[2024-01-24 14:13:01,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgdce43d43-f242-452a-9376-9b180ef9b465/dqc_reference
[2024-01-24 14:13:02,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,489] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgd005828c-308e-4ca4-a952-3a4cadf8f421/GCF_003012055.1_ASM301205v1_genomic.fna.gz | prodigal -d GCF_003012055.1_ASM301205v1_genomic.fna/cds.fna -a GCF_003012055.1_ASM301205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:05,956] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:05,957] [INFO] Task started: HMMsearch
[2024-01-24 14:13:05,957] [INFO] Running command: hmmsearch --tblout GCF_003012055.1_ASM301205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdce43d43-f242-452a-9376-9b180ef9b465/dqc_reference/reference_markers.hmm GCF_003012055.1_ASM301205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:06,189] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:06,191] [INFO] Found 6/6 markers.
[2024-01-24 14:13:06,224] [INFO] Query marker FASTA was written to GCF_003012055.1_ASM301205v1_genomic.fna/markers.fasta
[2024-01-24 14:13:06,224] [INFO] Task started: Blastn
[2024-01-24 14:13:06,224] [INFO] Running command: blastn -query GCF_003012055.1_ASM301205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdce43d43-f242-452a-9376-9b180ef9b465/dqc_reference/reference_markers.fasta -out GCF_003012055.1_ASM301205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:06,798] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:06,801] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:06,801] [INFO] Target genome list was writen to GCF_003012055.1_ASM301205v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:06,890] [INFO] Task started: fastANI
[2024-01-24 14:13:06,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgd005828c-308e-4ca4-a952-3a4cadf8f421/GCF_003012055.1_ASM301205v1_genomic.fna.gz --refList GCF_003012055.1_ASM301205v1_genomic.fna/target_genomes.txt --output GCF_003012055.1_ASM301205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:10,859] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:10,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdce43d43-f242-452a-9376-9b180ef9b465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:10,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdce43d43-f242-452a-9376-9b180ef9b465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:10,869] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:10,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:10,869] [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 russellii	strain=RT-10B	GCA_003012055.1	215200	215200	type	True	100.0	688	688	95	conclusive
Peptostreptococcus anaerobius	strain=NCTC11460	GCA_900454605.1	1261	1261	type	True	79.0363	136	688	95	below_threshold
Peptostreptococcus anaerobius	strain=VPI 4330	GCA_000318115.1	1261	1261	type	True	78.7663	127	688	95	below_threshold
Peptostreptococcus anaerobius	strain=DSM 2949	GCA_000381525.1	1261	1261	type	True	78.7587	134	688	95	below_threshold
Peptostreptococcus stomatis	strain=DSM 17678	GCA_000147675.2	341694	341694	type	True	78.7543	112	688	95	below_threshold
Peptostreptococcus porci	strain=WCA-SAB-591-4A-A	GCA_009695815.1	2652282	2652282	type	True	77.9356	132	688	95	below_threshold
Peptostreptococcus canis	strain=DSM 27025	GCA_014229965.1	1159213	1159213	type	True	77.6797	162	688	95	below_threshold
Peptacetobacter hiranonis	strain=DSM 13275	GCA_008151785.1	89152	89152	type	True	77.572	67	688	95	below_threshold
Peptostreptococcus canis	strain=DSM 27025	GCA_017874285.1	1159213	1159213	type	True	77.4985	166	688	95	below_threshold
Peptacetobacter hiranonis	strain=DSM 13275	GCA_000156055.1	89152	89152	type	True	76.8719	63	688	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	76.5739	89	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:10,871] [INFO] DFAST Taxonomy check result was written to GCF_003012055.1_ASM301205v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:10,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:10,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:10,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdce43d43-f242-452a-9376-9b180ef9b465/dqc_reference/checkm_data
[2024-01-24 14:13:10,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:10,901] [INFO] Task started: CheckM
[2024-01-24 14:13:10,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012055.1_ASM301205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012055.1_ASM301205v1_genomic.fna/checkm_input GCF_003012055.1_ASM301205v1_genomic.fna/checkm_result
[2024-01-24 14:13:29,654] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:29,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:29,675] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:29,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:29,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012055.1_ASM301205v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:29,676] [INFO] Task started: Blastn
[2024-01-24 14:13:29,676] [INFO] Running command: blastn -query GCF_003012055.1_ASM301205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdce43d43-f242-452a-9376-9b180ef9b465/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012055.1_ASM301205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:30,573] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:30,576] [INFO] Selected 14 target genomes.
[2024-01-24 14:13:30,576] [INFO] Target genome list was writen to GCF_003012055.1_ASM301205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:30,600] [INFO] Task started: fastANI
[2024-01-24 14:13:30,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgd005828c-308e-4ca4-a952-3a4cadf8f421/GCF_003012055.1_ASM301205v1_genomic.fna.gz --refList GCF_003012055.1_ASM301205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012055.1_ASM301205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:36,876] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:36,896] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:36,897] [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_003012055.1	s__Peptostreptococcus russellii	100.0	688	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	98.54	98.54	0.93	0.93	2	conclusive
GCF_900110295.1	s__Peptostreptococcus russellii_A	79.6251	309	688	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_000381525.1	s__Peptostreptococcus anaerobius	78.7618	133	688	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_000147675.1	s__Peptostreptococcus stomatis	78.7543	112	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptostreptococcus	95.0	97.69	97.69	0.87	0.87	2	-
GCA_900759325.1	s__Peptostreptococcus sp900759325	78.5147	108	688	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_000758885.1	s__Peptostreptococcus sp000758885	78.4552	107	688	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_009695815.1	s__Peptostreptococcus porci	77.9107	133	688	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_900112955.1	s__Peptostreptococcus sp900112955	77.8527	125	688	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_014229965.1	s__Peptostreptococcus canis	77.6797	162	688	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_008151785.1	s__Peptacetobacter hiranonis	77.5605	68	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	97.84	95.69	0.88	0.73	5	-
GCA_018336475.1	s__Romboutsia sp018336475	76.9458	79	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362365.1	s__GCA-900066495 sp902362365	76.6696	75	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550335.1	s__Peptacetobacter sp900550335	76.5283	56	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	99.93	99.93	0.85	0.85	2	-
GCF_900015215.1	s__Romboutsia ilealis	76.497	88	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:36,900] [INFO] GTDB search result was written to GCF_003012055.1_ASM301205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:36,901] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:36,907] [INFO] DFAST_QC result json was written to GCF_003012055.1_ASM301205v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:36,908] [INFO] DFAST_QC completed!
[2024-01-24 14:13:36,908] [INFO] Total running time: 0h0m36s