[2024-01-24 11:26:54,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg907d6233-70a9-41e8-8710-2a2f5796ccb7/dqc_reference
[2024-01-24 11:26:58,224] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,225] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,226] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e0d3b6d-fd1f-4d87-af9d-873124e6285f/GCF_900155585.1_PRJEB18033_genomic.fna.gz | prodigal -d GCF_900155585.1_PRJEB18033_genomic.fna/cds.fna -a GCF_900155585.1_PRJEB18033_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:03,122] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:03,122] [INFO] Task started: HMMsearch
[2024-01-24 11:27:03,123] [INFO] Running command: hmmsearch --tblout GCF_900155585.1_PRJEB18033_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg907d6233-70a9-41e8-8710-2a2f5796ccb7/dqc_reference/reference_markers.hmm GCF_900155585.1_PRJEB18033_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:03,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:03,371] [INFO] Found 6/6 markers.
[2024-01-24 11:27:03,389] [INFO] Query marker FASTA was written to GCF_900155585.1_PRJEB18033_genomic.fna/markers.fasta
[2024-01-24 11:27:03,390] [INFO] Task started: Blastn
[2024-01-24 11:27:03,390] [INFO] Running command: blastn -query GCF_900155585.1_PRJEB18033_genomic.fna/markers.fasta -db /var/lib/cwl/stg907d6233-70a9-41e8-8710-2a2f5796ccb7/dqc_reference/reference_markers.fasta -out GCF_900155585.1_PRJEB18033_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:03,974] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:03,978] [INFO] Selected 9 target genomes.
[2024-01-24 11:27:03,978] [INFO] Target genome list was writen to GCF_900155585.1_PRJEB18033_genomic.fna/target_genomes.txt
[2024-01-24 11:27:03,988] [INFO] Task started: fastANI
[2024-01-24 11:27:03,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0d3b6d-fd1f-4d87-af9d-873124e6285f/GCF_900155585.1_PRJEB18033_genomic.fna.gz --refList GCF_900155585.1_PRJEB18033_genomic.fna/target_genomes.txt --output GCF_900155585.1_PRJEB18033_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:07,883] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:07,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg907d6233-70a9-41e8-8710-2a2f5796ccb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:07,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg907d6233-70a9-41e8-8710-2a2f5796ccb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:07,889] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:07,889] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:07,889] [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 urinimassiliensis	strain=Marseille-P3195	GCA_900155585.1	1871017	1871017	type	True	100.0	605	605	95	conclusive
Peptoniphilus pacaensis	strain=Kh-D5	GCA_900088125.1	1776390	1776390	type	True	92.1605	509	605	95	below_threshold
Peptoniphilus rachelemmaiella	strain=EMRHCC_23	GCA_943169845.1	2811779	2811779	type	True	85.9137	462	605	95	below_threshold
Peptoniphilus nemausensis	strain=1804121828	GCA_903819165.1	2582829	2582829	type	True	79.5432	252	605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:07,891] [INFO] DFAST Taxonomy check result was written to GCF_900155585.1_PRJEB18033_genomic.fna/tc_result.tsv
[2024-01-24 11:27:07,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:07,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:07,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg907d6233-70a9-41e8-8710-2a2f5796ccb7/dqc_reference/checkm_data
[2024-01-24 11:27:07,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:07,920] [INFO] Task started: CheckM
[2024-01-24 11:27:07,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155585.1_PRJEB18033_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155585.1_PRJEB18033_genomic.fna/checkm_input GCF_900155585.1_PRJEB18033_genomic.fna/checkm_result
[2024-01-24 11:27:30,716] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:30,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,739] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:30,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:30,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155585.1_PRJEB18033_genomic.fna/markers.fasta)
[2024-01-24 11:27:30,740] [INFO] Task started: Blastn
[2024-01-24 11:27:30,740] [INFO] Running command: blastn -query GCF_900155585.1_PRJEB18033_genomic.fna/markers.fasta -db /var/lib/cwl/stg907d6233-70a9-41e8-8710-2a2f5796ccb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155585.1_PRJEB18033_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:31,648] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:31,652] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:31,652] [INFO] Target genome list was writen to GCF_900155585.1_PRJEB18033_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:31,669] [INFO] Task started: fastANI
[2024-01-24 11:27:31,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e0d3b6d-fd1f-4d87-af9d-873124e6285f/GCF_900155585.1_PRJEB18033_genomic.fna.gz --refList GCF_900155585.1_PRJEB18033_genomic.fna/target_genomes_gtdb.txt --output GCF_900155585.1_PRJEB18033_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:35,568] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:35,575] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:35,575] [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_900155585.1	s__Peptoniphilus_C urinimassiliensis	100.0	605	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900088125.1	s__Peptoniphilus_C pacaensis	92.1636	508	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363535.1	s__Peptoniphilus_C sp902363535	86.0561	447	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	97.41	97.41	0.94	0.94	2	-
GCF_900343085.1	s__Peptoniphilus_C sp900343085	85.6708	439	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903819165.1	s__Peptoniphilus_C nemausensis	79.5432	252	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900638585.1	s__Peptoniphilus_C ivorii	78.1769	178	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:35,577] [INFO] GTDB search result was written to GCF_900155585.1_PRJEB18033_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:35,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:35,580] [INFO] DFAST_QC result json was written to GCF_900155585.1_PRJEB18033_genomic.fna/dqc_result.json
[2024-01-24 11:27:35,580] [INFO] DFAST_QC completed!
[2024-01-24 11:27:35,581] [INFO] Total running time: 0h0m41s