[2024-01-25 17:50:35,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:35,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:35,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg31606573-364b-45ea-9393-62483d7ea0be/dqc_reference
[2024-01-25 17:50:36,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:36,682] [INFO] Task started: Prodigal
[2024-01-25 17:50:36,682] [INFO] Running command: gunzip -c /var/lib/cwl/stge2425f02-b205-4bd2-bf28-2a1869d77a82/GCF_002259705.1_ASM225970v1_genomic.fna.gz | prodigal -d GCF_002259705.1_ASM225970v1_genomic.fna/cds.fna -a GCF_002259705.1_ASM225970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:41,213] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:41,213] [INFO] Task started: HMMsearch
[2024-01-25 17:50:41,213] [INFO] Running command: hmmsearch --tblout GCF_002259705.1_ASM225970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31606573-364b-45ea-9393-62483d7ea0be/dqc_reference/reference_markers.hmm GCF_002259705.1_ASM225970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:41,389] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:41,390] [INFO] Found 6/6 markers.
[2024-01-25 17:50:41,409] [INFO] Query marker FASTA was written to GCF_002259705.1_ASM225970v1_genomic.fna/markers.fasta
[2024-01-25 17:50:41,410] [INFO] Task started: Blastn
[2024-01-25 17:50:41,410] [INFO] Running command: blastn -query GCF_002259705.1_ASM225970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31606573-364b-45ea-9393-62483d7ea0be/dqc_reference/reference_markers.fasta -out GCF_002259705.1_ASM225970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:41,985] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:41,989] [INFO] Selected 29 target genomes.
[2024-01-25 17:50:41,989] [INFO] Target genome list was writen to GCF_002259705.1_ASM225970v1_genomic.fna/target_genomes.txt
[2024-01-25 17:50:42,001] [INFO] Task started: fastANI
[2024-01-25 17:50:42,002] [INFO] Running command: fastANI --query /var/lib/cwl/stge2425f02-b205-4bd2-bf28-2a1869d77a82/GCF_002259705.1_ASM225970v1_genomic.fna.gz --refList GCF_002259705.1_ASM225970v1_genomic.fna/target_genomes.txt --output GCF_002259705.1_ASM225970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:50:57,148] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:57,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31606573-364b-45ea-9393-62483d7ea0be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:50:57,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31606573-364b-45ea-9393-62483d7ea0be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:50:57,157] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:50:57,157] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:50:57,157] [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
Alloscardovia macacae	strain=DSM 24762	GCA_002259705.1	1160091	1160091	type	True	100.0	622	622	95	conclusive
Alloscardovia theropitheci	strain=GLDI4/2	GCA_004332295.1	2496842	2496842	type	True	79.301	99	622	95	below_threshold
Alloscardovia omnicolens	strain=DSM 21503	GCA_000420505.1	419015	419015	type	True	78.5319	109	622	95	below_threshold
Bifidobacterium simiiventris	strain=81T8	GCA_019331715.1	2834434	2834434	type	True	76.8247	58	622	95	below_threshold
Bifidobacterium saimiriisciurei	strain=SMA1	GCA_010667655.1	2661627	2661627	type	True	76.8165	64	622	95	below_threshold
Bifidobacterium castoris	strain=2020B	GCA_003952025.1	2306972	2306972	type	True	76.7428	55	622	95	below_threshold
Bifidobacterium primatium	strain=TRE 1	GCA_002802875.1	2045438	2045438	type	True	76.721	65	622	95	below_threshold
Pseudoscardovia radai	strain=DSM 24742	GCA_002259605.1	987066	987066	type	True	76.6716	55	622	95	below_threshold
Bifidobacterium simiarum	strain=TRI 7	GCA_002802905.1	2045441	2045441	type	True	76.4643	63	622	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	76.4524	52	622	95	below_threshold
Bifidobacterium merycicum	strain=DSM 6492	GCA_900129045.1	78345	78345	type	True	76.3376	59	622	95	below_threshold
Bifidobacterium saguinibicoloris	strain=79T10	GCA_019331725.1	2834433	2834433	type	True	76.3303	65	622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:50:57,159] [INFO] DFAST Taxonomy check result was written to GCF_002259705.1_ASM225970v1_genomic.fna/tc_result.tsv
