[2023-06-13 09:49:02,743] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:49:02,746] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:49:02,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd94273f-aedb-4ea6-9edd-3a1bcf1707b8/dqc_reference
[2023-06-13 09:49:04,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:49:04,091] [INFO] Task started: Prodigal
[2023-06-13 09:49:04,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgaef6661f-c936-4cb9-a8df-7ce1f7795e28/GCA_022722575.1_ASM2272257v1_genomic.fna.gz | prodigal -d GCA_022722575.1_ASM2272257v1_genomic.fna/cds.fna -a GCA_022722575.1_ASM2272257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:49:10,228] [INFO] Task succeeded: Prodigal
[2023-06-13 09:49:10,228] [INFO] Task started: HMMsearch
[2023-06-13 09:49:10,228] [INFO] Running command: hmmsearch --tblout GCA_022722575.1_ASM2272257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd94273f-aedb-4ea6-9edd-3a1bcf1707b8/dqc_reference/reference_markers.hmm GCA_022722575.1_ASM2272257v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:49:10,475] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:49:10,477] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaef6661f-c936-4cb9-a8df-7ce1f7795e28/GCA_022722575.1_ASM2272257v1_genomic.fna.gz]
[2023-06-13 09:49:10,502] [INFO] Query marker FASTA was written to GCA_022722575.1_ASM2272257v1_genomic.fna/markers.fasta
[2023-06-13 09:49:10,503] [INFO] Task started: Blastn
[2023-06-13 09:49:10,503] [INFO] Running command: blastn -query GCA_022722575.1_ASM2272257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd94273f-aedb-4ea6-9edd-3a1bcf1707b8/dqc_reference/reference_markers.fasta -out GCA_022722575.1_ASM2272257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:11,250] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:11,255] [INFO] Selected 10 target genomes.
[2023-06-13 09:49:11,256] [INFO] Target genome list was writen to GCA_022722575.1_ASM2272257v1_genomic.fna/target_genomes.txt
[2023-06-13 09:49:11,259] [INFO] Task started: fastANI
[2023-06-13 09:49:11,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef6661f-c936-4cb9-a8df-7ce1f7795e28/GCA_022722575.1_ASM2272257v1_genomic.fna.gz --refList GCA_022722575.1_ASM2272257v1_genomic.fna/target_genomes.txt --output GCA_022722575.1_ASM2272257v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:49:16,469] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:16,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd94273f-aedb-4ea6-9edd-3a1bcf1707b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:49:16,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd94273f-aedb-4ea6-9edd-3a1bcf1707b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:49:16,483] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2023-06-13 09:49:16,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 09:49:16,483] [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 bifidum	strain=NCTC13001	GCA_900637095.1	1681	1681	type	True	99.138	583	602	95	conclusive
Bifidobacterium bifidum	strain=LMG 11041	GCA_000741085.1	1681	1681	type	True	99.1237	586	602	95	conclusive
Bifidobacterium bifidum	strain=JCM 1255	GCA_001025135.1	1681	1681	type	True	99.106	584	602	95	conclusive
Bifidobacterium bifidum	strain=ATCC 29521	GCA_000466525.1	1681	1681	type	True	99.0578	583	602	95	conclusive
Bifidobacterium bifidum	strain=DSM 20456	GCA_000771485.1	1681	1681	type	True	99.0509	574	602	95	conclusive
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.8873	364	602	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.0779	338	602	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.1501	217	602	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.0562	109	602	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.0177	66	602	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:49:16,486] [INFO] DFAST Taxonomy check result was written to GCA_022722575.1_ASM2272257v1_genomic.fna/tc_result.tsv
[2023-06-13 09:49:16,487] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:49:16,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:49:16,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd94273f-aedb-4ea6-9edd-3a1bcf1707b8/dqc_reference/checkm_data
[2023-06-13 09:49:16,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:49:16,513] [INFO] Task started: CheckM
[2023-06-13 09:49:16,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022722575.1_ASM2272257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022722575.1_ASM2272257v1_genomic.fna/checkm_input GCA_022722575.1_ASM2272257v1_genomic.fna/checkm_result
[2023-06-13 09:49:40,904] [INFO] Task succeeded: CheckM
[2023-06-13 09:49:40,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.50%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:49:40,934] [INFO] ===== Completeness check finished =====
[2023-06-13 09:49:40,934] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:49:40,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022722575.1_ASM2272257v1_genomic.fna/markers.fasta)
[2023-06-13 09:49:40,935] [INFO] Task started: Blastn
[2023-06-13 09:49:40,935] [INFO] Running command: blastn -query GCA_022722575.1_ASM2272257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd94273f-aedb-4ea6-9edd-3a1bcf1707b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022722575.1_ASM2272257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:42,016] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:42,032] [INFO] Selected 15 target genomes.
[2023-06-13 09:49:42,032] [INFO] Target genome list was writen to GCA_022722575.1_ASM2272257v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:49:42,037] [INFO] Task started: fastANI
[2023-06-13 09:49:42,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef6661f-c936-4cb9-a8df-7ce1f7795e28/GCA_022722575.1_ASM2272257v1_genomic.fna.gz --refList GCA_022722575.1_ASM2272257v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022722575.1_ASM2272257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:49:49,957] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:49,975] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:49:49,975] [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_001025135.1	s__Bifidobacterium bifidum	99.106	584	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.04	98.27	0.95	0.91	128	conclusive
GCF_009193355.1	s__Bifidobacterium leontopitheci	82.8836	452	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667645.1	s__Bifidobacterium platyrrhinorum	82.0376	343	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042635.1	s__Bifidobacterium scardovii	82.0037	394	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_009299505.1	s__Bifidobacterium ramosum	81.8934	374	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010667685.1	s__Bifidobacterium aerophilum	81.7894	379	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018555335.1	s__Bifidobacterium sp018555335	81.6321	356	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952945.1	s__Bifidobacterium samirii	81.6296	343	602	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	81.593	357	602	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	81.5427	356	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741165.1	s__Bifidobacterium biavatii	81.542	367	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_018555385.1	s__Bifidobacterium sp018555385	81.5147	362	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009078285.1	s__Bifidobacterium jacchi	81.1107	361	602	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	80.8382	282	602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_003951095.1	s__Bifidobacterium goeldii	80.3102	232	602	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 09:49:49,977] [INFO] GTDB search result was written to GCA_022722575.1_ASM2272257v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:49:49,978] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:49:49,981] [INFO] DFAST_QC result json was written to GCA_022722575.1_ASM2272257v1_genomic.fna/dqc_result.json
[2023-06-13 09:49:49,981] [INFO] DFAST_QC completed!
[2023-06-13 09:49:49,981] [INFO] Total running time: 0h0m47s