[2023-06-13 00:09:31,415] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:09:31,417] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:09:31,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f5186e8-9355-44f4-a10d-562ecff01ea2/dqc_reference
[2023-06-13 00:09:33,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:09:33,282] [INFO] Task started: Prodigal
[2023-06-13 00:09:33,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg69edc5d1-e7f9-4fa4-a0b5-462c84a7361f/GCA_928721925.1_min17_bin42_genomic.fna.gz | prodigal -d GCA_928721925.1_min17_bin42_genomic.fna/cds.fna -a GCA_928721925.1_min17_bin42_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:09:38,969] [INFO] Task succeeded: Prodigal
[2023-06-13 00:09:38,970] [INFO] Task started: HMMsearch
[2023-06-13 00:09:38,970] [INFO] Running command: hmmsearch --tblout GCA_928721925.1_min17_bin42_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f5186e8-9355-44f4-a10d-562ecff01ea2/dqc_reference/reference_markers.hmm GCA_928721925.1_min17_bin42_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:09:39,173] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:09:39,174] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg69edc5d1-e7f9-4fa4-a0b5-462c84a7361f/GCA_928721925.1_min17_bin42_genomic.fna.gz]
[2023-06-13 00:09:39,205] [INFO] Query marker FASTA was written to GCA_928721925.1_min17_bin42_genomic.fna/markers.fasta
[2023-06-13 00:09:39,205] [INFO] Task started: Blastn
[2023-06-13 00:09:39,206] [INFO] Running command: blastn -query GCA_928721925.1_min17_bin42_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f5186e8-9355-44f4-a10d-562ecff01ea2/dqc_reference/reference_markers.fasta -out GCA_928721925.1_min17_bin42_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:09:40,011] [INFO] Task succeeded: Blastn
[2023-06-13 00:09:40,028] [INFO] Selected 8 target genomes.
[2023-06-13 00:09:40,029] [INFO] Target genome list was writen to GCA_928721925.1_min17_bin42_genomic.fna/target_genomes.txt
[2023-06-13 00:09:40,031] [INFO] Task started: fastANI
[2023-06-13 00:09:40,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg69edc5d1-e7f9-4fa4-a0b5-462c84a7361f/GCA_928721925.1_min17_bin42_genomic.fna.gz --refList GCA_928721925.1_min17_bin42_genomic.fna/target_genomes.txt --output GCA_928721925.1_min17_bin42_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:09:43,584] [INFO] Task succeeded: fastANI
[2023-06-13 00:09:43,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f5186e8-9355-44f4-a10d-562ecff01ea2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:09:43,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f5186e8-9355-44f4-a10d-562ecff01ea2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:09:43,601] [INFO] Found 8 fastANI hits (8 hits with ANI > threshold)
[2023-06-13 00:09:43,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 00:09:43,602] [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 longum	strain=DSM 20219	GCA_900104835.1	216816	216816	type	True	98.6274	502	569	95	conclusive
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	98.5952	506	569	95	conclusive
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	98.5932	505	569	95	conclusive
Bifidobacterium longum subsp. longum	strain=KCTC 3128	GCA_017132775.1	1679	216816	type	True	98.5475	506	569	95	conclusive
Bifidobacterium longum subsp. longum	strain=LMG 13197	GCA_000741245.1	1679	216816	type	True	98.5247	504	569	95	conclusive
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	96.6262	470	569	95	conclusive
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	96.5244	465	569	95	conclusive
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	96.4119	463	569	95	conclusive
--------------------------------------------------------------------------------
[2023-06-13 00:09:43,605] [INFO] DFAST Taxonomy check result was written to GCA_928721925.1_min17_bin42_genomic.fna/tc_result.tsv
[2023-06-13 00:09:43,605] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:09:43,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:09:43,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f5186e8-9355-44f4-a10d-562ecff01ea2/dqc_reference/checkm_data
[2023-06-13 00:09:43,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:09:43,639] [INFO] Task started: CheckM
[2023-06-13 00:09:43,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_928721925.1_min17_bin42_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_928721925.1_min17_bin42_genomic.fna/checkm_input GCA_928721925.1_min17_bin42_genomic.fna/checkm_result
[2023-06-13 00:10:06,466] [INFO] Task succeeded: CheckM
[2023-06-13 00:10:06,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:10:06,493] [INFO] ===== Completeness check finished =====
[2023-06-13 00:10:06,493] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:10:06,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_928721925.1_min17_bin42_genomic.fna/markers.fasta)
[2023-06-13 00:10:06,494] [INFO] Task started: Blastn
[2023-06-13 00:10:06,494] [INFO] Running command: blastn -query GCA_928721925.1_min17_bin42_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f5186e8-9355-44f4-a10d-562ecff01ea2/dqc_reference/reference_markers_gtdb.fasta -out GCA_928721925.1_min17_bin42_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:10:07,619] [INFO] Task succeeded: Blastn
[2023-06-13 00:10:07,624] [INFO] Selected 9 target genomes.
[2023-06-13 00:10:07,624] [INFO] Target genome list was writen to GCA_928721925.1_min17_bin42_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:10:07,626] [INFO] Task started: fastANI
[2023-06-13 00:10:07,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg69edc5d1-e7f9-4fa4-a0b5-462c84a7361f/GCA_928721925.1_min17_bin42_genomic.fna.gz --refList GCA_928721925.1_min17_bin42_genomic.fna/target_genomes_gtdb.txt --output GCA_928721925.1_min17_bin42_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:10:12,127] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:12,139] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 00:10:12,139] [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_000196555.1	s__Bifidobacterium longum	98.5932	505	569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	inconclusive
GCF_000269965.1	s__Bifidobacterium infantis	95.1146	444	569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	inconclusive
GCF_001025175.1	s__Bifidobacterium breve	86.8639	383	569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_018555355.1	s__Bifidobacterium sp018555355	84.2166	394	569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	83.9229	378	569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259745.1	s__Bifidobacterium myosotis	83.2631	373	569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_009193305.1	s__Bifidobacterium cebidarum	83.1059	325	569	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	81.4857	313	569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:10:12,142] [INFO] GTDB search result was written to GCA_928721925.1_min17_bin42_genomic.fna/result_gtdb.tsv
[2023-06-13 00:10:12,143] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:10:12,147] [INFO] DFAST_QC result json was written to GCA_928721925.1_min17_bin42_genomic.fna/dqc_result.json
[2023-06-13 00:10:12,148] [INFO] DFAST_QC completed!
[2023-06-13 00:10:12,148] [INFO] Total running time: 0h0m41s