[2024-01-24 12:23:03,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,953] [INFO] DQC Reference Directory: /var/lib/cwl/stg72538924-e2a5-42b4-aeec-036f54983fe8/dqc_reference
[2024-01-24 12:23:05,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,440] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg49086764-e928-4cc4-8c79-29f704dae75f/GCF_019795105.1_ASM1979510v1_genomic.fna.gz | prodigal -d GCF_019795105.1_ASM1979510v1_genomic.fna/cds.fna -a GCF_019795105.1_ASM1979510v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:11,281] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:11,282] [INFO] Task started: HMMsearch
[2024-01-24 12:23:11,282] [INFO] Running command: hmmsearch --tblout GCF_019795105.1_ASM1979510v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72538924-e2a5-42b4-aeec-036f54983fe8/dqc_reference/reference_markers.hmm GCF_019795105.1_ASM1979510v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:11,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:11,514] [INFO] Found 6/6 markers.
[2024-01-24 12:23:11,538] [INFO] Query marker FASTA was written to GCF_019795105.1_ASM1979510v1_genomic.fna/markers.fasta
[2024-01-24 12:23:11,539] [INFO] Task started: Blastn
[2024-01-24 12:23:11,539] [INFO] Running command: blastn -query GCF_019795105.1_ASM1979510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72538924-e2a5-42b4-aeec-036f54983fe8/dqc_reference/reference_markers.fasta -out GCF_019795105.1_ASM1979510v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:12,152] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:12,157] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:12,157] [INFO] Target genome list was writen to GCF_019795105.1_ASM1979510v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:12,164] [INFO] Task started: fastANI
[2024-01-24 12:23:12,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg49086764-e928-4cc4-8c79-29f704dae75f/GCF_019795105.1_ASM1979510v1_genomic.fna.gz --refList GCF_019795105.1_ASM1979510v1_genomic.fna/target_genomes.txt --output GCF_019795105.1_ASM1979510v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:20,916] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72538924-e2a5-42b4-aeec-036f54983fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:20,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72538924-e2a5-42b4-aeec-036f54983fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:20,926] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:20,927] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:20,927] [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
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	78.72	77	642	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	78.1087	56	642	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	77.2926	56	642	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	77.2708	57	642	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	77.0823	55	642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:20,928] [INFO] DFAST Taxonomy check result was written to GCF_019795105.1_ASM1979510v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:20,929] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:20,929] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:20,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72538924-e2a5-42b4-aeec-036f54983fe8/dqc_reference/checkm_data
[2024-01-24 12:23:20,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:20,951] [INFO] Task started: CheckM
[2024-01-24 12:23:20,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019795105.1_ASM1979510v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019795105.1_ASM1979510v1_genomic.fna/checkm_input GCF_019795105.1_ASM1979510v1_genomic.fna/checkm_result
[2024-01-24 12:23:44,550] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:44,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:44,573] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:44,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:44,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019795105.1_ASM1979510v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:44,574] [INFO] Task started: Blastn
[2024-01-24 12:23:44,574] [INFO] Running command: blastn -query GCF_019795105.1_ASM1979510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72538924-e2a5-42b4-aeec-036f54983fe8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019795105.1_ASM1979510v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:45,465] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:45,469] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:45,469] [INFO] Target genome list was writen to GCF_019795105.1_ASM1979510v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:45,504] [INFO] Task started: fastANI
[2024-01-24 12:23:45,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg49086764-e928-4cc4-8c79-29f704dae75f/GCF_019795105.1_ASM1979510v1_genomic.fna.gz --refList GCF_019795105.1_ASM1979510v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019795105.1_ASM1979510v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:53,317] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:53,328] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:53,328] [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_900176655.1	s__Collinsella vaginalis	78.72	77	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.31	99.31	0.99	0.99	2	-
GCF_902501965.1	s__Collinsella sp900556495	78.1724	58	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.47	98.05	0.92	0.92	3	-
GCA_015062655.1	s__Collinsella sp015062655	77.8912	73	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018889955.1	s__Collinsella sp018889955	77.6029	71	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541195.1	s__Collinsella sp900541195	77.2308	51	642	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:53,330] [INFO] GTDB search result was written to GCF_019795105.1_ASM1979510v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:53,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:53,334] [INFO] DFAST_QC result json was written to GCF_019795105.1_ASM1979510v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:53,334] [INFO] DFAST_QC completed!
[2024-01-24 12:23:53,334] [INFO] Total running time: 0h0m49s