[2023-06-29 19:20:13,696] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:20:13,699] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:20:13,700] [INFO] DQC Reference Directory: /var/lib/cwl/stg64feb8a6-69bc-4c0f-a042-cf829370cb2f/dqc_reference
[2023-06-29 19:20:15,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:20:15,073] [INFO] Task started: Prodigal
[2023-06-29 19:20:15,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg982c73d7-a070-4038-aa87-771f3b157a6a/GCA_025348365.1_ASM2534836v1_genomic.fna.gz | prodigal -d GCA_025348365.1_ASM2534836v1_genomic.fna/cds.fna -a GCA_025348365.1_ASM2534836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:20:16,449] [INFO] Task succeeded: Prodigal
[2023-06-29 19:20:16,449] [INFO] Task started: HMMsearch
[2023-06-29 19:20:16,449] [INFO] Running command: hmmsearch --tblout GCA_025348365.1_ASM2534836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64feb8a6-69bc-4c0f-a042-cf829370cb2f/dqc_reference/reference_markers.hmm GCA_025348365.1_ASM2534836v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:20:16,563] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:20:16,564] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg982c73d7-a070-4038-aa87-771f3b157a6a/GCA_025348365.1_ASM2534836v1_genomic.fna.gz]
[2023-06-29 19:20:16,573] [INFO] Query marker FASTA was written to GCA_025348365.1_ASM2534836v1_genomic.fna/markers.fasta
[2023-06-29 19:20:16,573] [INFO] Task started: Blastn
[2023-06-29 19:20:16,573] [INFO] Running command: blastn -query GCA_025348365.1_ASM2534836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64feb8a6-69bc-4c0f-a042-cf829370cb2f/dqc_reference/reference_markers.fasta -out GCA_025348365.1_ASM2534836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:20:17,070] [INFO] Task succeeded: Blastn
[2023-06-29 19:20:17,074] [INFO] Selected 11 target genomes.
[2023-06-29 19:20:17,074] [INFO] Target genome list was writen to GCA_025348365.1_ASM2534836v1_genomic.fna/target_genomes.txt
[2023-06-29 19:20:17,078] [INFO] Task started: fastANI
[2023-06-29 19:20:17,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg982c73d7-a070-4038-aa87-771f3b157a6a/GCA_025348365.1_ASM2534836v1_genomic.fna.gz --refList GCA_025348365.1_ASM2534836v1_genomic.fna/target_genomes.txt --output GCA_025348365.1_ASM2534836v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:20:20,347] [INFO] Task succeeded: fastANI
[2023-06-29 19:20:20,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64feb8a6-69bc-4c0f-a042-cf829370cb2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:20:20,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64feb8a6-69bc-4c0f-a042-cf829370cb2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:20:20,352] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 19:20:20,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 19:20:20,353] [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
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.9643	91	97	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.8557	89	97	95	conclusive
--------------------------------------------------------------------------------
[2023-06-29 19:20:20,355] [INFO] DFAST Taxonomy check result was written to GCA_025348365.1_ASM2534836v1_genomic.fna/tc_result.tsv
[2023-06-29 19:20:20,355] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:20:20,355] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:20:20,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64feb8a6-69bc-4c0f-a042-cf829370cb2f/dqc_reference/checkm_data
[2023-06-29 19:20:20,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:20:20,367] [INFO] Task started: CheckM
[2023-06-29 19:20:20,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025348365.1_ASM2534836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025348365.1_ASM2534836v1_genomic.fna/checkm_input GCA_025348365.1_ASM2534836v1_genomic.fna/checkm_result
[2023-06-29 19:20:33,392] [INFO] Task succeeded: CheckM
[2023-06-29 19:20:33,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:20:33,420] [INFO] ===== Completeness check finished =====
[2023-06-29 19:20:33,420] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:20:33,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025348365.1_ASM2534836v1_genomic.fna/markers.fasta)
[2023-06-29 19:20:33,421] [INFO] Task started: Blastn
[2023-06-29 19:20:33,421] [INFO] Running command: blastn -query GCA_025348365.1_ASM2534836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64feb8a6-69bc-4c0f-a042-cf829370cb2f/dqc_reference/reference_markers_gtdb.fasta -out GCA_025348365.1_ASM2534836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:20:33,881] [INFO] Task succeeded: Blastn
[2023-06-29 19:20:33,885] [INFO] Selected 13 target genomes.
[2023-06-29 19:20:33,885] [INFO] Target genome list was writen to GCA_025348365.1_ASM2534836v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:20:33,927] [INFO] Task started: fastANI
[2023-06-29 19:20:33,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg982c73d7-a070-4038-aa87-771f3b157a6a/GCA_025348365.1_ASM2534836v1_genomic.fna.gz --refList GCA_025348365.1_ASM2534836v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025348365.1_ASM2534836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:20:37,383] [INFO] Task succeeded: fastANI
[2023-06-29 19:20:37,386] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:20:37,386] [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_000160875.1	s__Lactobacillus iners	98.9643	91	97	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
--------------------------------------------------------------------------------
[2023-06-29 19:20:37,389] [INFO] GTDB search result was written to GCA_025348365.1_ASM2534836v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:20:37,389] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:20:37,392] [INFO] DFAST_QC result json was written to GCA_025348365.1_ASM2534836v1_genomic.fna/dqc_result.json
[2023-06-29 19:20:37,392] [INFO] DFAST_QC completed!
[2023-06-29 19:20:37,392] [INFO] Total running time: 0h0m24s