[2024-01-24 11:44:23,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,775] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,776] [INFO] DQC Reference Directory: /var/lib/cwl/stge0765dde-af70-4e33-ba02-04b3cc692ca9/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/stg35b93623-fd45-410e-826c-c22e89f55cb1/GCF_024741235.1_ASM2474123v1_genomic.fna.gz | prodigal -d GCF_024741235.1_ASM2474123v1_genomic.fna/cds.fna -a GCF_024741235.1_ASM2474123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:34,512] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:34,513] [INFO] Task started: HMMsearch
[2024-01-24 11:44:34,513] [INFO] Running command: hmmsearch --tblout GCF_024741235.1_ASM2474123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0765dde-af70-4e33-ba02-04b3cc692ca9/dqc_reference/reference_markers.hmm GCF_024741235.1_ASM2474123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,753] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,781] [INFO] Query marker FASTA was written to GCF_024741235.1_ASM2474123v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,782] [INFO] Task started: Blastn
[2024-01-24 11:44:34,782] [INFO] Running command: blastn -query GCF_024741235.1_ASM2474123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0765dde-af70-4e33-ba02-04b3cc692ca9/dqc_reference/reference_markers.fasta -out GCF_024741235.1_ASM2474123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,424] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,428] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:35,428] [INFO] Target genome list was writen to GCF_024741235.1_ASM2474123v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:35,469] [INFO] Task started: fastANI
[2024-01-24 11:44:35,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg35b93623-fd45-410e-826c-c22e89f55cb1/GCF_024741235.1_ASM2474123v1_genomic.fna.gz --refList GCF_024741235.1_ASM2474123v1_genomic.fna/target_genomes.txt --output GCF_024741235.1_ASM2474123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:41,760] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:41,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0765dde-af70-4e33-ba02-04b3cc692ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:41,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0765dde-af70-4e33-ba02-04b3cc692ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:41,778] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:41,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:41,778] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.891	311	813	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.8594	306	813	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.6888	266	813	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.6135	295	813	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.4644	261	813	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.1815	232	813	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	79.0595	250	813	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	79.0173	234	813	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.9018	243	813	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	78.4482	142	813	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	77.959	177	813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,780] [INFO] DFAST Taxonomy check result was written to GCF_024741235.1_ASM2474123v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:41,781] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:41,781] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:41,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0765dde-af70-4e33-ba02-04b3cc692ca9/dqc_reference/checkm_data
[2024-01-24 11:44:41,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:41,809] [INFO] Task started: CheckM
[2024-01-24 11:44:41,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024741235.1_ASM2474123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024741235.1_ASM2474123v1_genomic.fna/checkm_input GCF_024741235.1_ASM2474123v1_genomic.fna/checkm_result
[2024-01-24 11:45:09,596] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:09,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:09,619] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:09,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:09,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024741235.1_ASM2474123v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:09,620] [INFO] Task started: Blastn
[2024-01-24 11:45:09,620] [INFO] Running command: blastn -query GCF_024741235.1_ASM2474123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0765dde-af70-4e33-ba02-04b3cc692ca9/dqc_reference/reference_markers_gtdb.fasta -out GCF_024741235.1_ASM2474123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:10,647] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:10,651] [INFO] Selected 9 target genomes.
[2024-01-24 11:45:10,651] [INFO] Target genome list was writen to GCF_024741235.1_ASM2474123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:10,658] [INFO] Task started: fastANI
[2024-01-24 11:45:10,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg35b93623-fd45-410e-826c-c22e89f55cb1/GCF_024741235.1_ASM2474123v1_genomic.fna.gz --refList GCF_024741235.1_ASM2474123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024741235.1_ASM2474123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:16,198] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:16,210] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:16,211] [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
GCA_900768455.1	s__Tractidigestivibacter sp900768455	97.5295	571	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	97.35	97.35	0.93	0.93	2	conclusive
GCA_000752675.2	s__Tractidigestivibacter sp000752675	94.9812	697	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCA_902834555.1	s__Tractidigestivibacter sp902834555	92.649	651	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900770865.1	s__Tractidigestivibacter sp900770865	92.2237	430	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773995.1	s__Tractidigestivibacter sp902773995	91.8743	589	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.13	97.55	0.87	0.83	4	-
GCF_001494635.1	s__Tractidigestivibacter scatoligenes	91.101	626	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119625.1	s__Tractidigestivibacter sp900119625	90.7261	629	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	96.91	96.91	0.78	0.78	2	-
GCF_900111695.1	s__Tractidigestivibacter sp900111695	88.5127	638	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557505.1	s__Tractidigestivibacter sp004557505	86.434	558	813	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:16,212] [INFO] GTDB search result was written to GCF_024741235.1_ASM2474123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:16,213] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:16,216] [INFO] DFAST_QC result json was written to GCF_024741235.1_ASM2474123v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:16,216] [INFO] DFAST_QC completed!
[2024-01-24 11:45:16,216] [INFO] Total running time: 0h0m52s