[2023-06-13 17:55:52,602] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:55:52,605] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:55:52,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgceeea125-aacd-4790-91d7-c98ac1548993/dqc_reference
[2023-06-13 17:55:53,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:55:53,862] [INFO] Task started: Prodigal
[2023-06-13 17:55:53,862] [INFO] Running command: gunzip -c /var/lib/cwl/stgb69e734c-9a1e-4d38-bd29-d7113485072f/GCA_022716855.1_ASM2271685v1_genomic.fna.gz | prodigal -d GCA_022716855.1_ASM2271685v1_genomic.fna/cds.fna -a GCA_022716855.1_ASM2271685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:56:00,166] [INFO] Task succeeded: Prodigal
[2023-06-13 17:56:00,166] [INFO] Task started: HMMsearch
[2023-06-13 17:56:00,167] [INFO] Running command: hmmsearch --tblout GCA_022716855.1_ASM2271685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceeea125-aacd-4790-91d7-c98ac1548993/dqc_reference/reference_markers.hmm GCA_022716855.1_ASM2271685v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:56:00,362] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:56:00,363] [INFO] Found 6/6 markers.
[2023-06-13 17:56:00,385] [INFO] Query marker FASTA was written to GCA_022716855.1_ASM2271685v1_genomic.fna/markers.fasta
[2023-06-13 17:56:00,385] [INFO] Task started: Blastn
[2023-06-13 17:56:00,385] [INFO] Running command: blastn -query GCA_022716855.1_ASM2271685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceeea125-aacd-4790-91d7-c98ac1548993/dqc_reference/reference_markers.fasta -out GCA_022716855.1_ASM2271685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:01,161] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:01,165] [INFO] Selected 14 target genomes.
[2023-06-13 17:56:01,165] [INFO] Target genome list was writen to GCA_022716855.1_ASM2271685v1_genomic.fna/target_genomes.txt
[2023-06-13 17:56:01,166] [INFO] Task started: fastANI
[2023-06-13 17:56:01,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgb69e734c-9a1e-4d38-bd29-d7113485072f/GCA_022716855.1_ASM2271685v1_genomic.fna.gz --refList GCA_022716855.1_ASM2271685v1_genomic.fna/target_genomes.txt --output GCA_022716855.1_ASM2271685v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:56:07,539] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:07,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceeea125-aacd-4790-91d7-c98ac1548993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:56:07,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceeea125-aacd-4790-91d7-c98ac1548993/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:56:07,550] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2023-06-13 17:56:07,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 17:56:07,550] [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 catenulatum subsp. kashiwanohense	strain=JCM 15439	GCA_001042615.1	630129	1686	type	True	95.3097	469	556	95	conclusive
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000741605.1	630129	1686	type	True	95.2989	468	556	95	conclusive
Bifidobacterium catenulatum subsp. kashiwanohense	strain=DSM 21854	GCA_000771545.1	630129	1686	type	True	95.18	471	556	95	conclusive
Bifidobacterium catenulatum	strain=JCM 1194	GCA_001025195.1	1686	1686	type	True	94.6078	439	556	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000173455.1	1686	1686	type	True	94.5965	440	556	95	below_threshold
Bifidobacterium catenulatum	strain=LMG 11043	GCA_000741565.1	1686	1686	type	True	94.5688	443	556	95	below_threshold
Bifidobacterium catenulatum	strain=DSM 16992	GCA_000771025.1	1686	1686	type	True	94.495	419	556	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000173435.1	28026	28026	type	True	92.4236	450	556	95	below_threshold
Bifidobacterium pseudocatenulatum	strain=DSM 20438	GCA_000771445.1	28026	28026	type	True	92.3776	450	556	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	80.0587	216	556	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	80.0311	224	556	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.6116	73	556	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:56:07,553] [INFO] DFAST Taxonomy check result was written to GCA_022716855.1_ASM2271685v1_genomic.fna/tc_result.tsv
[2023-06-13 17:56:07,554] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:56:07,554] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:56:07,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceeea125-aacd-4790-91d7-c98ac1548993/dqc_reference/checkm_data
[2023-06-13 17:56:07,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:56:07,578] [INFO] Task started: CheckM
[2023-06-13 17:56:07,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022716855.1_ASM2271685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022716855.1_ASM2271685v1_genomic.fna/checkm_input GCA_022716855.1_ASM2271685v1_genomic.fna/checkm_result
[2023-06-13 17:56:32,003] [INFO] Task succeeded: CheckM
[2023-06-13 17:56:32,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:56:32,026] [INFO] ===== Completeness check finished =====
[2023-06-13 17:56:32,027] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:56:32,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022716855.1_ASM2271685v1_genomic.fna/markers.fasta)
[2023-06-13 17:56:32,027] [INFO] Task started: Blastn
[2023-06-13 17:56:32,027] [INFO] Running command: blastn -query GCA_022716855.1_ASM2271685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceeea125-aacd-4790-91d7-c98ac1548993/dqc_reference/reference_markers_gtdb.fasta -out GCA_022716855.1_ASM2271685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:33,107] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:33,112] [INFO] Selected 5 target genomes.
[2023-06-13 17:56:33,112] [INFO] Target genome list was writen to GCA_022716855.1_ASM2271685v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:56:33,113] [INFO] Task started: fastANI
[2023-06-13 17:56:33,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgb69e734c-9a1e-4d38-bd29-d7113485072f/GCA_022716855.1_ASM2271685v1_genomic.fna.gz --refList GCA_022716855.1_ASM2271685v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022716855.1_ASM2271685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:56:35,528] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:35,534] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:56:35,535] [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_000800455.1	s__Bifidobacterium kashiwanohense_A	96.6391	488	556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.1942	N/A	N/A	N/A	N/A	1	conclusive
GCF_001042615.1	s__Bifidobacterium kashiwanohense	95.3097	469	556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.07	97.92	0.95	0.91	5	-
GCF_001025195.1	s__Bifidobacterium catenulatum	94.6078	439	556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	96.3948	99.04	98.03	0.94	0.87	12	-
GCF_002742445.1	s__Bifidobacterium sp002742445	94.1684	451	556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.43	96.66	0.87	0.84	9	-
GCF_001025215.1	s__Bifidobacterium pseudocatenulatum	92.2744	462	556	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.12	96.90	0.90	0.83	112	-
--------------------------------------------------------------------------------
[2023-06-13 17:56:35,536] [INFO] GTDB search result was written to GCA_022716855.1_ASM2271685v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:56:35,537] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:56:35,540] [INFO] DFAST_QC result json was written to GCA_022716855.1_ASM2271685v1_genomic.fna/dqc_result.json
[2023-06-13 17:56:35,541] [INFO] DFAST_QC completed!
[2023-06-13 17:56:35,541] [INFO] Total running time: 0h0m43s