[2024-01-24 15:02:33,920] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg6277990e-8571-406c-af0e-134240a1689f/dqc_reference
[2024-01-24 15:02:35,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:35,206] [INFO] Task started: Prodigal
[2024-01-24 15:02:35,206] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f9c5904-a694-48d6-bb19-3f90829ad449/GCF_003788975.1_ASM378897v1_genomic.fna.gz | prodigal -d GCF_003788975.1_ASM378897v1_genomic.fna/cds.fna -a GCF_003788975.1_ASM378897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:45,725] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:45,725] [INFO] Task started: HMMsearch
[2024-01-24 15:02:45,725] [INFO] Running command: hmmsearch --tblout GCF_003788975.1_ASM378897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6277990e-8571-406c-af0e-134240a1689f/dqc_reference/reference_markers.hmm GCF_003788975.1_ASM378897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:45,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:45,994] [INFO] Found 6/6 markers.
[2024-01-24 15:02:46,022] [INFO] Query marker FASTA was written to GCF_003788975.1_ASM378897v1_genomic.fna/markers.fasta
[2024-01-24 15:02:46,023] [INFO] Task started: Blastn
[2024-01-24 15:02:46,023] [INFO] Running command: blastn -query GCF_003788975.1_ASM378897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6277990e-8571-406c-af0e-134240a1689f/dqc_reference/reference_markers.fasta -out GCF_003788975.1_ASM378897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:46,843] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:46,846] [INFO] Selected 9 target genomes.
[2024-01-24 15:02:46,847] [INFO] Target genome list was writen to GCF_003788975.1_ASM378897v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:46,851] [INFO] Task started: fastANI
[2024-01-24 15:02:46,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f9c5904-a694-48d6-bb19-3f90829ad449/GCF_003788975.1_ASM378897v1_genomic.fna.gz --refList GCF_003788975.1_ASM378897v1_genomic.fna/target_genomes.txt --output GCF_003788975.1_ASM378897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:54,714] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:54,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6277990e-8571-406c-af0e-134240a1689f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:54,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6277990e-8571-406c-af0e-134240a1689f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:54,724] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:54,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:54,725] [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
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	100.0	1068	1070	95	conclusive
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	99.9971	1070	1070	95	conclusive
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	93.4538	870	1070	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	85.0947	681	1070	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	84.9826	689	1070	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	83.8581	617	1070	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	83.7881	620	1070	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	83.7214	627	1070	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	83.7084	648	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:54,726] [INFO] DFAST Taxonomy check result was written to GCF_003788975.1_ASM378897v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:54,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:54,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:54,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6277990e-8571-406c-af0e-134240a1689f/dqc_reference/checkm_data
[2024-01-24 15:02:54,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:54,765] [INFO] Task started: CheckM
[2024-01-24 15:02:54,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003788975.1_ASM378897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003788975.1_ASM378897v1_genomic.fna/checkm_input GCF_003788975.1_ASM378897v1_genomic.fna/checkm_result
[2024-01-24 15:03:28,835] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:28,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:28,865] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:28,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:28,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003788975.1_ASM378897v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:28,867] [INFO] Task started: Blastn
[2024-01-24 15:03:28,867] [INFO] Running command: blastn -query GCF_003788975.1_ASM378897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6277990e-8571-406c-af0e-134240a1689f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003788975.1_ASM378897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:30,318] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:30,322] [INFO] Selected 12 target genomes.
[2024-01-24 15:03:30,323] [INFO] Target genome list was writen to GCF_003788975.1_ASM378897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:30,331] [INFO] Task started: fastANI
[2024-01-24 15:03:30,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f9c5904-a694-48d6-bb19-3f90829ad449/GCF_003788975.1_ASM378897v1_genomic.fna.gz --refList GCF_003788975.1_ASM378897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003788975.1_ASM378897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:40,755] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:40,773] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:40,773] [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_900199375.1	s__Gordonibacter urolithinfaciens	99.9971	1070	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	conclusive
GCF_000210055.1	s__Gordonibacter pamelaeae	93.4688	869	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
GCA_900170005.1	s__Gordonibacter massiliensis	86.9815	852	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.56	97.12	0.94	0.89	3	-
GCF_003339845.1	s__Gordonibacter sp003339845	86.8649	818	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902386925.1	s__Arabia massiliensis	85.2327	657	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900184265.1	s__Eggerthella timonensis	85.0719	683	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834925.2	s__Eggerthella sp014287365	85.0532	684	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_002899715.1	s__Enteroscipio rubneri	84.2369	529	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Enteroscipio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000024265.1	s__Eggerthella lenta	83.7559	626	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_003339815.1	s__Eggerthella sinensis	83.713	647	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCA_019113915.1	s__Gordonibacter avicola	81.736	575	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420215.1	s__CAJFUR01 sp904420215	81.2251	395	1070	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAJFUR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:40,775] [INFO] GTDB search result was written to GCF_003788975.1_ASM378897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:40,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:40,779] [INFO] DFAST_QC result json was written to GCF_003788975.1_ASM378897v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:40,779] [INFO] DFAST_QC completed!
[2024-01-24 15:03:40,779] [INFO] Total running time: 0h1m7s