[2024-01-24 14:21:50,767] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,769] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0cd2f0b-c67b-449f-bfde-654fc6629bb2/dqc_reference
[2024-01-24 14:21:52,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,172] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,172] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b2c158c-fa4e-4743-9a25-30ba9f81b8db/GCF_016552165.1_ASM1655216v1_genomic.fna.gz | prodigal -d GCF_016552165.1_ASM1655216v1_genomic.fna/cds.fna -a GCF_016552165.1_ASM1655216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:21:55,154] [INFO] Task succeeded: Prodigal
[2024-01-24 14:21:55,155] [INFO] Task started: HMMsearch
[2024-01-24 14:21:55,155] [INFO] Running command: hmmsearch --tblout GCF_016552165.1_ASM1655216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0cd2f0b-c67b-449f-bfde-654fc6629bb2/dqc_reference/reference_markers.hmm GCF_016552165.1_ASM1655216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:21:55,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:21:55,383] [INFO] Found 6/6 markers.
[2024-01-24 14:21:55,403] [INFO] Query marker FASTA was written to GCF_016552165.1_ASM1655216v1_genomic.fna/markers.fasta
[2024-01-24 14:21:55,403] [INFO] Task started: Blastn
[2024-01-24 14:21:55,403] [INFO] Running command: blastn -query GCF_016552165.1_ASM1655216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cd2f0b-c67b-449f-bfde-654fc6629bb2/dqc_reference/reference_markers.fasta -out GCF_016552165.1_ASM1655216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:55,991] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:55,994] [INFO] Selected 15 target genomes.
[2024-01-24 14:21:55,995] [INFO] Target genome list was writen to GCF_016552165.1_ASM1655216v1_genomic.fna/target_genomes.txt
[2024-01-24 14:21:56,057] [INFO] Task started: fastANI
[2024-01-24 14:21:56,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2c158c-fa4e-4743-9a25-30ba9f81b8db/GCF_016552165.1_ASM1655216v1_genomic.fna.gz --refList GCF_016552165.1_ASM1655216v1_genomic.fna/target_genomes.txt --output GCF_016552165.1_ASM1655216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:01,153] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:01,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0cd2f0b-c67b-449f-bfde-654fc6629bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:01,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0cd2f0b-c67b-449f-bfde-654fc6629bb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:01,160] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:01,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:01,161] [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
Parvimonas parva	strain=S3374	GCA_016552165.1	2769485	2769485	type	True	100.0	547	548	95	conclusive
Parvimonas micra	strain=NCTC11808	GCA_900637905.1	33033	33033	type	True	85.4228	378	548	95	below_threshold
Parvimonas micra	strain=ATCC 33270	GCA_000154405.1	33033	33033	type	True	85.42	377	548	95	below_threshold
Peptoniphilus gorbachii	strain=DSM 21461	GCA_016908115.1	411567	411567	type	True	77.1264	54	548	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:01,164] [INFO] DFAST Taxonomy check result was written to GCF_016552165.1_ASM1655216v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:01,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:01,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:01,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0cd2f0b-c67b-449f-bfde-654fc6629bb2/dqc_reference/checkm_data
[2024-01-24 14:22:01,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:01,188] [INFO] Task started: CheckM
[2024-01-24 14:22:01,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016552165.1_ASM1655216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016552165.1_ASM1655216v1_genomic.fna/checkm_input GCF_016552165.1_ASM1655216v1_genomic.fna/checkm_result
[2024-01-24 14:22:18,973] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:18,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:18,995] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:18,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:18,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016552165.1_ASM1655216v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:18,996] [INFO] Task started: Blastn
[2024-01-24 14:22:18,996] [INFO] Running command: blastn -query GCF_016552165.1_ASM1655216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cd2f0b-c67b-449f-bfde-654fc6629bb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016552165.1_ASM1655216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:19,866] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:19,879] [INFO] Selected 7 target genomes.
[2024-01-24 14:22:19,879] [INFO] Target genome list was writen to GCF_016552165.1_ASM1655216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:19,889] [INFO] Task started: fastANI
[2024-01-24 14:22:19,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b2c158c-fa4e-4743-9a25-30ba9f81b8db/GCF_016552165.1_ASM1655216v1_genomic.fna.gz --refList GCF_016552165.1_ASM1655216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016552165.1_ASM1655216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:22,821] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:22,828] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:22,828] [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_001553085.1	s__Parvimonas sp001553085	97.7663	442	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	97.94	97.94	0.87	0.87	2	conclusive
GCF_000223315.1	s__Parvimonas sp000223315	85.693	367	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637905.1	s__Parvimonas micra	85.4118	379	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	98.21	97.17	0.92	0.77	11	-
GCF_000214475.1	s__Parvimonas sp000214475	85.1409	369	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	97.82	97.68	0.91	0.90	3	-
GCA_015257355.1	s__Parvimonas sp015257355	84.0807	276	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001552895.1	s__Parvimonas sp001552895	81.6355	250	548	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Parvimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:22,832] [INFO] GTDB search result was written to GCF_016552165.1_ASM1655216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:22,833] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:22,836] [INFO] DFAST_QC result json was written to GCF_016552165.1_ASM1655216v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:22,837] [INFO] DFAST_QC completed!
[2024-01-24 14:22:22,837] [INFO] Total running time: 0h0m32s