[2024-01-24 15:27:41,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg43c11b0a-648a-4535-a07e-2e079fadb0dc/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,884] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ff732a6-7829-4477-9131-24e760568325/GCF_019331775.1_ASM1933177v1_genomic.fna.gz | prodigal -d GCF_019331775.1_ASM1933177v1_genomic.fna/cds.fna -a GCF_019331775.1_ASM1933177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:51,765] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:51,765] [INFO] Task started: HMMsearch
[2024-01-24 15:27:51,765] [INFO] Running command: hmmsearch --tblout GCF_019331775.1_ASM1933177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43c11b0a-648a-4535-a07e-2e079fadb0dc/dqc_reference/reference_markers.hmm GCF_019331775.1_ASM1933177v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:52,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:52,004] [INFO] Found 6/6 markers.
[2024-01-24 15:27:52,029] [INFO] Query marker FASTA was written to GCF_019331775.1_ASM1933177v1_genomic.fna/markers.fasta
[2024-01-24 15:27:52,030] [INFO] Task started: Blastn
[2024-01-24 15:27:52,030] [INFO] Running command: blastn -query GCF_019331775.1_ASM1933177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43c11b0a-648a-4535-a07e-2e079fadb0dc/dqc_reference/reference_markers.fasta -out GCF_019331775.1_ASM1933177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:53,254] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:53,257] [INFO] Selected 20 target genomes.
[2024-01-24 15:27:53,257] [INFO] Target genome list was writen to GCF_019331775.1_ASM1933177v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:53,287] [INFO] Task started: fastANI
[2024-01-24 15:27:53,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff732a6-7829-4477-9131-24e760568325/GCF_019331775.1_ASM1933177v1_genomic.fna.gz --refList GCF_019331775.1_ASM1933177v1_genomic.fna/target_genomes.txt --output GCF_019331775.1_ASM1933177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:04,142] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:04,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43c11b0a-648a-4535-a07e-2e079fadb0dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:04,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43c11b0a-648a-4535-a07e-2e079fadb0dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:04,162] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:04,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:04,162] [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 phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	100.0	874	876	95	conclusive
Bifidobacterium pullorum subsp. gallinarum	strain=DSM 20670	GCA_000771505.1	78344	78448	type	True	85.0019	520	876	95	below_threshold
Bifidobacterium pullorum subsp. saeculare	strain=LMG 14934	GCA_000741375.1	78257	78448	type	True	84.8886	542	876	95	below_threshold
Bifidobacterium pullorum subsp. saeculare	strain=DSM 6531	GCA_000770965.1	78257	78448	type	True	84.8835	542	876	95	below_threshold
Bifidobacterium pullorum subsp. gallinarum	strain=LMG 11586	GCA_000741215.1	78344	78448	type	True	84.8585	524	876	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	83.2312	471	876	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	83.2038	465	876	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	83.1236	471	876	95	below_threshold
Bifidobacterium scardovii	strain=JCM 12489	GCA_001042635.1	158787	158787	type	True	83.1102	470	876	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	82.9196	448	876	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	82.8938	469	876	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	82.5978	466	876	95	below_threshold
Bifidobacterium stellenboschense	strain=DSM 23968	GCA_000741785.1	762211	762211	type	True	82.471	438	876	95	below_threshold
Bifidobacterium parmae	strain=Uis4E	GCA_002860365.1	361854	361854	type	True	82.4426	445	876	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	82.0185	426	876	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.8447	440	876	95	below_threshold
Bifidobacterium italicum	strain=Rab10A	GCA_002286915.1	1960968	1960968	type	True	81.6881	365	876	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	80.4797	304	876	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.5087	177	876	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.4424	215	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:04,164] [INFO] DFAST Taxonomy check result was written to GCF_019331775.1_ASM1933177v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:04,164] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:04,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:04,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43c11b0a-648a-4535-a07e-2e079fadb0dc/dqc_reference/checkm_data
[2024-01-24 15:28:04,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:04,196] [INFO] Task started: CheckM
[2024-01-24 15:28:04,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019331775.1_ASM1933177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019331775.1_ASM1933177v1_genomic.fna/checkm_input GCF_019331775.1_ASM1933177v1_genomic.fna/checkm_result
[2024-01-24 15:28:32,609] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:32,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:32,633] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:32,634] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:32,636] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019331775.1_ASM1933177v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:32,636] [INFO] Task started: Blastn
[2024-01-24 15:28:32,637] [INFO] Running command: blastn -query GCF_019331775.1_ASM1933177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43c11b0a-648a-4535-a07e-2e079fadb0dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_019331775.1_ASM1933177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:34,551] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:34,555] [INFO] Selected 14 target genomes.
[2024-01-24 15:28:34,555] [INFO] Target genome list was writen to GCF_019331775.1_ASM1933177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:34,567] [INFO] Task started: fastANI
[2024-01-24 15:28:34,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff732a6-7829-4477-9131-24e760568325/GCF_019331775.1_ASM1933177v1_genomic.fna.gz --refList GCF_019331775.1_ASM1933177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019331775.1_ASM1933177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:42,470] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:42,483] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:28:42,484] [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_000741215.1	s__Bifidobacterium pullorum_B	84.8778	523	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.16	95.67	0.87	0.83	17	-
GCF_000771405.1	s__Bifidobacterium pullorum	84.8115	526	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_003952945.1	s__Bifidobacterium samirii	83.1681	476	876	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	83.1108	470	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_016899725.1	s__Bifidobacterium pullorum_C	83.0803	432	876	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	82.9102	448	876	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	82.851	472	876	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	82.4604	444	876	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	82.435	440	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193355.1	s__Bifidobacterium leontopitheci	82.2547	421	876	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	82.1014	423	876	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	81.8244	427	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898175.1	s__Bifidobacterium lemurum	81.8228	468	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002286915.1	s__Bifidobacterium italicum	81.6502	366	876	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:42,486] [INFO] GTDB search result was written to GCF_019331775.1_ASM1933177v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:42,486] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:42,491] [INFO] DFAST_QC result json was written to GCF_019331775.1_ASM1933177v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:42,491] [INFO] DFAST_QC completed!
[2024-01-24 15:28:42,491] [INFO] Total running time: 0h1m1s