[2020-07-03 14:34:25,255] [INFO] DFAST_QC pipeline started.
[2020-07-03 14:34:25,256] [INFO] DFAST_QC version: 0.2.4
[2020-07-03 14:34:25,256] [INFO] DQC Reference Directory: /home/www/dfast_qc/dqc_reference
[2020-07-03 14:34:25,556] [INFO] ===== Start taxonomy check using ANI =====
[2020-07-03 14:34:25,556] [INFO] Task started: Prodigal
[2020-07-03 14:34:25,556] [INFO] Running command: cat /home/www/dfast/jobs/77608a70-12ff-40ce-a6a1-2edf2c5fc896/result/genome.fna | prodigal -d dqc_result/cds.fna -a dqc_result/protein.faa -g 11 -q > /dev/null
[2020-07-03 14:34:37,503] [INFO] Task succeeded: Prodigal
[2020-07-03 14:34:37,504] [INFO] Task started: HMMsearch
[2020-07-03 14:34:37,504] [INFO] Running command: hmmsearch --tblout dqc_result/hmmer_result.tsv -E 1E-5 /home/www/dfast_qc/dqc_reference/reference_markers.hmm dqc_result/protein.faa > /dev/null
[2020-07-03 14:34:37,820] [INFO] Task succeeded: HMMsearch
[2020-07-03 14:34:37,821] [INFO] Found 6/6 markers.
[2020-07-03 14:34:37,901] [INFO] Query marker FASTA was written to dqc_result/markers.fasta
[2020-07-03 14:34:37,901] [INFO] Task started: Blastn
[2020-07-03 14:34:37,902] [INFO] Running command: blastn -query dqc_result/markers.fasta -db /home/www/dfast_qc/dqc_reference/reference_markers.fasta -out dqc_result/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2020-07-03 14:34:38,257] [INFO] Task succeeded: Blastn
[2020-07-03 14:34:38,258] [INFO] Selected 10 target genomes.
[2020-07-03 14:34:38,259] [INFO] Target genome list was writen to dqc_result/target_genomes.txt
[2020-07-03 14:34:39,419] [INFO] Task started: fastANI
[2020-07-03 14:34:39,419] [INFO] Running command: fastANI --query result/genome.fna --refList dqc_result/target_genomes.txt --output dqc_result/fastani_result.tsv --threads 1
[2020-07-03 14:34:46,815] [INFO] Task succeeded: fastANI
[2020-07-03 14:34:46,913] [INFO] Found 10 fastANI hits (10 hits with ANI > 95%)
[2020-07-03 14:34:46,914] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_000192165.1	29397	1584	type	True	99.976	649	680
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_001434635.1	29397	1584	type	True	99.8134	524	680
Lactobacillus delbrueckii subsp. lactis	strain=DSM 20072	GCA_002278095.1	29397	1584	type	True	99.4802	653	680
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_004354615.1	1537158	1584	type	True	97.8401	511	680
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001433875.1	83684	1584	type	True	97.8322	476	680
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001888965.1	1050107	1584	type	True	97.6588	555	680
Lactobacillus delbrueckii subsp. delbrueckii	strain=NBRC 3202	GCA_006740305.1	83684	1584	type	True	97.6477	554	680
Lactobacillus delbrueckii subsp. jakobsenii	strain=DSM 26046	GCA_001888925.1	1537158	1584	type	True	97.6384	538	680
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001190005.1	1050107	1584	type	True	97.5865	549	680
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001908495.1	83684	1584	type	True	97.5152	543	680
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[2020-07-03 14:34:46,914] [INFO] DFAST Taxonomy check result was written to dqc_result/tc_result.tsv
[2020-07-03 14:34:46,914] [INFO] ===== Taxonomy check completed =====
[2020-07-03 14:34:46,914] [INFO] Taxid for CheckM is set to 1584.
[2020-07-03 14:34:46,915] [INFO] ===== Start completeness check using CheckM =====
[2020-07-03 14:34:46,925] [INFO] Selected 'Lactobacillus delbrueckii' markers (species, taxid=1584) for CheckM
[2020-07-03 14:34:46,928] [INFO] Task started: CheckM
[2020-07-03 14:34:46,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f dqc_result/cc_result.tsv -t 1 species "Lactobacillus delbrueckii" dqc_result/checkm_input dqc_result/checkm_result
[2020-07-03 14:37:30,488] [INFO] Task succeeded: CheckM
[2020-07-03 14:37:30,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2020-07-03 14:37:30,491] [INFO] ===== Completeness check finished =====
[2020-07-03 14:37:30,492] [INFO] DFAST_QC result json was written to dqc_result/dqc_result.json
[2020-07-03 14:37:30,492] [INFO] DFAST_QC completed!
[2020-07-03 14:37:30,492] [INFO] Total running time: 0h3m5s