[2023-06-13 11:16:46,800] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:16:46,803] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:16:46,803] [INFO] DQC Reference Directory: /var/lib/cwl/stgc42bc553-2948-4c6e-9e64-0a2311238cff/dqc_reference
[2023-06-13 11:16:48,053] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:16:48,054] [INFO] Task started: Prodigal
[2023-06-13 11:16:48,054] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbdba489-5fa3-4da2-b82d-821565de49ec/GCA_022775445.1_ASM2277544v1_genomic.fna.gz | prodigal -d GCA_022775445.1_ASM2277544v1_genomic.fna/cds.fna -a GCA_022775445.1_ASM2277544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:16:53,500] [INFO] Task succeeded: Prodigal
[2023-06-13 11:16:53,501] [INFO] Task started: HMMsearch
[2023-06-13 11:16:53,501] [INFO] Running command: hmmsearch --tblout GCA_022775445.1_ASM2277544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc42bc553-2948-4c6e-9e64-0a2311238cff/dqc_reference/reference_markers.hmm GCA_022775445.1_ASM2277544v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:16:53,706] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:16:53,708] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfbdba489-5fa3-4da2-b82d-821565de49ec/GCA_022775445.1_ASM2277544v1_genomic.fna.gz]
[2023-06-13 11:16:53,737] [INFO] Query marker FASTA was written to GCA_022775445.1_ASM2277544v1_genomic.fna/markers.fasta
[2023-06-13 11:16:53,737] [INFO] Task started: Blastn
[2023-06-13 11:16:53,737] [INFO] Running command: blastn -query GCA_022775445.1_ASM2277544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc42bc553-2948-4c6e-9e64-0a2311238cff/dqc_reference/reference_markers.fasta -out GCA_022775445.1_ASM2277544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:16:54,328] [INFO] Task succeeded: Blastn
[2023-06-13 11:16:54,331] [INFO] Selected 8 target genomes.
[2023-06-13 11:16:54,331] [INFO] Target genome list was writen to GCA_022775445.1_ASM2277544v1_genomic.fna/target_genomes.txt
[2023-06-13 11:16:54,334] [INFO] Task started: fastANI
[2023-06-13 11:16:54,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbdba489-5fa3-4da2-b82d-821565de49ec/GCA_022775445.1_ASM2277544v1_genomic.fna.gz --refList GCA_022775445.1_ASM2277544v1_genomic.fna/target_genomes.txt --output GCA_022775445.1_ASM2277544v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:16:58,614] [INFO] Task succeeded: fastANI
[2023-06-13 11:16:58,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc42bc553-2948-4c6e-9e64-0a2311238cff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:16:58,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc42bc553-2948-4c6e-9e64-0a2311238cff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:16:58,619] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:16:58,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:16:58,619] [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
Lentihominibacter faecis	strain=BX16	GCA_014306095.1	2764712	2764712	type	True	78.3776	91	716	95	below_threshold
Lentihominibacter hominis	strain=NSJ-24	GCA_014385065.1	2763645	2763645	type	True	77.4578	82	716	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:16:58,624] [INFO] DFAST Taxonomy check result was written to GCA_022775445.1_ASM2277544v1_genomic.fna/tc_result.tsv
[2023-06-13 11:16:58,625] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:16:58,625] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:16:58,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc42bc553-2948-4c6e-9e64-0a2311238cff/dqc_reference/checkm_data
[2023-06-13 11:16:58,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:16:58,657] [INFO] Task started: CheckM
[2023-06-13 11:16:58,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022775445.1_ASM2277544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022775445.1_ASM2277544v1_genomic.fna/checkm_input GCA_022775445.1_ASM2277544v1_genomic.fna/checkm_result
[2023-06-13 11:17:21,246] [INFO] Task succeeded: CheckM
[2023-06-13 11:17:21,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:17:21,269] [INFO] ===== Completeness check finished =====
[2023-06-13 11:17:21,269] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:17:21,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022775445.1_ASM2277544v1_genomic.fna/markers.fasta)
[2023-06-13 11:17:21,270] [INFO] Task started: Blastn
[2023-06-13 11:17:21,270] [INFO] Running command: blastn -query GCA_022775445.1_ASM2277544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc42bc553-2948-4c6e-9e64-0a2311238cff/dqc_reference/reference_markers_gtdb.fasta -out GCA_022775445.1_ASM2277544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:17:22,115] [INFO] Task succeeded: Blastn
[2023-06-13 11:17:22,126] [INFO] Selected 13 target genomes.
[2023-06-13 11:17:22,126] [INFO] Target genome list was writen to GCA_022775445.1_ASM2277544v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:17:22,132] [INFO] Task started: fastANI
[2023-06-13 11:17:22,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbdba489-5fa3-4da2-b82d-821565de49ec/GCA_022775445.1_ASM2277544v1_genomic.fna.gz --refList GCA_022775445.1_ASM2277544v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022775445.1_ASM2277544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:17:28,577] [INFO] Task succeeded: fastANI
[2023-06-13 11:17:28,585] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:17:28,585] [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_905193765.1	s__Copromorpha sp905193765	98.4862	543	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902362435.1	s__Copromorpha sp900066305	78.8134	186	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.11	98.22	0.97	0.95	3	-
GCA_014306095.1	s__Copromorpha sp900549125	78.3776	91	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	97.82	97.60	0.83	0.80	4	-
GCA_017416795.1	s__Copromorpha sp017416795	78.2758	102	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	95.76	95.76	0.88	0.88	2	-
GCA_012513435.1	s__Copromorpha sp012513435	77.8606	69	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543485.1	s__Copromorpha excrementipullorum	77.4838	99	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.13	99.09	0.94	0.94	3	-
GCA_900542385.1	s__Copromorpha excrementavium	77.0755	68	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Copromorpha	95.0	99.28	99.27	0.88	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-13 11:17:28,587] [INFO] GTDB search result was written to GCA_022775445.1_ASM2277544v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:17:28,588] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:17:28,591] [INFO] DFAST_QC result json was written to GCA_022775445.1_ASM2277544v1_genomic.fna/dqc_result.json
[2023-06-13 11:17:28,591] [INFO] DFAST_QC completed!
[2023-06-13 11:17:28,591] [INFO] Total running time: 0h0m42s