[2024-01-25 18:13:20,583] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e1f4d49-8fc6-41db-9208-cdc070896a78/dqc_reference
[2024-01-25 18:13:21,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,712] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg97c0adcc-212c-4a19-a74f-64d9e71ef95d/GCF_009676995.1_ASM967699v1_genomic.fna.gz | prodigal -d GCF_009676995.1_ASM967699v1_genomic.fna/cds.fna -a GCF_009676995.1_ASM967699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:28,331] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:28,331] [INFO] Task started: HMMsearch
[2024-01-25 18:13:28,331] [INFO] Running command: hmmsearch --tblout GCF_009676995.1_ASM967699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e1f4d49-8fc6-41db-9208-cdc070896a78/dqc_reference/reference_markers.hmm GCF_009676995.1_ASM967699v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:28,508] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:28,509] [INFO] Found 6/6 markers.
[2024-01-25 18:13:28,530] [INFO] Query marker FASTA was written to GCF_009676995.1_ASM967699v1_genomic.fna/markers.fasta
[2024-01-25 18:13:28,530] [INFO] Task started: Blastn
[2024-01-25 18:13:28,530] [INFO] Running command: blastn -query GCF_009676995.1_ASM967699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e1f4d49-8fc6-41db-9208-cdc070896a78/dqc_reference/reference_markers.fasta -out GCF_009676995.1_ASM967699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:29,153] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:29,156] [INFO] Selected 8 target genomes.
[2024-01-25 18:13:29,157] [INFO] Target genome list was writen to GCF_009676995.1_ASM967699v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:29,166] [INFO] Task started: fastANI
[2024-01-25 18:13:29,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c0adcc-212c-4a19-a74f-64d9e71ef95d/GCF_009676995.1_ASM967699v1_genomic.fna.gz --refList GCF_009676995.1_ASM967699v1_genomic.fna/target_genomes.txt --output GCF_009676995.1_ASM967699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:33,221] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:33,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e1f4d49-8fc6-41db-9208-cdc070896a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:33,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e1f4d49-8fc6-41db-9208-cdc070896a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:33,229] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:13:33,229] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:13:33,230] [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
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	100.0	766	768	95	inconclusive
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	96.0138	637	768	95	inconclusive
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	82.0264	385	768	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	81.9115	385	768	95	below_threshold
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	81.6597	364	768	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.5437	255	768	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.4694	245	768	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.1799	177	768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:33,231] [INFO] DFAST Taxonomy check result was written to GCF_009676995.1_ASM967699v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:33,232] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:33,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:33,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e1f4d49-8fc6-41db-9208-cdc070896a78/dqc_reference/checkm_data
[2024-01-25 18:13:33,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:33,259] [INFO] Task started: CheckM
[2024-01-25 18:13:33,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009676995.1_ASM967699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009676995.1_ASM967699v1_genomic.fna/checkm_input GCF_009676995.1_ASM967699v1_genomic.fna/checkm_result
[2024-01-25 18:13:56,262] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:56,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:56,280] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:56,280] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:56,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009676995.1_ASM967699v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:56,281] [INFO] Task started: Blastn
[2024-01-25 18:13:56,281] [INFO] Running command: blastn -query GCF_009676995.1_ASM967699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e1f4d49-8fc6-41db-9208-cdc070896a78/dqc_reference/reference_markers_gtdb.fasta -out GCF_009676995.1_ASM967699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:57,379] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:57,383] [INFO] Selected 11 target genomes.
[2024-01-25 18:13:57,383] [INFO] Target genome list was writen to GCF_009676995.1_ASM967699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:57,412] [INFO] Task started: fastANI
[2024-01-25 18:13:57,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c0adcc-212c-4a19-a74f-64d9e71ef95d/GCF_009676995.1_ASM967699v1_genomic.fna.gz --refList GCF_009676995.1_ASM967699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009676995.1_ASM967699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:02,505] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:02,513] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:02,513] [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_000311845.1	s__Enorma massiliensis	96.0138	637	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	97.43	96.04	0.89	0.84	11	conclusive
GCF_902150035.1	s__Enorma burkinafasonensis	82.0117	385	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333815.1	s__Enorma sp000333815	81.8755	384	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCF_900186505.1	s__Enorma phocaeensis	81.6597	364	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900538305.1	s__Enorma sp900538305	81.5135	348	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210055.1	s__Enorma sp900751795	81.1474	299	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	99.77	99.77	0.84	0.84	2	-
GCF_016901575.1	s__Limicola phocaeensis_A	80.3752	331	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160065.1	s__Limicola sp002160065	80.271	299	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900375.1	s__Collinsella sp002305035	80.2011	298	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCF_002161805.1	s__Coprousia sp002161805	80.1118	302	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715125.1	s__Coprousia avicola	79.9861	289	768	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:02,514] [INFO] GTDB search result was written to GCF_009676995.1_ASM967699v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:02,515] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:02,517] [INFO] DFAST_QC result json was written to GCF_009676995.1_ASM967699v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:02,517] [INFO] DFAST_QC completed!
[2024-01-25 18:14:02,517] [INFO] Total running time: 0h0m42s