[2024-01-24 12:45:20,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,736] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb132b65-d559-4b64-8981-816170e695d4/dqc_reference
[2024-01-24 12:45:22,071] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:22,071] [INFO] Task started: Prodigal
[2024-01-24 12:45:22,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg52202ec6-6021-4bdb-a6dd-5072211f30e3/GCF_014229965.1_ASM1422996v1_genomic.fna.gz | prodigal -d GCF_014229965.1_ASM1422996v1_genomic.fna/cds.fna -a GCF_014229965.1_ASM1422996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:25,690] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:25,691] [INFO] Task started: HMMsearch
[2024-01-24 12:45:25,691] [INFO] Running command: hmmsearch --tblout GCF_014229965.1_ASM1422996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb132b65-d559-4b64-8981-816170e695d4/dqc_reference/reference_markers.hmm GCF_014229965.1_ASM1422996v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:25,920] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:25,921] [INFO] Found 6/6 markers.
[2024-01-24 12:45:25,949] [INFO] Query marker FASTA was written to GCF_014229965.1_ASM1422996v1_genomic.fna/markers.fasta
[2024-01-24 12:45:25,949] [INFO] Task started: Blastn
[2024-01-24 12:45:25,949] [INFO] Running command: blastn -query GCF_014229965.1_ASM1422996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb132b65-d559-4b64-8981-816170e695d4/dqc_reference/reference_markers.fasta -out GCF_014229965.1_ASM1422996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:26,535] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:26,540] [INFO] Selected 13 target genomes.
[2024-01-24 12:45:26,541] [INFO] Target genome list was writen to GCF_014229965.1_ASM1422996v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:26,555] [INFO] Task started: fastANI
[2024-01-24 12:45:26,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg52202ec6-6021-4bdb-a6dd-5072211f30e3/GCF_014229965.1_ASM1422996v1_genomic.fna.gz --refList GCF_014229965.1_ASM1422996v1_genomic.fna/target_genomes.txt --output GCF_014229965.1_ASM1422996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:31,926] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:31,927] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb132b65-d559-4b64-8981-816170e695d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:31,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb132b65-d559-4b64-8981-816170e695d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:31,938] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:31,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:31,938] [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_014229965.1	1159213	1159213	type	True	100.0	672	672	95	conclusive
Peptostreptococcus canis	strain=DSM 27025	GCA_017874285.1	1159213	1159213	type	True	99.9914	666	672	95	conclusive
Peptostreptococcus stomatis	strain=DSM 17678	GCA_000147675.2	341694	341694	type	True	79.5513	113	672	95	below_threshold
Peptostreptococcus anaerobius	strain=NCTC11460	GCA_900454605.1	1261	1261	type	True	78.8833	114	672	95	below_threshold
Peptostreptococcus anaerobius	strain=DSM 2949	GCA_000381525.1	1261	1261	type	True	78.6479	114	672	95	below_threshold
Peptostreptococcus anaerobius	strain=VPI 4330	GCA_000318115.1	1261	1261	type	True	78.5499	107	672	95	below_threshold
Peptostreptococcus porci	strain=WCA-SAB-591-4A-A	GCA_009695815.1	2652282	2652282	type	True	78.2414	170	672	95	below_threshold
Peptostreptococcus russellii	strain=RT-10B	GCA_003012055.1	215200	215200	type	True	77.6225	161	672	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	76.5472	77	672	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	76.4035	66	672	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	76.1536	70	672	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	76.021	74	672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:31,941] [INFO] DFAST Taxonomy check result was written to GCF_014229965.1_ASM1422996v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:31,941] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:31,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:31,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb132b65-d559-4b64-8981-816170e695d4/dqc_reference/checkm_data
[2024-01-24 12:45:31,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:31,965] [INFO] Task started: CheckM
[2024-01-24 12:45:31,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014229965.1_ASM1422996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014229965.1_ASM1422996v1_genomic.fna/checkm_input GCF_014229965.1_ASM1422996v1_genomic.fna/checkm_result
[2024-01-24 12:45:50,329] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:50,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:50,345] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:50,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:50,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014229965.1_ASM1422996v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:50,346] [INFO] Task started: Blastn
[2024-01-24 12:45:50,346] [INFO] Running command: blastn -query GCF_014229965.1_ASM1422996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb132b65-d559-4b64-8981-816170e695d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014229965.1_ASM1422996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:51,143] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:51,147] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:51,147] [INFO] Target genome list was writen to GCF_014229965.1_ASM1422996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:51,182] [INFO] Task started: fastANI
[2024-01-24 12:45:51,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg52202ec6-6021-4bdb-a6dd-5072211f30e3/GCF_014229965.1_ASM1422996v1_genomic.fna.gz --refList GCF_014229965.1_ASM1422996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014229965.1_ASM1422996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:58,585] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:58,597] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:58,598] [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	100.0	672	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	79.5967	112	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	79.0902	95	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_000381525.1	s__Peptostreptococcus anaerobius	78.6859	113	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	-
GCA_900759325.1	s__Peptostreptococcus sp900759325	78.3545	85	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_009695815.1	s__Peptostreptococcus porci	78.2414	170	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	77.8768	178	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	77.6225	161	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	76.4257	78	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_900106845.1	s__Romboutsia timonensis	76.4035	66	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_006802875.1	s__Paraclostridium bifermentans	76.3842	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_000439105.1	s__Terrisporobacter glycolicus	76.1536	70	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_015668515.1	s__Paraclostridium tenue	76.1374	68	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_002250835.2	s__Romboutsia_A weinsteinii	75.9911	53	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 12:45:58,599] [INFO] GTDB search result was written to GCF_014229965.1_ASM1422996v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:58,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:58,604] [INFO] DFAST_QC result json was written to GCF_014229965.1_ASM1422996v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:58,604] [INFO] DFAST_QC completed!
[2024-01-24 12:45:58,604] [INFO] Total running time: 0h0m38s