[2024-01-24 13:09:34,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a14bb56-db8e-40c7-bf25-5991f141e13c/dqc_reference
[2024-01-24 13:09:35,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,377] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg36c54596-4777-48d5-beef-d3515a37fec0/GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna.gz | prodigal -d GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/cds.fna -a GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:42,045] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:42,045] [INFO] Task started: HMMsearch
[2024-01-24 13:09:42,046] [INFO] Running command: hmmsearch --tblout GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a14bb56-db8e-40c7-bf25-5991f141e13c/dqc_reference/reference_markers.hmm GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:42,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:42,336] [INFO] Found 6/6 markers.
[2024-01-24 13:09:42,365] [INFO] Query marker FASTA was written to GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/markers.fasta
[2024-01-24 13:09:42,365] [INFO] Task started: Blastn
[2024-01-24 13:09:42,366] [INFO] Running command: blastn -query GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a14bb56-db8e-40c7-bf25-5991f141e13c/dqc_reference/reference_markers.fasta -out GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:43,042] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:43,046] [INFO] Selected 15 target genomes.
[2024-01-24 13:09:43,046] [INFO] Target genome list was writen to GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/target_genomes.txt
[2024-01-24 13:09:43,055] [INFO] Task started: fastANI
[2024-01-24 13:09:43,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg36c54596-4777-48d5-beef-d3515a37fec0/GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna.gz --refList GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/target_genomes.txt --output GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:50,203] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:50,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a14bb56-db8e-40c7-bf25-5991f141e13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:50,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a14bb56-db8e-40c7-bf25-5991f141e13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:50,214] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:09:50,215] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:09:50,215] [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
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.5468	270	713	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	79.4182	293	713	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	79.019	186	713	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.9837	192	713	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.9421	188	713	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.8576	242	713	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.8064	217	713	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.3446	162	713	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.2709	134	713	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	77.7375	119	713	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.7375	119	713	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.3084	60	713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:50,217] [INFO] DFAST Taxonomy check result was written to GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/tc_result.tsv
[2024-01-24 13:09:50,218] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:50,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:50,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a14bb56-db8e-40c7-bf25-5991f141e13c/dqc_reference/checkm_data
[2024-01-24 13:09:50,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:50,244] [INFO] Task started: CheckM
[2024-01-24 13:09:50,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/checkm_input GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/checkm_result
[2024-01-24 13:10:14,193] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:14,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:14,211] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:14,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:14,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/markers.fasta)
[2024-01-24 13:10:14,212] [INFO] Task started: Blastn
[2024-01-24 13:10:14,212] [INFO] Running command: blastn -query GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a14bb56-db8e-40c7-bf25-5991f141e13c/dqc_reference/reference_markers_gtdb.fasta -out GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:15,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:15,153] [INFO] Selected 17 target genomes.
[2024-01-24 13:10:15,153] [INFO] Target genome list was writen to GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:15,170] [INFO] Task started: fastANI
[2024-01-24 13:10:15,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg36c54596-4777-48d5-beef-d3515a37fec0/GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna.gz --refList GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/target_genomes_gtdb.txt --output GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:23,175] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:23,190] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:23,190] [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_905219705.1	s__Marseille-P3106 sp905219705	98.4221	573	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900543935.1	s__Marseille-P3106 sp900543935	81.4895	376	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169975.1	s__Marseille-P3106 sp900169975	80.6914	341	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588975.1	s__Marseille-P3106 sp910588975	80.5269	284	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587345.1	s__Marseille-P3106 sp910587345	80.5002	263	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577415.1	s__Marseille-P3106 sp910577415	80.361	270	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549565.1	s__UMGS1202 sp900549565	79.6903	290	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117605.1	s__Intestinimonas stercoravium	79.6035	233	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCF_016899775.1	s__Lawsonibacter sp900545895	79.5916	227	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.62	96.12	0.85	0.79	4	-
GCA_910585735.1	s__Marseille-P3106 sp910585735	79.5447	238	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626145.1	s__Intestinimonas timonensis	79.4955	257	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161085.1	s__Flavonifractor avicola	79.441	242	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.94	96.68	0.83	0.78	7	-
GCF_002160305.1	s__Lawsonibacter pullicola	79.425	225	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.22	97.83	0.90	0.75	8	-
GCF_016901735.1	s__An92 sp016901735	79.2155	246	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.81	98.81	0.85	0.85	2	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	79.0974	233	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCA_904420465.1	s__Lawsonibacter sp904420465	78.7514	173	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584395.1	s__MGBC124762 sp910584395	78.3135	169	713	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__MGBC124762	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:23,192] [INFO] GTDB search result was written to GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:23,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:23,196] [INFO] DFAST_QC result json was written to GCF_943193085.1_Oscillospiraceae_gen_nov_DSM112226_genomic.fna/dqc_result.json
[2024-01-24 13:10:23,197] [INFO] DFAST_QC completed!
[2024-01-24 13:10:23,197] [INFO] Total running time: 0h0m49s