[2024-01-24 11:27:19,064] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,066] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg17e2c385-1c17-4645-8255-d7351eecd9bf/dqc_reference
[2024-01-24 11:27:20,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:20,290] [INFO] Task started: Prodigal
[2024-01-24 11:27:20,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg3378e891-c929-4e5a-acf0-1cb13f48c437/GCF_014207605.1_ASM1420760v1_genomic.fna.gz | prodigal -d GCF_014207605.1_ASM1420760v1_genomic.fna/cds.fna -a GCF_014207605.1_ASM1420760v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:24,485] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:24,486] [INFO] Task started: HMMsearch
[2024-01-24 11:27:24,486] [INFO] Running command: hmmsearch --tblout GCF_014207605.1_ASM1420760v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17e2c385-1c17-4645-8255-d7351eecd9bf/dqc_reference/reference_markers.hmm GCF_014207605.1_ASM1420760v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:24,697] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:24,698] [INFO] Found 6/6 markers.
[2024-01-24 11:27:24,717] [INFO] Query marker FASTA was written to GCF_014207605.1_ASM1420760v1_genomic.fna/markers.fasta
[2024-01-24 11:27:24,718] [INFO] Task started: Blastn
[2024-01-24 11:27:24,718] [INFO] Running command: blastn -query GCF_014207605.1_ASM1420760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e2c385-1c17-4645-8255-d7351eecd9bf/dqc_reference/reference_markers.fasta -out GCF_014207605.1_ASM1420760v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:25,388] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:25,391] [INFO] Selected 17 target genomes.
[2024-01-24 11:27:25,391] [INFO] Target genome list was writen to GCF_014207605.1_ASM1420760v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:25,481] [INFO] Task started: fastANI
[2024-01-24 11:27:25,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg3378e891-c929-4e5a-acf0-1cb13f48c437/GCF_014207605.1_ASM1420760v1_genomic.fna.gz --refList GCF_014207605.1_ASM1420760v1_genomic.fna/target_genomes.txt --output GCF_014207605.1_ASM1420760v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:33,513] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17e2c385-1c17-4645-8255-d7351eecd9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:33,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17e2c385-1c17-4645-8255-d7351eecd9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:33,517] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:33,517] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:33,517] [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
Negativicoccus succinicivorans	strain=DSM 21255	GCA_014207605.1	620903	620903	type	True	100.0	463	464	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,518] [INFO] DFAST Taxonomy check result was written to GCF_014207605.1_ASM1420760v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:33,519] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:33,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:33,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17e2c385-1c17-4645-8255-d7351eecd9bf/dqc_reference/checkm_data
[2024-01-24 11:27:33,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:33,535] [INFO] Task started: CheckM
[2024-01-24 11:27:33,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207605.1_ASM1420760v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207605.1_ASM1420760v1_genomic.fna/checkm_input GCF_014207605.1_ASM1420760v1_genomic.fna/checkm_result
[2024-01-24 11:27:53,024] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:53,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,047] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:53,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:53,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207605.1_ASM1420760v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:53,049] [INFO] Task started: Blastn
[2024-01-24 11:27:53,049] [INFO] Running command: blastn -query GCF_014207605.1_ASM1420760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17e2c385-1c17-4645-8255-d7351eecd9bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207605.1_ASM1420760v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:53,920] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:53,924] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:53,924] [INFO] Target genome list was writen to GCF_014207605.1_ASM1420760v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:53,973] [INFO] Task started: fastANI
[2024-01-24 11:27:53,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg3378e891-c929-4e5a-acf0-1cb13f48c437/GCF_014207605.1_ASM1420760v1_genomic.fna.gz --refList GCF_014207605.1_ASM1420760v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207605.1_ASM1420760v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:58,404] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:58,412] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:58,413] [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_902506685.1	s__Negativicoccus succinicivorans	99.9929	464	464	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Negativicoccaceae;g__Negativicoccus	95.0	97.99	97.21	0.96	0.91	6	conclusive
GCA_900556745.1	s__Negativicoccus sp900556745	94.411	249	464	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Negativicoccaceae;g__Negativicoccus	95.0	98.29	98.29	0.98	0.98	2	-
GCA_900155405.1	s__Negativicoccus massiliensis	93.8035	421	464	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Negativicoccaceae;g__Negativicoccus	95.0	95.18	95.18	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:58,414] [INFO] GTDB search result was written to GCF_014207605.1_ASM1420760v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:58,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:58,417] [INFO] DFAST_QC result json was written to GCF_014207605.1_ASM1420760v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:58,417] [INFO] DFAST_QC completed!
[2024-01-24 11:27:58,417] [INFO] Total running time: 0h0m39s