[2024-01-24 12:00:36,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a7febf9-bc38-43bb-a47a-bc1958a47e7a/dqc_reference
[2024-01-24 12:00:39,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,376] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg656b0481-53d1-4d00-a6e4-57878f544388/GCF_017874285.1_ASM1787428v1_genomic.fna.gz | prodigal -d GCF_017874285.1_ASM1787428v1_genomic.fna/cds.fna -a GCF_017874285.1_ASM1787428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:42,977] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:42,978] [INFO] Task started: HMMsearch
[2024-01-24 12:00:42,978] [INFO] Running command: hmmsearch --tblout GCF_017874285.1_ASM1787428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a7febf9-bc38-43bb-a47a-bc1958a47e7a/dqc_reference/reference_markers.hmm GCF_017874285.1_ASM1787428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:43,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:43,202] [INFO] Found 6/6 markers.
[2024-01-24 12:00:43,232] [INFO] Query marker FASTA was written to GCF_017874285.1_ASM1787428v1_genomic.fna/markers.fasta
[2024-01-24 12:00:43,233] [INFO] Task started: Blastn
[2024-01-24 12:00:43,233] [INFO] Running command: blastn -query GCF_017874285.1_ASM1787428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a7febf9-bc38-43bb-a47a-bc1958a47e7a/dqc_reference/reference_markers.fasta -out GCF_017874285.1_ASM1787428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:45,178] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:45,181] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:45,182] [INFO] Target genome list was writen to GCF_017874285.1_ASM1787428v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:45,237] [INFO] Task started: fastANI
[2024-01-24 12:00:45,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg656b0481-53d1-4d00-a6e4-57878f544388/GCF_017874285.1_ASM1787428v1_genomic.fna.gz --refList GCF_017874285.1_ASM1787428v1_genomic.fna/target_genomes.txt --output GCF_017874285.1_ASM1787428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:50,748] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:50,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a7febf9-bc38-43bb-a47a-bc1958a47e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:50,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a7febf9-bc38-43bb-a47a-bc1958a47e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:50,764] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:00:50,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:50,765] [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 canis	strain=DSM 27025	GCA_017874285.1	1159213	1159213	type	True	100.0	669	672	95	conclusive
Peptostreptococcus canis	strain=DSM 27025	GCA_014229965.1	1159213	1159213	type	True	99.995	667	672	95	conclusive
Peptostreptococcus stomatis	strain=DSM 17678	GCA_000147675.2	341694	341694	type	True	79.359	114	672	95	below_threshold
Peptostreptococcus anaerobius	strain=NCTC11460	GCA_900454605.1	1261	1261	type	True	78.5636	122	672	95	below_threshold
Peptostreptococcus anaerobius	strain=DSM 2949	GCA_000381525.1	1261	1261	type	True	78.442	125	672	95	below_threshold
Peptostreptococcus porci	strain=WCA-SAB-591-4A-A	GCA_009695815.1	2652282	2652282	type	True	78.4346	164	672	95	below_threshold
Peptostreptococcus anaerobius	strain=VPI 4330	GCA_000318115.1	1261	1261	type	True	78.414	117	672	95	below_threshold
Peptostreptococcus russellii	strain=RT-10B	GCA_003012055.1	215200	215200	type	True	77.525	165	672	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	76.5174	70	672	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	76.2696	67	672	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	75.8496	77	672	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	75.7942	80	672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:50,767] [INFO] DFAST Taxonomy check result was written to GCF_017874285.1_ASM1787428v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:50,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:50,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:50,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a7febf9-bc38-43bb-a47a-bc1958a47e7a/dqc_reference/checkm_data
[2024-01-24 12:00:50,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:50,792] [INFO] Task started: CheckM
[2024-01-24 12:00:50,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874285.1_ASM1787428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874285.1_ASM1787428v1_genomic.fna/checkm_input GCF_017874285.1_ASM1787428v1_genomic.fna/checkm_result
[2024-01-24 12:01:08,769] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:08,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:08,790] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:08,790] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:08,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874285.1_ASM1787428v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:08,791] [INFO] Task started: Blastn
[2024-01-24 12:01:08,791] [INFO] Running command: blastn -query GCF_017874285.1_ASM1787428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a7febf9-bc38-43bb-a47a-bc1958a47e7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874285.1_ASM1787428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:09,569] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:09,574] [INFO] Selected 20 target genomes.
[2024-01-24 12:01:09,574] [INFO] Target genome list was writen to GCF_017874285.1_ASM1787428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:09,635] [INFO] Task started: fastANI
[2024-01-24 12:01:09,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg656b0481-53d1-4d00-a6e4-57878f544388/GCF_017874285.1_ASM1787428v1_genomic.fna.gz --refList GCF_017874285.1_ASM1787428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874285.1_ASM1787428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:17,460] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:17,477] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:17,478] [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_014229965.1	s__Peptostreptococcus canis	99.995	667	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000147675.1	s__Peptostreptococcus stomatis	79.359	114	672	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	78.7997	99	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759325.1	s__Peptostreptococcus sp900759325	78.5566	82	672	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_000381525.1	s__Peptostreptococcus anaerobius	78.4741	124	672	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_009695815.1	s__Peptostreptococcus porci	78.4352	164	672	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_900110295.1	s__Peptostreptococcus russellii_A	77.8802	177	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.51	98.15	0.92	0.90	3	-
GCF_003012055.1	s__Peptostreptococcus russellii	77.5425	164	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_000452245.2	s__Paraclostridium bifermentans_A	76.4782	70	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.39	96.64	0.88	0.81	7	-
GCF_006861675.1	s__Peptacetobacter hominis	76.4255	56	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006802875.1	s__Paraclostridium bifermentans	76.3035	65	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCF_015668515.1	s__Paraclostridium tenue	76.0795	70	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.58	97.73	0.92	0.87	8	-
GCF_900106845.1	s__Romboutsia timonensis	75.8496	77	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
GCF_000439105.1	s__Terrisporobacter glycolicus	75.7942	80	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
GCF_002250835.2	s__Romboutsia_A weinsteinii	75.7012	58	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:17,479] [INFO] GTDB search result was written to GCF_017874285.1_ASM1787428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:17,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:17,485] [INFO] DFAST_QC result json was written to GCF_017874285.1_ASM1787428v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:17,485] [INFO] DFAST_QC completed!
[2024-01-24 12:01:17,485] [INFO] Total running time: 0h0m41s