Getting Started with Deconseq

Question

[stu111392]

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

[sara.zahran]

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?

[Kevin Blighe]

Hey Sara, please post as a new question.

[sara.zahran]

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

[Kevin Blighe]

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.

Answer 1

[TriS]

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

[stu111392]

Thanks for the answer. I solved the problem today.