[2024-01-25 20:17:35,790] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:35,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:35,792] [INFO] DQC Reference Directory: /var/lib/cwl/stgad9fdc30-54eb-43e6-b179-6b7be7b888be/dqc_reference
[2024-01-25 20:17:36,920] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:36,921] [INFO] Task started: Prodigal
[2024-01-25 20:17:36,921] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a4d2cef-1ad0-478a-963a-cb3cbd9f146b/GCF_000321025.1_ASM32102v1_genomic.fna.gz | prodigal -d GCF_000321025.1_ASM32102v1_genomic.fna/cds.fna -a GCF_000321025.1_ASM32102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:39,939] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:39,939] [INFO] Task started: HMMsearch
[2024-01-25 20:17:39,939] [INFO] Running command: hmmsearch --tblout GCF_000321025.1_ASM32102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad9fdc30-54eb-43e6-b179-6b7be7b888be/dqc_reference/reference_markers.hmm GCF_000321025.1_ASM32102v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:40,124] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:40,126] [INFO] Found 6/6 markers.
[2024-01-25 20:17:40,144] [INFO] Query marker FASTA was written to GCF_000321025.1_ASM32102v1_genomic.fna/markers.fasta
[2024-01-25 20:17:40,145] [INFO] Task started: Blastn
[2024-01-25 20:17:40,145] [INFO] Running command: blastn -query GCF_000321025.1_ASM32102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad9fdc30-54eb-43e6-b179-6b7be7b888be/dqc_reference/reference_markers.fasta -out GCF_000321025.1_ASM32102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:40,689] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:40,695] [INFO] Selected 8 target genomes.
[2024-01-25 20:17:40,696] [INFO] Target genome list was writen to GCF_000321025.1_ASM32102v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:40,702] [INFO] Task started: fastANI
[2024-01-25 20:17:40,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4d2cef-1ad0-478a-963a-cb3cbd9f146b/GCF_000321025.1_ASM32102v1_genomic.fna.gz --refList GCF_000321025.1_ASM32102v1_genomic.fna/target_genomes.txt --output GCF_000321025.1_ASM32102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:44,036] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:44,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad9fdc30-54eb-43e6-b179-6b7be7b888be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:44,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad9fdc30-54eb-43e6-b179-6b7be7b888be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:44,043] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:44,043] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:44,043] [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 senegalensis	strain=type strain: JC140	GCA_000321025.1	1465757	1465757	type	True	99.9987	606	611	95	conclusive
Peptoniphilus grossensis	strain=ph5	GCA_000311825.1	1465756	1465756	type	True	88.396	487	611	95	below_threshold
Peptoniphilus gorbachii	strain=DSM 21461	GCA_016908115.1	411567	411567	type	True	87.5959	471	611	95	below_threshold
Peptoniphilus harei	strain=NCTC13076	GCA_900454685.1	54005	54005	suspected-type	True	83.2343	402	611	95	below_threshold
Peptoniphilus phoceensis	strain=SIT15	GCA_001517665.2	1720298	1720298	type	True	83.2055	399	611	95	below_threshold
Peptoniphilus timonensis	strain=JC401	GCA_000312025.1	1268254	1268254	type	True	82.978	393	611	95	below_threshold
Peptoniphilus vaginalis	strain=KhD- 2	GCA_900176605.1	1756987	1756987	type	True	82.42	375	611	95	below_threshold
Peptoniphilus stercorisuis	strain=DSM 27563	GCA_017874395.1	1436965	1436965	type	True	76.1931	95	611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:44,044] [INFO] DFAST Taxonomy check result was written to GCF_000321025.1_ASM32102v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:44,045] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:44,045] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:44,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad9fdc30-54eb-43e6-b179-6b7be7b888be/dqc_reference/checkm_data
[2024-01-25 20:17:44,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:44,067] [INFO] Task started: CheckM
[2024-01-25 20:17:44,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000321025.1_ASM32102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000321025.1_ASM32102v1_genomic.fna/checkm_input GCF_000321025.1_ASM32102v1_genomic.fna/checkm_result
[2024-01-25 20:17:59,444] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:59,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:59,458] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:59,458] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:59,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000321025.1_ASM32102v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:59,459] [INFO] Task started: Blastn
[2024-01-25 20:17:59,459] [INFO] Running command: blastn -query GCF_000321025.1_ASM32102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad9fdc30-54eb-43e6-b179-6b7be7b888be/dqc_reference/reference_markers_gtdb.fasta -out GCF_000321025.1_ASM32102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:00,221] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:00,224] [INFO] Selected 8 target genomes.
[2024-01-25 20:18:00,224] [INFO] Target genome list was writen to GCF_000321025.1_ASM32102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:00,231] [INFO] Task started: fastANI
[2024-01-25 20:18:00,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4d2cef-1ad0-478a-963a-cb3cbd9f146b/GCF_000321025.1_ASM32102v1_genomic.fna.gz --refList GCF_000321025.1_ASM32102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000321025.1_ASM32102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:03,618] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:03,624] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:03,625] [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_000321025.1	s__Peptoniphilus_A senegalensis	99.9987	606	611	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	conclusive
GCF_000311825.1	s__Peptoniphilus_A grossensis	88.396	487	611	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_016908115.1	s__Peptoniphilus_A gorbachii	87.5959	471	611	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_012976305.1	s__Peptoniphilus_A faecalis	83.9467	412	611	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_001517665.2	s__Peptoniphilus_A phoceensis	83.208	398	611	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_000312025.1	s__Peptoniphilus_A timonensis	82.9563	394	611	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	82.4713	372	611	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	-
GCF_900106515.1	s__Peptoniphilus_A lacydonensis	82.455	378	611	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	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:03,626] [INFO] GTDB search result was written to GCF_000321025.1_ASM32102v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:03,628] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:03,630] [INFO] DFAST_QC result json was written to GCF_000321025.1_ASM32102v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:03,630] [INFO] DFAST_QC completed!
[2024-01-25 20:18:03,631] [INFO] Total running time: 0h0m28s