[2024-01-24 11:44:23,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ce7cf54-25be-467e-824d-fb8d101eac1c/dqc_reference
[2024-01-24 11:44:26,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,341] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg75c1f218-c263-4525-af70-1407c00e6553/GCF_000738005.1_ASM73800v1_genomic.fna.gz | prodigal -d GCF_000738005.1_ASM73800v1_genomic.fna/cds.fna -a GCF_000738005.1_ASM73800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:34,228] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:34,228] [INFO] Task started: HMMsearch
[2024-01-24 11:44:34,228] [INFO] Running command: hmmsearch --tblout GCF_000738005.1_ASM73800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ce7cf54-25be-467e-824d-fb8d101eac1c/dqc_reference/reference_markers.hmm GCF_000738005.1_ASM73800v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,472] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,474] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,498] [INFO] Query marker FASTA was written to GCF_000738005.1_ASM73800v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,499] [INFO] Task started: Blastn
[2024-01-24 11:44:34,499] [INFO] Running command: blastn -query GCF_000738005.1_ASM73800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ce7cf54-25be-467e-824d-fb8d101eac1c/dqc_reference/reference_markers.fasta -out GCF_000738005.1_ASM73800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,275] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,278] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:35,278] [INFO] Target genome list was writen to GCF_000738005.1_ASM73800v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:35,301] [INFO] Task started: fastANI
[2024-01-24 11:44:35,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c1f218-c263-4525-af70-1407c00e6553/GCF_000738005.1_ASM73800v1_genomic.fna.gz --refList GCF_000738005.1_ASM73800v1_genomic.fna/target_genomes.txt --output GCF_000738005.1_ASM73800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:44,741] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:44,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ce7cf54-25be-467e-824d-fb8d101eac1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:44,742] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ce7cf54-25be-467e-824d-fb8d101eac1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:44,762] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:44,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:44,762] [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 crudilactis	strain=LMG 23609	GCA_000738005.1	327277	327277	type	True	100.0	785	785	95	conclusive
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_002813205.1	218140	218140	type	True	80.9617	399	785	95	below_threshold
Bifidobacterium psychraerophilum	strain=DSM 22366	GCA_000771565.1	218140	218140	type	True	80.9005	380	785	95	below_threshold
Bifidobacterium psychraerophilum	strain=LMG 21775	GCA_000741705.1	218140	218140	type	True	80.8555	385	785	95	below_threshold
Bifidobacterium aquikefiri	strain=LMG 28769	GCA_002259795.1	1653207	1653207	type	True	78.5471	120	785	95	below_threshold
Bifidobacterium lemurum	strain=DSM 28807	GCA_002259665.1	1603886	1603886	type	True	78.1085	129	785	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_014898155.1	1765219	1765219	type	True	78.0174	140	785	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	77.8652	146	785	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	77.8361	145	785	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	77.8339	143	785	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	77.8338	142	785	95	below_threshold
Bifidobacterium eulemuris	strain=DSM 100216	GCA_002259685.1	1765219	1765219	type	True	77.8124	137	785	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	77.7431	130	785	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	77.678	100	785	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000741165.1	762212	762212	type	True	77.6258	116	785	95	below_threshold
Bifidobacterium actinocoloniiforme	strain=DSM 22766	GCA_000771585.1	638619	638619	type	True	77.5432	91	785	95	below_threshold
Bifidobacterium biavatii	strain=DSM 23969	GCA_000771645.1	762212	762212	type	True	77.4925	120	785	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	77.2684	113	785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:44,764] [INFO] DFAST Taxonomy check result was written to GCF_000738005.1_ASM73800v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:44,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:44,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:44,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ce7cf54-25be-467e-824d-fb8d101eac1c/dqc_reference/checkm_data
[2024-01-24 11:44:44,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:44,791] [INFO] Task started: CheckM
[2024-01-24 11:44:44,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000738005.1_ASM73800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000738005.1_ASM73800v1_genomic.fna/checkm_input GCF_000738005.1_ASM73800v1_genomic.fna/checkm_result
[2024-01-24 11:45:12,928] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:12,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:12,949] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:12,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:12,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000738005.1_ASM73800v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:12,951] [INFO] Task started: Blastn
[2024-01-24 11:45:12,951] [INFO] Running command: blastn -query GCF_000738005.1_ASM73800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ce7cf54-25be-467e-824d-fb8d101eac1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000738005.1_ASM73800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:14,068] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:14,072] [INFO] Selected 25 target genomes.
[2024-01-24 11:45:14,073] [INFO] Target genome list was writen to GCF_000738005.1_ASM73800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:14,091] [INFO] Task started: fastANI
[2024-01-24 11:45:14,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg75c1f218-c263-4525-af70-1407c00e6553/GCF_000738005.1_ASM73800v1_genomic.fna.gz --refList GCF_000738005.1_ASM73800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000738005.1_ASM73800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:24,373] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:24,398] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:24,399] [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_000738005.1	s__Bifidobacterium crudilactis	100.0	785	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	97.51	97.51	0.90	0.90	2	conclusive
GCF_000741705.1	s__Bifidobacterium psychraerophilum	80.8555	385	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000741285.1	s__Bifidobacterium mongoliense	79.2276	151	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.45	98.93	0.93	0.89	3	-
GCF_002259795.1	s__Bifidobacterium aquikefiri	78.5437	119	785	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	78.1692	133	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014898155.1	s__Bifidobacterium eulemuris	78.0174	140	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001042635.1	s__Bifidobacterium scardovii	77.9384	147	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_002802905.1	s__Galliscardovia simiarum	77.8711	147	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_002802875.1	s__Galliscardovia primatium	77.848	147	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000706765.1	s__Bifidobacterium indicum	77.8068	110	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.17	97.45	0.96	0.94	8	-
GCF_009193305.1	s__Bifidobacterium cebidarum	77.7972	119	785	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	77.7418	146	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.70	97.42	0.94	0.89	3	-
GCF_000770925.1	s__Bifidobacterium ruminantium	77.7169	139	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.91	97.77	0.92	0.85	6	-
GCF_001263395.1	s__Bifidobacterium actinocoloniiforme	77.7067	90	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	77.6678	154	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCA_000771265.1	s__Bifidobacterium thermophilum	77.6329	123	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.72	95.35	0.90	0.87	15	-
GCF_000741165.1	s__Bifidobacterium biavatii	77.6315	115	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000522505.1	s__Bifidobacterium moukalabense	77.5992	143	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.37	98.94	0.93	0.88	13	-
GCF_009683175.1	s__Bifidobacterium asteroides_H	77.5378	102	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042595.1	s__Bifidobacterium dentium	77.4653	147	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.95	98.47	0.92	0.86	50	-
GCF_000967265.1	s__Bifidobacterium asteroides_A	77.4539	103	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.98	96.98	0.90	0.90	2	-
GCF_003202755.1	s__Bifidobacterium asteroides_F	77.4408	109	785	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000499285.1	s__Bifidobacterium sp000499285	77.3133	106	785	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 11:45:24,401] [INFO] GTDB search result was written to GCF_000738005.1_ASM73800v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:24,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:24,405] [INFO] DFAST_QC result json was written to GCF_000738005.1_ASM73800v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:24,406] [INFO] DFAST_QC completed!
[2024-01-24 11:45:24,406] [INFO] Total running time: 0h1m1s