[2024-01-24 15:18:27,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,480] [INFO] DQC Reference Directory: /var/lib/cwl/stgecbddd31-47fb-4d88-92c0-ef4496d21ca6/dqc_reference
[2024-01-24 15:18:28,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,819] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg962f6314-8a1f-4cc9-8d03-73ca921a4d4d/GCF_002802905.1_ASM280290v1_genomic.fna.gz | prodigal -d GCF_002802905.1_ASM280290v1_genomic.fna/cds.fna -a GCF_002802905.1_ASM280290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:37,880] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:37,880] [INFO] Task started: HMMsearch
[2024-01-24 15:18:37,881] [INFO] Running command: hmmsearch --tblout GCF_002802905.1_ASM280290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecbddd31-47fb-4d88-92c0-ef4496d21ca6/dqc_reference/reference_markers.hmm GCF_002802905.1_ASM280290v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:38,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:38,226] [INFO] Found 6/6 markers.
[2024-01-24 15:18:38,270] [INFO] Query marker FASTA was written to GCF_002802905.1_ASM280290v1_genomic.fna/markers.fasta
[2024-01-24 15:18:38,271] [INFO] Task started: Blastn
[2024-01-24 15:18:38,271] [INFO] Running command: blastn -query GCF_002802905.1_ASM280290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecbddd31-47fb-4d88-92c0-ef4496d21ca6/dqc_reference/reference_markers.fasta -out GCF_002802905.1_ASM280290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:39,470] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:39,473] [INFO] Selected 17 target genomes.
[2024-01-24 15:18:39,474] [INFO] Target genome list was writen to GCF_002802905.1_ASM280290v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:39,505] [INFO] Task started: fastANI
[2024-01-24 15:18:39,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg962f6314-8a1f-4cc9-8d03-73ca921a4d4d/GCF_002802905.1_ASM280290v1_genomic.fna.gz --refList GCF_002802905.1_ASM280290v1_genomic.fna/target_genomes.txt --output GCF_002802905.1_ASM280290v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:49,892] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:49,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecbddd31-47fb-4d88-92c0-ef4496d21ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:49,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecbddd31-47fb-4d88-92c0-ef4496d21ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:49,909] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:49,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:49,910] [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 simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	100.0	895	895	95	conclusive
Bifidobacterium margollesii	strain=Uis1B	GCA_002860355.1	2020964	2020964	type	True	87.0669	671	895	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	84.8833	564	895	95	below_threshold
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	84.8433	569	895	95	below_threshold
Bifidobacterium vansinderenii	strain=Tam10B	GCA_002234915.1	1984871	1984871	type	True	84.0437	544	895	95	below_threshold
Bifidobacterium callimiconis	strain=2028B	GCA_003952005.1	2306973	2306973	type	True	83.8186	539	895	95	below_threshold
Bifidobacterium tissieri	strain=DSM 100201	GCA_002259645.1	1630162	1630162	type	True	82.9335	489	895	95	below_threshold
Bifidobacterium avesanii	strain=TREC	GCA_010667745.1	1798157	1798157	type	True	82.4918	413	895	95	below_threshold
Bifidobacterium avesanii	strain=DSM 100685	GCA_009299475.1	1798157	1798157	type	True	82.4715	421	895	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_000770985.1	158787	158787	type	True	81.7629	392	895	95	below_threshold
Bifidobacterium amazonense	strain=MA1	GCA_018555435.2	2809027	2809027	type	True	81.7402	413	895	95	below_threshold
Bifidobacterium scardovii	strain=DSM 13734	GCA_001005065.1	158787	158787	type	True	81.7387	401	895	95	below_threshold
Bifidobacterium miconisargentati	strain=82T25	GCA_019331675.1	2834437	2834437	type	True	81.7141	425	895	95	below_threshold
Bifidobacterium samirii	strain=2033B	GCA_003952945.1	2306974	2306974	type	True	81.3413	373	895	95	below_threshold
Bifidobacterium pseudolongum subsp. pseudolongum	strain=ATCC 25526	GCA_022691205.1	31954	1694	type	True	79.6443	247	895	95	below_threshold
Bifidobacterium mizhiense	strain=S053-2	GCA_020884755.1	2879940	2879940	type	True	78.1818	172	895	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.1177	109	895	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:49,918] [INFO] DFAST Taxonomy check result was written to GCF_002802905.1_ASM280290v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:49,919] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:49,919] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:49,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecbddd31-47fb-4d88-92c0-ef4496d21ca6/dqc_reference/checkm_data
[2024-01-24 15:18:49,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:49,984] [INFO] Task started: CheckM
[2024-01-24 15:18:49,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002802905.1_ASM280290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002802905.1_ASM280290v1_genomic.fna/checkm_input GCF_002802905.1_ASM280290v1_genomic.fna/checkm_result
[2024-01-24 15:19:20,030] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:20,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:20,052] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:20,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:20,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002802905.1_ASM280290v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:20,053] [INFO] Task started: Blastn
[2024-01-24 15:19:20,053] [INFO] Running command: blastn -query GCF_002802905.1_ASM280290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecbddd31-47fb-4d88-92c0-ef4496d21ca6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002802905.1_ASM280290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:21,644] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:21,652] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:21,652] [INFO] Target genome list was writen to GCF_002802905.1_ASM280290v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:21,661] [INFO] Task started: fastANI
[2024-01-24 15:19:21,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg962f6314-8a1f-4cc9-8d03-73ca921a4d4d/GCF_002802905.1_ASM280290v1_genomic.fna.gz --refList GCF_002802905.1_ASM280290v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002802905.1_ASM280290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:30,135] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:30,151] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:30,151] [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_002802905.1	s__Galliscardovia simiarum	100.0	895	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	conclusive
GCF_002860355.1	s__Galliscardovia margollesii	87.0369	673	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	84.87	562	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002802875.1	s__Galliscardovia primatium	84.8257	570	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234915.1	s__Galliscardovia vansinderenii	84.0395	544	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952005.1	s__Galliscardovia callimiconis	83.8226	539	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.12	98.12	0.92	0.92	2	-
GCF_003129925.1	s__Galliscardovia catulorum	83.7719	472	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259645.1	s__Galliscardovia tissieri	82.9335	489	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	96.74	96.02	0.89	0.88	4	-
GCF_009299475.1	s__Bifidobacterium avesanii	82.5283	420	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012932365.1	s__Bifidobacterium sp012932365	82.1939	427	895	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	82.1455	435	895	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	81.6887	404	895	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.51	98.97	0.97	0.93	7	-
GCF_003952945.1	s__Bifidobacterium samirii	81.3158	375	895	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 15:19:30,153] [INFO] GTDB search result was written to GCF_002802905.1_ASM280290v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:30,153] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:30,157] [INFO] DFAST_QC result json was written to GCF_002802905.1_ASM280290v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:30,157] [INFO] DFAST_QC completed!
[2024-01-24 15:19:30,157] [INFO] Total running time: 0h1m3s