[2024-01-25 17:34:07,126] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg50bc154b-8602-4d46-a469-a38dbd1e9f44/dqc_reference
[2024-01-25 17:34:08,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,951] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbc8841d-83ef-4ed5-80b9-71aaa78d590f/GCF_016791605.1_ASM1679160v1_genomic.fna.gz | prodigal -d GCF_016791605.1_ASM1679160v1_genomic.fna/cds.fna -a GCF_016791605.1_ASM1679160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:12,910] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:12,911] [INFO] Task started: HMMsearch
[2024-01-25 17:34:12,911] [INFO] Running command: hmmsearch --tblout GCF_016791605.1_ASM1679160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50bc154b-8602-4d46-a469-a38dbd1e9f44/dqc_reference/reference_markers.hmm GCF_016791605.1_ASM1679160v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:13,179] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:13,180] [INFO] Found 6/6 markers.
[2024-01-25 17:34:13,220] [INFO] Query marker FASTA was written to GCF_016791605.1_ASM1679160v1_genomic.fna/markers.fasta
[2024-01-25 17:34:13,221] [INFO] Task started: Blastn
[2024-01-25 17:34:13,221] [INFO] Running command: blastn -query GCF_016791605.1_ASM1679160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50bc154b-8602-4d46-a469-a38dbd1e9f44/dqc_reference/reference_markers.fasta -out GCF_016791605.1_ASM1679160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:14,059] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:14,062] [INFO] Selected 7 target genomes.
[2024-01-25 17:34:14,062] [INFO] Target genome list was writen to GCF_016791605.1_ASM1679160v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:14,179] [INFO] Task started: fastANI
[2024-01-25 17:34:14,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbc8841d-83ef-4ed5-80b9-71aaa78d590f/GCF_016791605.1_ASM1679160v1_genomic.fna.gz --refList GCF_016791605.1_ASM1679160v1_genomic.fna/target_genomes.txt --output GCF_016791605.1_ASM1679160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:25,021] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:25,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50bc154b-8602-4d46-a469-a38dbd1e9f44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:25,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50bc154b-8602-4d46-a469-a38dbd1e9f44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:25,030] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:25,030] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:25,030] [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 asaccharolyticus	strain=FDAARGOS_1135	GCA_016791605.1	1258	1258	type	True	100.0	763	771	95	conclusive
Peptoniphilus asaccharolyticus	strain=DSM 20463	GCA_900176115.1	1258	1258	type	True	99.9672	718	771	95	conclusive
Peptoniphilus indolicus	strain=NCTC11088	GCA_900454665.1	33030	33030	type	True	84.5059	463	771	95	below_threshold
Peptoniphilus indolicus	strain=ATCC 29427	GCA_000227315.1	33030	33030	type	True	84.3964	443	771	95	below_threshold
Peptoniphilus grossensis	strain=ph5	GCA_000311825.1	1465756	1465756	type	True	80.9772	102	771	95	below_threshold
Peptoniphilus mikwangii	strain=ChDC B134	GCA_000468535.1	1354300	1354300	type	True	77.8181	111	771	95	below_threshold
Anaerosphaera massiliensis	strain=Marseille-P4592	GCA_902167235.1	2040296	2040296	type	True	76.6531	79	771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:25,031] [INFO] DFAST Taxonomy check result was written to GCF_016791605.1_ASM1679160v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:25,032] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:25,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:25,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50bc154b-8602-4d46-a469-a38dbd1e9f44/dqc_reference/checkm_data
[2024-01-25 17:34:25,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:25,065] [INFO] Task started: CheckM
[2024-01-25 17:34:25,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016791605.1_ASM1679160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016791605.1_ASM1679160v1_genomic.fna/checkm_input GCF_016791605.1_ASM1679160v1_genomic.fna/checkm_result
[2024-01-25 17:34:42,720] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:42,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 17:34:42,739] [INFO] ===== Completeness check finished =====
[2024-01-25 17:34:42,739] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:34:42,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016791605.1_ASM1679160v1_genomic.fna/markers.fasta)
[2024-01-25 17:34:42,740] [INFO] Task started: Blastn
[2024-01-25 17:34:42,740] [INFO] Running command: blastn -query GCF_016791605.1_ASM1679160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50bc154b-8602-4d46-a469-a38dbd1e9f44/dqc_reference/reference_markers_gtdb.fasta -out GCF_016791605.1_ASM1679160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:43,658] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:43,661] [INFO] Selected 17 target genomes.
[2024-01-25 17:34:43,661] [INFO] Target genome list was writen to GCF_016791605.1_ASM1679160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:34:43,672] [INFO] Task started: fastANI
[2024-01-25 17:34:43,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbc8841d-83ef-4ed5-80b9-71aaa78d590f/GCF_016791605.1_ASM1679160v1_genomic.fna.gz --refList GCF_016791605.1_ASM1679160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016791605.1_ASM1679160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:34:53,703] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:53,710] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:34:53,710] [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_900176115.1	s__Peptoniphilus asaccharolyticus	99.9672	718	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus	95.0	99.97	99.97	0.98	0.98	2	conclusive
GCF_000227315.1	s__Peptoniphilus indolicus	84.4093	442	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus	95.0	99.65	99.65	0.96	0.96	2	-
GCF_000311825.1	s__Peptoniphilus_A grossensis	80.9336	103	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.39	95.38	0.93	0.87	4	-
GCF_900454685.1	s__Peptoniphilus_A harei	80.8119	95	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.43	96.58	0.91	0.87	7	-
GCF_000478985.1	s__Peptoniphilus_B sp000478985	80.5329	87	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129925.1	s__Anaerosphaera aminiphila	77.8675	78	771	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_000468535.1	s__Anaerosphaera mikwangii	77.8242	112	771	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_004006535.1	s__Anaerosphaera multitolerans	77.467	69	771	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	76.705	97	771	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:34:53,712] [INFO] GTDB search result was written to GCF_016791605.1_ASM1679160v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:34:53,712] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:34:53,715] [INFO] DFAST_QC result json was written to GCF_016791605.1_ASM1679160v1_genomic.fna/dqc_result.json
[2024-01-25 17:34:53,715] [INFO] DFAST_QC completed!
[2024-01-25 17:34:53,715] [INFO] Total running time: 0h0m47s