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Getting Started with Deconseq

Hello out there,

I want to filter my Illumina reads for unwanted sequences and exclude them. I wanted to use deconseq for doing the job. Just for testing purposes I downloaded to my desktop pc and said the program to make a db out of the viral NCBI entrys.

With the command:

bwa64 index -p viren -a bwtsw virus_ti.fa >out.txt 2>&1 &

bwa generates a library containing of 8 files for the virus file. Just for testing purposes I wanted to use only the viral db to see if it works. But I get the following error:

ERROR: cannot find all database files for database "virus" in dir "/dcdata1/deconseq

But in the folder there are all files that where generated by the bwa command. Has anybody an idea what to do? And if anybody has experience with this program I would be very thankful for any advice.

With kind regards, Julian

sequence next-gen
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updated by Ram Ram • written by stu111392 • stu111392

if you please i want to know how you solved this problem as this mentioned command bwa64 index -p viren -a bwtsw virus_ti.fa >out.txt 2>&1 & generated only 5 files instead of 8, can you help me solve the problem?

• 1 views • link
written by sara.zahran • sara.zahran

Hey Sara, please post as a new question.

• 1 views • link
written by Kevin Blighe Kevin Blighe

if you please i need to know how you solved this problem as i tried to generate my database but i got only 5 files instead of 8

• 1 views • link
written by sara.zahran • sara.zahran

As per my comment yesterday, Sara, please post this as a new question. This thread is almost 4 years old.

When you post as a new question, please give as much details as possible.

• 1 views • link
written by Kevin Blighe Kevin Blighe

1 answer

this might help

https://groups.google.com/forum/#!topic/edwardslabtools/LSWMb_YqbaE

also, not sure this is what you look for but worth a try:

ERROR: cannot find all database files for database "db" in dir "directory".
Please make sure that the directory path does not start with the "~"-sign and does end with an "/"-sign. Specify the full path to the database directory if unsure from what directory the program will be used.

source: http://ribopicker.sourceforge.net/faq.html

• 0 views • link
updated by Ram Ram • written by TriS TriS

Thanks for the answer. I solved the problem today.

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written by stu111392 • stu111392

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