[2023-06-13 14:06:10,119] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:06:10,122] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:06:10,122] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcf92774-0053-4ff7-82fe-444b1e8aa353/dqc_reference
[2023-06-13 14:06:11,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:06:11,490] [INFO] Task started: Prodigal
[2023-06-13 14:06:11,490] [INFO] Running command: gunzip -c /var/lib/cwl/stg558ef862-33a6-4def-8a2f-a96deed1b12b/GCA_022739915.1_ASM2273991v1_genomic.fna.gz | prodigal -d GCA_022739915.1_ASM2273991v1_genomic.fna/cds.fna -a GCA_022739915.1_ASM2273991v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:06:18,807] [INFO] Task succeeded: Prodigal
[2023-06-13 14:06:18,807] [INFO] Task started: HMMsearch
[2023-06-13 14:06:18,808] [INFO] Running command: hmmsearch --tblout GCA_022739915.1_ASM2273991v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcf92774-0053-4ff7-82fe-444b1e8aa353/dqc_reference/reference_markers.hmm GCA_022739915.1_ASM2273991v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:06:19,054] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:06:19,055] [INFO] Found 6/6 markers.
[2023-06-13 14:06:19,083] [INFO] Query marker FASTA was written to GCA_022739915.1_ASM2273991v1_genomic.fna/markers.fasta
[2023-06-13 14:06:19,084] [INFO] Task started: Blastn
[2023-06-13 14:06:19,084] [INFO] Running command: blastn -query GCA_022739915.1_ASM2273991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf92774-0053-4ff7-82fe-444b1e8aa353/dqc_reference/reference_markers.fasta -out GCA_022739915.1_ASM2273991v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:20,006] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:20,010] [INFO] Selected 14 target genomes.
[2023-06-13 14:06:20,011] [INFO] Target genome list was writen to GCA_022739915.1_ASM2273991v1_genomic.fna/target_genomes.txt
[2023-06-13 14:06:20,012] [INFO] Task started: fastANI
[2023-06-13 14:06:20,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg558ef862-33a6-4def-8a2f-a96deed1b12b/GCA_022739915.1_ASM2273991v1_genomic.fna.gz --refList GCA_022739915.1_ASM2273991v1_genomic.fna/target_genomes.txt --output GCA_022739915.1_ASM2273991v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:06:27,060] [INFO] Task succeeded: fastANI
[2023-06-13 14:06:27,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcf92774-0053-4ff7-82fe-444b1e8aa353/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:06:27,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcf92774-0053-4ff7-82fe-444b1e8aa353/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:06:27,073] [INFO] Found 14 fastANI hits (7 hits with ANI > threshold)
[2023-06-13 14:06:27,073] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 14:06:27,073] [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 subsp. infantis	strain=DSM 20088	GCA_000771105.1	1682	216816	type	True	98.058	592	683	95	conclusive
Bifidobacterium longum subsp. infantis	strain=ATCC 15697	GCA_000020425.1	1682	216816	type	True	98.0017	624	683	95	conclusive
Bifidobacterium longum subsp. infantis	strain=NCTC11817	GCA_900637215.1	1682	216816	type	True	97.9704	628	683	95	conclusive
Bifidobacterium longum subsp. infantis	strain=JCM 1222	GCA_000269965.1	1682	216816	type	True	97.9553	630	683	95	conclusive
Bifidobacterium longum subsp. suillum	strain=JCM 19995	GCA_017132755.1	1931217	216816	type	True	95.8427	553	683	95	conclusive
Bifidobacterium longum subsp. suillum	strain=SU-851	GCA_016882605.1	1931217	216816	type	True	95.7727	550	683	95	conclusive
Bifidobacterium longum subsp. suis	strain=DSM 20211	GCA_000771285.1	1695	216816	type	True	95.4109	547	683	95	conclusive
Bifidobacterium longum	strain=NCTC11818	GCA_900637335.1	216816	216816	type	True	94.915	522	683	95	below_threshold
Bifidobacterium longum subsp. longum	strain=JCM 1217	GCA_000196555.1	1679	216816	type	True	94.8871	523	683	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	83.8188	452	683	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.4944	352	683	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	78.8419	193	683	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.6875	126	683	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.1648	58	683	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:06:27,075] [INFO] DFAST Taxonomy check result was written to GCA_022739915.1_ASM2273991v1_genomic.fna/tc_result.tsv
[2023-06-13 14:06:27,076] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:06:27,076] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:06:27,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcf92774-0053-4ff7-82fe-444b1e8aa353/dqc_reference/checkm_data
[2023-06-13 14:06:27,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:06:27,109] [INFO] Task started: CheckM
[2023-06-13 14:06:27,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022739915.1_ASM2273991v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022739915.1_ASM2273991v1_genomic.fna/checkm_input GCA_022739915.1_ASM2273991v1_genomic.fna/checkm_result
[2023-06-13 14:06:55,119] [INFO] Task succeeded: CheckM
[2023-06-13 14:06:55,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 2.89%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 14:06:55,150] [INFO] ===== Completeness check finished =====
[2023-06-13 14:06:55,151] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:06:55,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022739915.1_ASM2273991v1_genomic.fna/markers.fasta)
[2023-06-13 14:06:55,152] [INFO] Task started: Blastn
[2023-06-13 14:06:55,152] [INFO] Running command: blastn -query GCA_022739915.1_ASM2273991v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf92774-0053-4ff7-82fe-444b1e8aa353/dqc_reference/reference_markers_gtdb.fasta -out GCA_022739915.1_ASM2273991v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:06:56,551] [INFO] Task succeeded: Blastn
[2023-06-13 14:06:56,555] [INFO] Selected 9 target genomes.
[2023-06-13 14:06:56,555] [INFO] Target genome list was writen to GCA_022739915.1_ASM2273991v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:06:56,556] [INFO] Task started: fastANI
[2023-06-13 14:06:56,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg558ef862-33a6-4def-8a2f-a96deed1b12b/GCA_022739915.1_ASM2273991v1_genomic.fna.gz --refList GCA_022739915.1_ASM2273991v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022739915.1_ASM2273991v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:07:01,739] [INFO] Task succeeded: fastANI
[2023-06-13 14:07:01,752] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:07:01,753] [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_000269965.1	s__Bifidobacterium infantis	97.9553	630	683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.68	97.44	0.91	0.82	49	conclusive
GCF_000196555.1	s__Bifidobacterium longum	94.9154	522	683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.53	95.59	0.86	0.67	481	-
GCF_001025175.1	s__Bifidobacterium breve	86.3655	485	683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.58	97.75	0.90	0.86	170	-
GCF_003129905.1	s__Bifidobacterium callitrichidarum	83.8142	444	683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555355.1	s__Bifidobacterium sp018555355	83.6448	462	683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.26	96.26	0.85	0.85	2	-
GCF_000741695.1	s__Bifidobacterium reuteri	83.0163	418	683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.43	97.71	0.91	0.87	9	-
GCF_002259745.1	s__Bifidobacterium myosotis	83.004	435	683	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.86	96.74	0.90	0.89	3	-
GCF_012932425.1	s__Bifidobacterium sp012932425	81.2455	343	683	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 14:07:01,755] [INFO] GTDB search result was written to GCA_022739915.1_ASM2273991v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:07:01,755] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:07:01,761] [INFO] DFAST_QC result json was written to GCA_022739915.1_ASM2273991v1_genomic.fna/dqc_result.json
[2023-06-13 14:07:01,762] [INFO] DFAST_QC completed!
[2023-06-13 14:07:01,762] [INFO] Total running time: 0h0m52s