[2023-06-05 00:01:26,515] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:01:26,531] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:01:26,531] [INFO] DQC Reference Directory: /var/lib/cwl/stgb037b057-a164-407f-8f09-f0f8e1a855b9/dqc_reference
[2023-06-05 00:01:28,244] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:01:28,246] [INFO] Task started: Prodigal
[2023-06-05 00:01:28,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa4f3493-67ea-4e47-9151-6d880b324cc6/GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna.gz | prodigal -d GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/cds.fna -a GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:01:32,977] [INFO] Task succeeded: Prodigal
[2023-06-05 00:01:32,977] [INFO] Task started: HMMsearch
[2023-06-05 00:01:32,977] [INFO] Running command: hmmsearch --tblout GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb037b057-a164-407f-8f09-f0f8e1a855b9/dqc_reference/reference_markers.hmm GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:01:33,237] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:01:33,238] [INFO] Found 6/6 markers.
[2023-06-05 00:01:33,284] [INFO] Query marker FASTA was written to GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/markers.fasta
[2023-06-05 00:01:33,285] [INFO] Task started: Blastn
[2023-06-05 00:01:33,285] [INFO] Running command: blastn -query GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/markers.fasta -db /var/lib/cwl/stgb037b057-a164-407f-8f09-f0f8e1a855b9/dqc_reference/reference_markers.fasta -out GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:01:34,051] [INFO] Task succeeded: Blastn
[2023-06-05 00:01:34,055] [INFO] Selected 23 target genomes.
[2023-06-05 00:01:34,055] [INFO] Target genome list was writen to GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/target_genomes.txt
[2023-06-05 00:01:34,056] [INFO] Task started: fastANI
[2023-06-05 00:01:34,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa4f3493-67ea-4e47-9151-6d880b324cc6/GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna.gz --refList GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/target_genomes.txt --output GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:01:48,641] [INFO] Task succeeded: fastANI
[2023-06-05 00:01:48,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb037b057-a164-407f-8f09-f0f8e1a855b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:01:48,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb037b057-a164-407f-8f09-f0f8e1a855b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:01:48,659] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:01:48,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:01:48,659] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.2919	58	615	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.1845	71	615	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.1401	64	615	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.1286	65	615	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.0256	53	615	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	76.8256	62	615	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.7938	63	615	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.369	54	615	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.3459	52	615	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.324	54	615	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:01:48,662] [INFO] DFAST Taxonomy check result was written to GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/tc_result.tsv
[2023-06-05 00:01:48,663] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:01:48,663] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:01:48,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb037b057-a164-407f-8f09-f0f8e1a855b9/dqc_reference/checkm_data
[2023-06-05 00:01:48,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:01:48,696] [INFO] Task started: CheckM
[2023-06-05 00:01:48,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/checkm_input GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/checkm_result
[2023-06-05 00:02:09,419] [INFO] Task succeeded: CheckM
[2023-06-05 00:02:09,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:02:09,442] [INFO] ===== Completeness check finished =====
[2023-06-05 00:02:09,443] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:02:09,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/markers.fasta)
[2023-06-05 00:02:09,444] [INFO] Task started: Blastn
[2023-06-05 00:02:09,444] [INFO] Running command: blastn -query GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/markers.fasta -db /var/lib/cwl/stgb037b057-a164-407f-8f09-f0f8e1a855b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:02:10,752] [INFO] Task succeeded: Blastn
[2023-06-05 00:02:10,757] [INFO] Selected 14 target genomes.
[2023-06-05 00:02:10,757] [INFO] Target genome list was writen to GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:02:10,811] [INFO] Task started: fastANI
[2023-06-05 00:02:10,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa4f3493-67ea-4e47-9151-6d880b324cc6/GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna.gz --refList GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/target_genomes_gtdb.txt --output GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:02:16,446] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:16,463] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:02:16,463] [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_900315595.1	s__Faecousia sp900315595	97.5596	555	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.62	97.05	0.87	0.79	33	conclusive
GCA_017425545.1	s__Faecousia sp017425545	82.2402	255	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017519005.1	s__Faecousia sp017519005	80.4391	278	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.84	97.84	0.75	0.75	2	-
GCA_902767915.1	s__Faecousia sp902767915	80.3881	263	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.86	97.78	0.84	0.82	3	-
GCA_016292255.1	s__Faecousia sp016292255	80.2152	280	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540945.1	s__Faecousia sp017540945	80.176	260	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.32	98.32	0.76	0.76	2	-
GCA_017541995.1	s__Faecousia sp017541995	80.0516	285	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795195.1	s__Faecousia sp902795195	79.5134	229	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017614755.1	s__Faecousia sp017614755	78.7414	211	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395865.1	s__Avoscillospira_A sp904395865	76.8996	96	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904395905.1	s__Avoscillospira_A sp904395905	76.6705	80	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436785.1	s__Faecousia sp017436785	76.2468	62	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:02:16,466] [INFO] GTDB search result was written to GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/result_gtdb.tsv
[2023-06-05 00:02:16,466] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:02:16,470] [INFO] DFAST_QC result json was written to GCA_902761255.1_Rumen_uncultured_genome_RUG10643_genomic.fna/dqc_result.json
[2023-06-05 00:02:16,470] [INFO] DFAST_QC completed!
[2023-06-05 00:02:16,470] [INFO] Total running time: 0h0m50s