[2024-01-24 13:25:27,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:27,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:27,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg0737bd98-a506-4588-90ae-6f18200934b5/dqc_reference
[2024-01-24 13:25:28,536] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:28,537] [INFO] Task started: Prodigal
[2024-01-24 13:25:28,537] [INFO] Running command: gunzip -c /var/lib/cwl/stga5720e6c-4c9c-40fd-841c-642aa90e66e0/GCF_018919265.1_ASM1891926v1_genomic.fna.gz | prodigal -d GCF_018919265.1_ASM1891926v1_genomic.fna/cds.fna -a GCF_018919265.1_ASM1891926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:32,351] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:32,352] [INFO] Task started: HMMsearch
[2024-01-24 13:25:32,352] [INFO] Running command: hmmsearch --tblout GCF_018919265.1_ASM1891926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0737bd98-a506-4588-90ae-6f18200934b5/dqc_reference/reference_markers.hmm GCF_018919265.1_ASM1891926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:32,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:32,602] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga5720e6c-4c9c-40fd-841c-642aa90e66e0/GCF_018919265.1_ASM1891926v1_genomic.fna.gz]
[2024-01-24 13:25:32,625] [INFO] Query marker FASTA was written to GCF_018919265.1_ASM1891926v1_genomic.fna/markers.fasta
[2024-01-24 13:25:32,625] [INFO] Task started: Blastn
[2024-01-24 13:25:32,625] [INFO] Running command: blastn -query GCF_018919265.1_ASM1891926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0737bd98-a506-4588-90ae-6f18200934b5/dqc_reference/reference_markers.fasta -out GCF_018919265.1_ASM1891926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:33,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:33,265] [INFO] Selected 8 target genomes.
[2024-01-24 13:25:33,265] [INFO] Target genome list was writen to GCF_018919265.1_ASM1891926v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:33,274] [INFO] Task started: fastANI
[2024-01-24 13:25:33,274] [INFO] Running command: fastANI --query /var/lib/cwl/stga5720e6c-4c9c-40fd-841c-642aa90e66e0/GCF_018919265.1_ASM1891926v1_genomic.fna.gz --refList GCF_018919265.1_ASM1891926v1_genomic.fna/target_genomes.txt --output GCF_018919265.1_ASM1891926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:36,427] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:36,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0737bd98-a506-4588-90ae-6f18200934b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:36,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0737bd98-a506-4588-90ae-6f18200934b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:36,436] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:36,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:36,437] [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 ovalis	strain=MSJ-1	GCA_018919265.1	2841503	2841503	type	True	100.0	693	694	95	conclusive
Peptoniphilus gorbachii	strain=DSM 21461	GCA_016908115.1	411567	411567	type	True	80.2324	285	694	95	below_threshold
Peptoniphilus grossensis	strain=ph5	GCA_000311825.1	1465756	1465756	type	True	80.2227	255	694	95	below_threshold
Peptoniphilus senegalensis	strain=type strain: JC140	GCA_000321025.1	1465757	1465757	type	True	80.147	283	694	95	below_threshold
Peptoniphilus phoceensis	strain=SIT15	GCA_001517665.2	1720298	1720298	type	True	80.0269	295	694	95	below_threshold
Peptoniphilus timonensis	strain=JC401	GCA_000312025.1	1268254	1268254	type	True	79.6118	278	694	95	below_threshold
Peptoniphilus vaginalis	strain=KhD- 2	GCA_900176605.1	1756987	1756987	type	True	78.9408	232	694	95	below_threshold
Peptoniphilus stercorisuis	strain=DSM 27563	GCA_017874395.1	1436965	1436965	type	True	76.7359	123	694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:36,438] [INFO] DFAST Taxonomy check result was written to GCF_018919265.1_ASM1891926v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:36,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:36,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:36,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0737bd98-a506-4588-90ae-6f18200934b5/dqc_reference/checkm_data
[2024-01-24 13:25:36,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:36,465] [INFO] Task started: CheckM
[2024-01-24 13:25:36,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018919265.1_ASM1891926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018919265.1_ASM1891926v1_genomic.fna/checkm_input GCF_018919265.1_ASM1891926v1_genomic.fna/checkm_result
[2024-01-24 13:25:55,371] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:55,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:55,391] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:55,392] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:55,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018919265.1_ASM1891926v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:55,393] [INFO] Task started: Blastn
[2024-01-24 13:25:55,393] [INFO] Running command: blastn -query GCF_018919265.1_ASM1891926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0737bd98-a506-4588-90ae-6f18200934b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_018919265.1_ASM1891926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:56,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:56,179] [INFO] Selected 10 target genomes.
[2024-01-24 13:25:56,179] [INFO] Target genome list was writen to GCF_018919265.1_ASM1891926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:56,187] [INFO] Task started: fastANI
[2024-01-24 13:25:56,187] [INFO] Running command: fastANI --query /var/lib/cwl/stga5720e6c-4c9c-40fd-841c-642aa90e66e0/GCF_018919265.1_ASM1891926v1_genomic.fna.gz --refList GCF_018919265.1_ASM1891926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018919265.1_ASM1891926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:00,112] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:00,127] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:00,127] [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_018919265.1	s__Peptoniphilus_A sp018919265	100.0	693	694	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000183565.1	s__Peptoniphilus_A harei_A	80.6013	260	694	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	-
GCF_016908115.1	s__Peptoniphilus_A gorbachii	80.2619	282	694	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_000311825.1	s__Peptoniphilus_A grossensis	80.2168	256	694	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_000321025.1	s__Peptoniphilus_A senegalensis	80.1047	284	694	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_001517665.2	s__Peptoniphilus_A phoceensis	80.0269	295	694	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_900106515.1	s__Peptoniphilus_A lacydonensis	79.8403	277	694	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_012976305.1	s__Peptoniphilus_A faecalis	79.7815	292	694	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	98.47	98.47	0.83	0.83	2	-
GCF_000312025.1	s__Peptoniphilus_A timonensis	79.6118	278	694	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_900176605.1	s__Peptoniphilus_A vaginalis	78.9437	232	694	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.24	97.24	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:00,129] [INFO] GTDB search result was written to GCF_018919265.1_ASM1891926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:00,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:00,133] [INFO] DFAST_QC result json was written to GCF_018919265.1_ASM1891926v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:00,134] [INFO] DFAST_QC completed!
[2024-01-24 13:26:00,134] [INFO] Total running time: 0h0m33s