[2024-01-24 13:28:00,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:00,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:00,204] [INFO] DQC Reference Directory: /var/lib/cwl/stgab299753-022f-4aa8-8c93-952e9b5c3aba/dqc_reference
[2024-01-24 13:28:01,506] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:01,507] [INFO] Task started: Prodigal
[2024-01-24 13:28:01,508] [INFO] Running command: gunzip -c /var/lib/cwl/stg89b26db0-2797-4f38-818c-9019ffc3c792/GCF_000227315.1_ASM22731v1_genomic.fna.gz | prodigal -d GCF_000227315.1_ASM22731v1_genomic.fna/cds.fna -a GCF_000227315.1_ASM22731v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:05,596] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:05,597] [INFO] Task started: HMMsearch
[2024-01-24 13:28:05,597] [INFO] Running command: hmmsearch --tblout GCF_000227315.1_ASM22731v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab299753-022f-4aa8-8c93-952e9b5c3aba/dqc_reference/reference_markers.hmm GCF_000227315.1_ASM22731v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:05,824] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:05,826] [INFO] Found 6/6 markers.
[2024-01-24 13:28:05,848] [INFO] Query marker FASTA was written to GCF_000227315.1_ASM22731v1_genomic.fna/markers.fasta
[2024-01-24 13:28:05,848] [INFO] Task started: Blastn
[2024-01-24 13:28:05,848] [INFO] Running command: blastn -query GCF_000227315.1_ASM22731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab299753-022f-4aa8-8c93-952e9b5c3aba/dqc_reference/reference_markers.fasta -out GCF_000227315.1_ASM22731v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:06,415] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:06,418] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:06,418] [INFO] Target genome list was writen to GCF_000227315.1_ASM22731v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:06,467] [INFO] Task started: fastANI
[2024-01-24 13:28:06,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b26db0-2797-4f38-818c-9019ffc3c792/GCF_000227315.1_ASM22731v1_genomic.fna.gz --refList GCF_000227315.1_ASM22731v1_genomic.fna/target_genomes.txt --output GCF_000227315.1_ASM22731v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:11,445] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:11,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab299753-022f-4aa8-8c93-952e9b5c3aba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:11,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab299753-022f-4aa8-8c93-952e9b5c3aba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:11,455] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:11,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:11,456] [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
Peptoniphilus indolicus	strain=ATCC 29427	GCA_000227315.1	33030	33030	type	True	99.9831	678	703	95	conclusive
Peptoniphilus indolicus	strain=NCTC11088	GCA_900454665.1	33030	33030	type	True	99.649	677	703	95	conclusive
Peptoniphilus asaccharolyticus	strain=FDAARGOS_1135	GCA_016791605.1	1258	1258	type	True	84.1369	460	703	95	below_threshold
Peptoniphilus asaccharolyticus	strain=DSM 20463	GCA_900176115.1	1258	1258	type	True	84.0949	462	703	95	below_threshold
Peptoniphilus senegalensis	strain=type strain: JC140	GCA_000321025.1	1465757	1465757	type	True	78.4129	105	703	95	below_threshold
Peptoniphilus obesi	strain=ph1	GCA_000311865.1	1472765	1472765	type	True	77.1636	108	703	95	below_threshold
Peptoniphilus mikwangii	strain=ChDC B134	GCA_000468535.1	1354300	1354300	type	True	76.8518	124	703	95	below_threshold
Anaerosphaera aminiphila	strain=DSM 21120	GCA_900129925.1	1120994	1120994	type	True	76.4564	102	703	95	below_threshold
Peptoniphilus stercorisuis	strain=DSM 27563	GCA_017874395.1	1436965	1436965	type	True	76.42	131	703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:11,458] [INFO] DFAST Taxonomy check result was written to GCF_000227315.1_ASM22731v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:11,458] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:11,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:11,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab299753-022f-4aa8-8c93-952e9b5c3aba/dqc_reference/checkm_data
[2024-01-24 13:28:11,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:11,485] [INFO] Task started: CheckM
[2024-01-24 13:28:11,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000227315.1_ASM22731v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000227315.1_ASM22731v1_genomic.fna/checkm_input GCF_000227315.1_ASM22731v1_genomic.fna/checkm_result
[2024-01-24 13:28:29,359] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:29,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,376] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:29,376] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:29,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000227315.1_ASM22731v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:29,377] [INFO] Task started: Blastn
[2024-01-24 13:28:29,377] [INFO] Running command: blastn -query GCF_000227315.1_ASM22731v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab299753-022f-4aa8-8c93-952e9b5c3aba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000227315.1_ASM22731v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:30,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:30,152] [INFO] Selected 17 target genomes.
[2024-01-24 13:28:30,153] [INFO] Target genome list was writen to GCF_000227315.1_ASM22731v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:30,223] [INFO] Task started: fastANI
[2024-01-24 13:28:30,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b26db0-2797-4f38-818c-9019ffc3c792/GCF_000227315.1_ASM22731v1_genomic.fna.gz --refList GCF_000227315.1_ASM22731v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000227315.1_ASM22731v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:36,494] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:36,507] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:36,507] [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_000227315.1	s__Peptoniphilus indolicus	99.9831	678	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus	95.0	99.65	99.65	0.96	0.96	2	conclusive
GCF_900176115.1	s__Peptoniphilus asaccharolyticus	84.069	464	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000321025.1	s__Peptoniphilus_A senegalensis	78.5464	101	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	98.73	97.46	0.94	0.88	3	-
GCF_901447155.2	s__Peptoniphilus_E catoniae	77.9361	82	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908115.1	s__Peptoniphilus_A gorbachii	77.8576	106	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	96.70	96.17	0.85	0.82	5	-
GCF_000311865.1	s__Peptoniphilus_E obesi	77.214	103	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000468535.1	s__Anaerosphaera mikwangii	76.904	120	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	99.03	99.03	0.96	0.96	2	-
GCF_001517665.2	s__Peptoniphilus_A phoceensis	76.7917	99	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	100.00	100.00	1.00	1.00	2	-
GCF_000183565.1	s__Peptoniphilus_A harei_A	76.7594	73	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	96.93	96.82	0.90	0.88	5	-
GCA_000952975.1	s__Peptoniphilus_E sp000952975	76.6396	69	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106515.1	s__Peptoniphilus_A lacydonensis	76.5705	103	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	99.18	98.94	0.92	0.87	4	-
GCF_000312025.1	s__Peptoniphilus_A timonensis	76.5362	97	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	N/A	N/A	N/A	N/A	1	-
GCF_900129925.1	s__Anaerosphaera aminiphila	76.5029	101	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874395.1	s__Anaerosphaera stercorisuis	76.4507	129	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001584565.1	s__Clostridium_Y paradoxum	75.5474	52	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridium_Y	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:36,509] [INFO] GTDB search result was written to GCF_000227315.1_ASM22731v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:36,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:36,513] [INFO] DFAST_QC result json was written to GCF_000227315.1_ASM22731v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:36,513] [INFO] DFAST_QC completed!
[2024-01-24 13:28:36,513] [INFO] Total running time: 0h0m36s