Jalal K. Siddiqui

We are working to implement PureCLIP in our pipelines. We have some questions to address first. 1. For our purposes, need information on the peaks in order to access the...

Error when running telescope assign

9

I tried to run telescope assign on one of my alignment files and get the following lines: Traceback (most recent call last): File "/users/PAS1143/osu8165/.conda/envs/telescope_env/bin/telescope", line 11, in load_entry_point('telescope-ngs==1.0.3', 'console_scripts', 'telescope')()...

I always have a segmentation fault when trying to build a krakenuniq database into bracken.. Any help will be appreciated. **(krakenuniq) [user@server bracken_testing]$ bracken-build -d krakenuniq_db/ -t 16 -k 31...

Viral neighbors download (Died)

2

I tried to create the viral neighbors database by this line **krakenuniq-download --db DB 'viral-neighbors' --rettype fasta -R --rsync** I get the following output. Downloading viral neighbors. Downloading DB/taxonomy/nucl_gb.accession2taxid.gz [curl...

I was downloading sequences from viral-neighbors and get errors like below: Downloading sequences 90001 to 100000 of 188678 ...https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=taxonomy&id=HM104174 HM104174: 239365 [/tmp/*] No mapping for sequence HM104174 - not writing...

Trouble downloading viral neighbors database

2

I tried to download the "viral neighbors" database (as well as RefSeq) using the code below. krakenuniq-download --db DBDIR refseq/viral/Any viral-neighbors Unfortunately, we run into the following error below: Downloading...