[2024-01-25 20:11:35,364] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:35,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:35,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg21970b86-17f4-490e-ae24-5a4f811e3def/dqc_reference
[2024-01-25 20:11:36,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:36,523] [INFO] Task started: Prodigal
[2024-01-25 20:11:36,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg95d02652-ac69-4dc7-bd9d-df259303698e/GCF_030815095.1_ASM3081509v1_genomic.fna.gz | prodigal -d GCF_030815095.1_ASM3081509v1_genomic.fna/cds.fna -a GCF_030815095.1_ASM3081509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:11:40,451] [INFO] Task succeeded: Prodigal
[2024-01-25 20:11:40,451] [INFO] Task started: HMMsearch
[2024-01-25 20:11:40,451] [INFO] Running command: hmmsearch --tblout GCF_030815095.1_ASM3081509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21970b86-17f4-490e-ae24-5a4f811e3def/dqc_reference/reference_markers.hmm GCF_030815095.1_ASM3081509v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:11:40,633] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:11:40,634] [INFO] Found 6/6 markers.
[2024-01-25 20:11:40,650] [INFO] Query marker FASTA was written to GCF_030815095.1_ASM3081509v1_genomic.fna/markers.fasta
[2024-01-25 20:11:40,650] [INFO] Task started: Blastn
[2024-01-25 20:11:40,650] [INFO] Running command: blastn -query GCF_030815095.1_ASM3081509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21970b86-17f4-490e-ae24-5a4f811e3def/dqc_reference/reference_markers.fasta -out GCF_030815095.1_ASM3081509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:11:41,212] [INFO] Task succeeded: Blastn
[2024-01-25 20:11:41,215] [INFO] Selected 15 target genomes.
[2024-01-25 20:11:41,215] [INFO] Target genome list was writen to GCF_030815095.1_ASM3081509v1_genomic.fna/target_genomes.txt
[2024-01-25 20:11:41,255] [INFO] Task started: fastANI
[2024-01-25 20:11:41,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d02652-ac69-4dc7-bd9d-df259303698e/GCF_030815095.1_ASM3081509v1_genomic.fna.gz --refList GCF_030815095.1_ASM3081509v1_genomic.fna/target_genomes.txt --output GCF_030815095.1_ASM3081509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:11:49,904] [INFO] Task succeeded: fastANI
[2024-01-25 20:11:49,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21970b86-17f4-490e-ae24-5a4f811e3def/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:11:49,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21970b86-17f4-490e-ae24-5a4f811e3def/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:11:49,910] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:11:49,910] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:11:49,910] [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 pacaensis	strain=Kh-D5	GCA_900088125.1	1776390	1776390	type	True	78.0074	172	530	95	below_threshold
Peptoniphilus rachelemmaiella	strain=EMRHCC_23	GCA_943169845.1	2811779	2811779	type	True	77.9782	161	530	95	below_threshold
Peptoniphilus nemausensis	strain=1804121828	GCA_903819165.1	2582829	2582829	type	True	77.6712	131	530	95	below_threshold
Peptoniphilus urinimassiliensis	strain=Marseille-P3195	GCA_900155585.1	1871017	1871017	type	True	77.6567	169	530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:11:49,912] [INFO] DFAST Taxonomy check result was written to GCF_030815095.1_ASM3081509v1_genomic.fna/tc_result.tsv
[2024-01-25 20:11:49,912] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:11:49,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:11:49,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21970b86-17f4-490e-ae24-5a4f811e3def/dqc_reference/checkm_data
[2024-01-25 20:11:49,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:11:49,934] [INFO] Task started: CheckM
[2024-01-25 20:11:49,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030815095.1_ASM3081509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030815095.1_ASM3081509v1_genomic.fna/checkm_input GCF_030815095.1_ASM3081509v1_genomic.fna/checkm_result
[2024-01-25 20:12:06,725] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:06,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:06,744] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:06,744] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:06,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030815095.1_ASM3081509v1_genomic.fna/markers.fasta)
[2024-01-25 20:12:06,745] [INFO] Task started: Blastn
[2024-01-25 20:12:06,745] [INFO] Running command: blastn -query GCF_030815095.1_ASM3081509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21970b86-17f4-490e-ae24-5a4f811e3def/dqc_reference/reference_markers_gtdb.fasta -out GCF_030815095.1_ASM3081509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:07,564] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:07,567] [INFO] Selected 15 target genomes.
[2024-01-25 20:12:07,567] [INFO] Target genome list was writen to GCF_030815095.1_ASM3081509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:07,597] [INFO] Task started: fastANI
[2024-01-25 20:12:07,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d02652-ac69-4dc7-bd9d-df259303698e/GCF_030815095.1_ASM3081509v1_genomic.fna.gz --refList GCF_030815095.1_ASM3081509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030815095.1_ASM3081509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:13,873] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:13,879] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:13,879] [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_900638585.1	s__Peptoniphilus_C ivorii	99.4507	485	530	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_900343085.1	s__Peptoniphilus_C sp900343085	79.769	194	530	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	78.146	184	530	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_900088125.1	s__Peptoniphilus_C pacaensis	78.0074	172	530	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	77.6712	131	530	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_900155585.1	s__Peptoniphilus_C urinimassiliensis	77.6379	170	530	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_001553115.1	s__Peptoniphilus_C coxii	77.397	119	530	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	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:13,881] [INFO] GTDB search result was written to GCF_030815095.1_ASM3081509v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:13,881] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:13,883] [INFO] DFAST_QC result json was written to GCF_030815095.1_ASM3081509v1_genomic.fna/dqc_result.json
[2024-01-25 20:12:13,884] [INFO] DFAST_QC completed!
[2024-01-25 20:12:13,884] [INFO] Total running time: 0h0m39s