11,944] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:11,945] [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
GCA_000771265.1	s__Bifidobacterium thermophilum	95.3653	611	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	conclusive
GCA_000741495.1	s__Bifidobacterium thermophilum_A	88.0975	519	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299485.1	s__Bifidobacterium apri	87.3326	570	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741535.1	s__Bifidobacterium boum	86.6342	512	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.80	97.54	0.95	0.91	9	-
GCF_000010425.1	s__Bifidobacterium adolescentis	79.9359	273	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.09	95.61	0.87	0.77	128	-
GCF_010667685.1	s__Bifidobacterium aerophilum	79.9027	282	674	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	79.8631	287	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_000770925.1	s__Bifidobacterium ruminantium	79.8564	261	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_018555385.1	s__Bifidobacterium sp018555385	79.7979	265	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	79.7502	284	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	79.4833	261	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000771405.1	s__Bifidobacterium pullorum	79.2245	260	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_014898175.1	s__Bifidobacterium lemurum	79.1454	266	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000522505.1	s__Bifidobacterium moukalabense	78.9004	260	674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:11,947] [INFO] GTDB search result was written to GCF_000771045.1_DSM-17755_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:11,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:11,951] [INFO] DFAST_QC result json was written to GCF_000771045.1_DSM-17755_genomic.fna/dqc_result.json
[2024-01-24 12:55:11,951] [INFO] DFAST_QC completed!
[2024-01-24 12:55:11,951] [INFO] Total running time: 0h0m50s