[2024-01-24 12:21:36,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,040] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b71d281-efaa-4e4c-af41-ff61e3b7c3a7/dqc_reference
[2024-01-24 12:21:37,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,243] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg64a3e958-ccb9-475c-a75e-72bdad775e69/GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/cds.fna -a GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:44,872] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:44,872] [INFO] Task started: HMMsearch
[2024-01-24 12:21:44,872] [INFO] Running command: hmmsearch --tblout GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b71d281-efaa-4e4c-af41-ff61e3b7c3a7/dqc_reference/reference_markers.hmm GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:45,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:45,129] [INFO] Found 6/6 markers.
[2024-01-24 12:21:45,157] [INFO] Query marker FASTA was written to GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:21:45,158] [INFO] Task started: Blastn
[2024-01-24 12:21:45,158] [INFO] Running command: blastn -query GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b71d281-efaa-4e4c-af41-ff61e3b7c3a7/dqc_reference/reference_markers.fasta -out GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:46,010] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:46,014] [INFO] Selected 10 target genomes.
[2024-01-24 12:21:46,015] [INFO] Target genome list was writen to GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:21:46,061] [INFO] Task started: fastANI
[2024-01-24 12:21:46,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a3e958-ccb9-475c-a75e-72bdad775e69/GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna.gz --refList GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:51,815] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:51,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b71d281-efaa-4e4c-af41-ff61e3b7c3a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:51,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b71d281-efaa-4e4c-af41-ff61e3b7c3a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:51,830] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:21:51,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:51,831] [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 merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	100.0	751	751	95	conclusive
Bifidobacterium merycicum	strain=LMG 11341	GCA_000741615.1	78345	78345	type	True	99.9714	746	751	95	conclusive
Bifidobacterium merycicum	strain=DSM 6492	GCA_000770945.1	78345	78345	type	True	99.9712	731	751	95	conclusive
Bifidobacterium pongonis	strain=64T4	GCA_019331805.1	2834432	2834432	type	True	90.7467	589	751	95	below_threshold
Bifidobacterium angulatum	strain=LMG 11039	GCA_000741065.1	1683	1683	type	True	88.2576	548	751	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.7813	373	751	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.2864	58	751	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	75.7525	65	751	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	75.704	56	751	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:51,834] [INFO] DFAST Taxonomy check result was written to GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:21:51,835] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:51,835] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:51,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b71d281-efaa-4e4c-af41-ff61e3b7c3a7/dqc_reference/checkm_data
[2024-01-24 12:21:51,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:51,866] [INFO] Task started: CheckM
[2024-01-24 12:21:51,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/checkm_input GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:22:19,430] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:19,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:19,449] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:19,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:19,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:22:19,450] [INFO] Task started: Blastn
[2024-01-24 12:22:19,450] [INFO] Running command: blastn -query GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b71d281-efaa-4e4c-af41-ff61e3b7c3a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:20,688] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:20,692] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:20,692] [INFO] Target genome list was writen to GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:20,703] [INFO] Task started: fastANI
[2024-01-24 12:22:20,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg64a3e958-ccb9-475c-a75e-72bdad775e69/GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna.gz --refList GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:26,731] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:26,749] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:26,749] [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_900129045.1	s__Bifidobacterium merycicum	100.0	751	751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.68	99.29	0.97	0.90	6	conclusive
GCF_001025155.1	s__Bifidobacterium angulatum	88.1776	543	751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.71	95.22	0.93	0.74	7	-
GCF_012932675.1	s__Bifidobacterium sp012932675	87.0043	571	751	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	81.6393	399	751	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	81.5159	396	751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	81.4464	343	751	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	81.4308	388	751	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	81.4199	383	751	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	81.2761	391	751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932425.1	s__Bifidobacterium sp012932425	80.562	330	751	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	80.5197	266	751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741215.1	s__Bifidobacterium pullorum_B	80.3926	323	751	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:26,751] [INFO] GTDB search result was written to GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:26,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:26,754] [INFO] DFAST_QC result json was written to GCF_900129045.1_IMG-taxon_2563366502_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:22:26,754] [INFO] DFAST_QC completed!
[2024-01-24 12:22:26,754] [INFO] Total running time: 0h0m51s