[2024-01-25 17:50:57,159] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:50:57,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:50:57,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31606573-364b-45ea-9393-62483d7ea0be/dqc_reference/checkm_data
[2024-01-25 17:50:57,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:50:57,183] [INFO] Task started: CheckM
[2024-01-25 17:50:57,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002259705.1_ASM225970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002259705.1_ASM225970v1_genomic.fna/checkm_input GCF_002259705.1_ASM225970v1_genomic.fna/checkm_result
[2024-01-25 17:51:15,409] [INFO] Task succeeded: CheckM
[2024-01-25 17:51:15,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:51:15,425] [INFO] ===== Completeness check finished =====
[2024-01-25 17:51:15,425] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:51:15,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002259705.1_ASM225970v1_genomic.fna/markers.fasta)
[2024-01-25 17:51:15,425] [INFO] Task started: Blastn
[2024-01-25 17:51:15,425] [INFO] Running command: blastn -query GCF_002259705.1_ASM225970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31606573-364b-45ea-9393-62483d7ea0be/dqc_reference/reference_markers_gtdb.fasta -out GCF_002259705.1_ASM225970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:16,218] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:16,221] [INFO] Selected 23 target genomes.
[2024-01-25 17:51:16,221] [INFO] Target genome list was writen to GCF_002259705.1_ASM225970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:51:16,234] [INFO] Task started: fastANI
[2024-01-25 17:51:16,234] [INFO] Running command: fastANI --query /var/lib/cwl/stge2425f02-b205-4bd2-bf28-2a1869d77a82/GCF_002259705.1_ASM225970v1_genomic.fna.gz --refList GCF_002259705.1_ASM225970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002259705.1_ASM225970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:51:26,474] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:26,483] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:51:26,484] [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_002259705.1	s__Alloscardovia macacae	100.0	622	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	96.29	96.25	0.92	0.91	3	conclusive
GCF_004332295.1	s__Alloscardovia theropitheci	79.301	99	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376885.1	s__Alloscardovia criceti	79.0081	129	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420505.1	s__Alloscardovia omnicolens	78.5319	109	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Alloscardovia	95.0	98.68	97.50	0.93	0.88	12	-
GCF_012932365.1	s__Bifidobacterium sp012932365	77.0348	63	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299475.1	s__Bifidobacterium avesanii	76.8896	63	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010667655.1	s__Galliscardovia saimiriisciurei	76.8165	64	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003952025.1	s__Bifidobacterium castoris	76.7428	55	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000741135.1	s__Bifidobacterium choerinum	76.7381	52	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.70	99.15	0.96	0.91	4	-
GCF_002802875.1	s__Galliscardovia primatium	76.721	65	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002259605.1	s__Pseudoscardovia radai	76.6716	55	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802905.1	s__Galliscardovia simiarum	76.4643	63	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia	95.0	98.16	98.16	0.94	0.94	2	-
GCF_008698145.1	s__Bifidobacterium vespertilionis	76.4323	58	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.94	97.88	0.96	0.92	3	-
GCF_018555635.1	s__Bifidobacterium sp018555635	76.1601	67	622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:51:26,485] [INFO] GTDB search result was written to GCF_002259705.1_ASM225970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:51:26,486] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:51:26,488] [INFO] DFAST_QC result json was written to GCF_002259705.1_ASM225970v1_genomic.fna/dqc_result.json
[2024-01-25 17:51:26,489] [INFO] DFAST_QC completed!
[2024-01-25 17:51:26,489] [INFO] Total running time: 0h0m51s