[2023-06-17 16:42:55,282] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:42:55,284] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:42:55,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg954c544d-d50b-46f3-b834-57c51eb4c3ae/dqc_reference
[2023-06-17 16:42:56,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:42:56,650] [INFO] Task started: Prodigal
[2023-06-17 16:42:56,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg46d3d46c-64ed-4e3b-a33b-d8869c465d10/GCA_028722145.1_ASM2872214v1_genomic.fna.gz | prodigal -d GCA_028722145.1_ASM2872214v1_genomic.fna/cds.fna -a GCA_028722145.1_ASM2872214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:43:00,682] [INFO] Task succeeded: Prodigal
[2023-06-17 16:43:00,683] [INFO] Task started: HMMsearch
[2023-06-17 16:43:00,683] [INFO] Running command: hmmsearch --tblout GCA_028722145.1_ASM2872214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg954c544d-d50b-46f3-b834-57c51eb4c3ae/dqc_reference/reference_markers.hmm GCA_028722145.1_ASM2872214v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:43:00,939] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:43:00,940] [INFO] Found 6/6 markers.
[2023-06-17 16:43:00,963] [INFO] Query marker FASTA was written to GCA_028722145.1_ASM2872214v1_genomic.fna/markers.fasta
[2023-06-17 16:43:00,964] [INFO] Task started: Blastn
[2023-06-17 16:43:00,964] [INFO] Running command: blastn -query GCA_028722145.1_ASM2872214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954c544d-d50b-46f3-b834-57c51eb4c3ae/dqc_reference/reference_markers.fasta -out GCA_028722145.1_ASM2872214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:43:01,545] [INFO] Task succeeded: Blastn
[2023-06-17 16:43:01,550] [INFO] Selected 22 target genomes.
[2023-06-17 16:43:01,551] [INFO] Target genome list was writen to GCA_028722145.1_ASM2872214v1_genomic.fna/target_genomes.txt
[2023-06-17 16:43:01,558] [INFO] Task started: fastANI
[2023-06-17 16:43:01,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d3d46c-64ed-4e3b-a33b-d8869c465d10/GCA_028722145.1_ASM2872214v1_genomic.fna.gz --refList GCA_028722145.1_ASM2872214v1_genomic.fna/target_genomes.txt --output GCA_028722145.1_ASM2872214v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:43:11,813] [INFO] Task succeeded: fastANI
[2023-06-17 16:43:11,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg954c544d-d50b-46f3-b834-57c51eb4c3ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:43:11,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg954c544d-d50b-46f3-b834-57c51eb4c3ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:43:11,828] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 16:43:11,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 16:43:11,828] [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
Peptostreptococcus porci	strain=WCA-SAB-591-4A-A	GCA_009695815.1	2652282	2652282	type	True	98.1168	581	643	95	conclusive
Peptostreptococcus stomatis	strain=DSM 17678	GCA_000147675.2	341694	341694	type	True	78.8457	81	643	95	below_threshold
Peptostreptococcus anaerobius	strain=VPI 4330	GCA_000318115.1	1261	1261	type	True	78.7551	89	643	95	below_threshold
Peptostreptococcus anaerobius	strain=DSM 2949	GCA_000381525.1	1261	1261	type	True	78.6584	92	643	95	below_threshold
Peptostreptococcus anaerobius	strain=NCTC11460	GCA_900454605.1	1261	1261	type	True	78.5944	99	643	95	below_threshold
Peptostreptococcus canis	strain=DSM 27025	GCA_017874285.1	1159213	1159213	type	True	78.4741	154	643	95	below_threshold
Peptostreptococcus canis	strain=DSM 27025	GCA_014229965.1	1159213	1159213	type	True	78.3812	156	643	95	below_threshold
Peptostreptococcus russellii	strain=RT-10B	GCA_003012055.1	215200	215200	type	True	77.9474	112	643	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	75.957	54	643	95	below_threshold
Terrisporobacter petrolearius	strain=LAM0A37	GCA_020748185.1	1460447	1460447	type	True	75.8164	51	643	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	75.6028	55	643	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:43:11,831] [INFO] DFAST Taxonomy check result was written to GCA_028722145.1_ASM2872214v1_genomic.fna/tc_result.tsv
[2023-06-17 16:43:11,832] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:43:11,832] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:43:11,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg954c544d-d50b-46f3-b834-57c51eb4c3ae/dqc_reference/checkm_data
[2023-06-17 16:43:11,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:43:11,859] [INFO] Task started: CheckM
[2023-06-17 16:43:11,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028722145.1_ASM2872214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028722145.1_ASM2872214v1_genomic.fna/checkm_input GCA_028722145.1_ASM2872214v1_genomic.fna/checkm_result
[2023-06-17 16:43:31,756] [INFO] Task succeeded: CheckM
[2023-06-17 16:43:31,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:43:31,782] [INFO] ===== Completeness check finished =====
[2023-06-17 16:43:31,783] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:43:31,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028722145.1_ASM2872214v1_genomic.fna/markers.fasta)
[2023-06-17 16:43:31,783] [INFO] Task started: Blastn
[2023-06-17 16:43:31,784] [INFO] Running command: blastn -query GCA_028722145.1_ASM2872214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg954c544d-d50b-46f3-b834-57c51eb4c3ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_028722145.1_ASM2872214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:43:32,612] [INFO] Task succeeded: Blastn
[2023-06-17 16:43:32,616] [INFO] Selected 20 target genomes.
[2023-06-17 16:43:32,617] [INFO] Target genome list was writen to GCA_028722145.1_ASM2872214v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:43:32,625] [INFO] Task started: fastANI
[2023-06-17 16:43:32,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d3d46c-64ed-4e3b-a33b-d8869c465d10/GCA_028722145.1_ASM2872214v1_genomic.fna.gz --refList GCA_028722145.1_ASM2872214v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028722145.1_ASM2872214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:43:41,104] [INFO] Task succeeded: fastANI
[2023-06-17 16:43:41,118] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:43:41,118] [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_009695815.1	s__Peptostreptococcus porci	98.1168	581	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112955.1	s__Peptostreptococcus sp900112955	91.6748	525	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147675.1	s__Peptostreptococcus stomatis	78.8457	81	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCF_000758885.1	s__Peptostreptococcus sp000758885	78.7354	69	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381525.1	s__Peptostreptococcus anaerobius	78.6584	92	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	99.16	98.74	0.90	0.83	12	-
GCF_014229965.1	s__Peptostreptococcus canis	78.3911	157	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110295.1	s__Peptostreptococcus russellii_A	77.9878	109	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.51	98.15	0.92	0.90	3	-
GCA_900759325.1	s__Peptostreptococcus sp900759325	77.9662	81	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.17	97.99	0.91	0.90	4	-
GCF_003012055.1	s__Peptostreptococcus russellii	77.9474	112	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.54	98.54	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-17 16:43:41,120] [INFO] GTDB search result was written to GCA_028722145.1_ASM2872214v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:43:41,121] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:43:41,125] [INFO] DFAST_QC result json was written to GCA_028722145.1_ASM2872214v1_genomic.fna/dqc_result.json
[2023-06-17 16:43:41,125] [INFO] DFAST_QC completed!
[2023-06-17 16:43:41,125] [INFO] Total running time: 0h0m46s