[2024-01-25 19:43:20,651] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:20,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:20,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg77af6d00-cdd6-4cb4-8e7f-f60c4a4c9c11/dqc_reference
[2024-01-25 19:43:21,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:21,779] [INFO] Task started: Prodigal
[2024-01-25 19:43:21,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg114d2e62-6ec2-4b0e-8229-dfc1b0cb3daa/GCF_000741065.1_Bifang_genomic.fna.gz | prodigal -d GCF_000741065.1_Bifang_genomic.fna/cds.fna -a GCF_000741065.1_Bifang_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:28,116] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:28,117] [INFO] Task started: HMMsearch
[2024-01-25 19:43:28,117] [INFO] Running command: hmmsearch --tblout GCF_000741065.1_Bifang_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77af6d00-cdd6-4cb4-8e7f-f60c4a4c9c11/dqc_reference/reference_markers.hmm GCF_000741065.1_Bifang_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:28,332] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:28,333] [INFO] Found 6/6 markers.
[2024-01-25 19:43:28,352] [INFO] Query marker FASTA was written to GCF_000741065.1_Bifang_genomic.fna/markers.fasta
[2024-01-25 19:43:28,352] [INFO] Task started: Blastn
[2024-01-25 19:43:28,353] [INFO] Running command: blastn -query GCF_000741065.1_Bifang_genomic.fna/markers.fasta -db /var/lib/cwl/stg77af6d00-cdd6-4cb4-8e7f-f60c4a4c9c11/dqc_reference/reference_markers.fasta -out GCF_000741065.1_Bifang_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:29,108] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:29,111] [INFO] Selected 11 target genomes.
[2024-01-25 19:43:29,111] [INFO] Target genome list was writen to GCF_000741065.1_Bifang_genomic.fna/target_genomes.txt
[2024-01-25 19:43:29,117] [INFO] Task started: fastANI
[2024-01-25 19:43:29,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg114d2e62-6ec2-4b0e-8229-dfc1b0cb3daa/GCF_000741065.1_Bifang_genomic.fna.gz --refList GCF_000741065.1_Bifang_genomic.fna/target_genomes.txt --output GCF_000741065.1_Bifang_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:36,180] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:36,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77af6d00-cdd6-4cb4-8e7f-f60c4a4c9c11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:36,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77af6d00-cdd6-4cb4-8e7f-f60c4a4c9c11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:36,187] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:43:36,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:36,188] [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 angulatum	strain=LMG 11039	GCA_000741065.1	1683	1683	type	True	100.0	665	665	95	conclusive
Bifidobacterium angulatum	strain=JCM 7096	GCA_001025155.1	1683	1683	type	True	99.9823	665	665	95	conclusive
Bifidobacterium angulatum	strain=DSM 20098	GCA_000156635.1	1683	1683	type	True	99.9779	664	665	95	conclusive
Bifidobacterium angulatum	strain=DSM 20098	GCA_000771205.1	1683	1683	type	True	99.9658	648	665	95	conclusive
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	88.4062	532	665	95	below_threshold
Bifidobacterium pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	86.2464	497	665	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.8901	328	665	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	75.6007	54	665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:36,189] [INFO] DFAST Taxonomy check result was written to GCF_000741065.1_Bifang_genomic.fna/tc_result.tsv
[2024-01-25 19:43:36,189] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:36,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:36,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77af6d00-cdd6-4cb4-8e7f-f60c4a4c9c11/dqc_reference/checkm_data
[2024-01-25 19:43:36,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:36,214] [INFO] Task started: CheckM
[2024-01-25 19:43:36,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000741065.1_Bifang_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000741065.1_Bifang_genomic.fna/checkm_input GCF_000741065.1_Bifang_genomic.fna/checkm_result
[2024-01-25 19:43:58,560] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:58,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:58,575] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:58,575] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:58,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000741065.1_Bifang_genomic.fna/markers.fasta)
[2024-01-25 19:43:58,576] [INFO] Task started: Blastn
[2024-01-25 19:43:58,576] [INFO] Running command: blastn -query GCF_000741065.1_Bifang_genomic.fna/markers.fasta -db /var/lib/cwl/stg77af6d00-cdd6-4cb4-8e7f-f60c4a4c9c11/dqc_reference/reference_markers_gtdb.fasta -out GCF_000741065.1_Bifang_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:59,724] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:59,727] [INFO] Selected 13 target genomes.
[2024-01-25 19:43:59,727] [INFO] Target genome list was writen to GCF_000741065.1_Bifang_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:59,742] [INFO] Task started: fastANI
[2024-01-25 19:43:59,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg114d2e62-6ec2-4b0e-8229-dfc1b0cb3daa/GCF_000741065.1_Bifang_genomic.fna.gz --refList GCF_000741065.1_Bifang_genomic.fna/target_genomes_gtdb.txt --output GCF_000741065.1_Bifang_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:06,029] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:06,038] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:06,038] [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_001025155.1	s__Bifidobacterium angulatum	99.9823	665	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.71	95.22	0.93	0.74	7	conclusive
GCF_900129045.1	s__Bifidobacterium merycicum	88.4062	532	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	-
GCF_012932675.1	s__Bifidobacterium sp012932675	87.8254	562	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555385.1	s__Bifidobacterium sp018555385	81.1665	330	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741175.1	s__Bifidobacterium callitrichos	81.0654	320	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.40	96.52	0.91	0.88	6	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.0517	311	665	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	81.0002	346	665	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	80.9987	325	665	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	80.8579	348	665	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	80.7843	336	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932445.1	s__Bifidobacterium sp012932445	80.7159	251	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932375.1	s__Bifidobacterium sp012932375	80.4693	290	665	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	80.3142	292	665	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:06,040] [INFO] GTDB search result was written to GCF_000741065.1_Bifang_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:06,040] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:06,043] [INFO] DFAST_QC result json was written to GCF_000741065.1_Bifang_genomic.fna/dqc_result.json
[2024-01-25 19:44:06,043] [INFO] DFAST_QC completed!
[2024-01-25 19:44:06,043] [INFO] Total running time: 0h0m45s