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khuang28jhu / bs3

BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
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Can not find the index file in "./reference_genome/Sscrofa11.fa_snap/W_G2A and W_C2T" #13

Open xiaoxiaolongyuan opened 6 years ago

xiaoxiaolongyuan commented 6 years ago

Hi, I did bs3-build as "./bs3-build -f ./reference_genome/Sscrofa11.fa --aligner=snap". This command went well. However, I can not find the index file in "./reference_genome/Sscrofa11.fa_snap/W_G2A and W_C2T".

Thus "./bs3-align.py" said that "Loading index from directory... Unable to open file './reference_genome/Sscrofa11.fa_snap/W_C2T/GenomeIndex' for read. Index load failed, aborting."

"Loading index from directory... Unable to open file './reference_genome/Sscrofa11.fa_snap/W_G2A/GenomeIndex' for read. Index load failed, aborting." So How should I do to solve this problem. Look forward to hearing from you soon.

freshlearner commented 5 years ago

Did you solve the problem yet? i met the same error .

xiaoxiaolongyuan commented 5 years ago

Not yet.

I think there must be some wrong in their pipeline "BS-Seeker3"

Department of Animal genetics, Breeding and Reproduction College of Animal Science South China Agricultural University On behalf of "yxl@scua.edu.cn"

On 11/23/2018 10:09，freshlearnernotifications@github.com wrote：

Did you solve the problem yet? i met the same error .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

freshlearner commented 5 years ago

Not yet. I think there must be some wrong in their pipeline "BS-Seeker3" Department of Animal genetics, Breeding and Reproduction College of Animal Science South China Agricultural University On behalf of "yxl@scua.edu.cn" On 11/23/2018 10:09，freshlearnernotifications@github.com wrote： Did you solve the problem yet? i met the same error . — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

I seemed to know what the problem was . building index need sufficient memory .I used 120 gigabytes of memory to index the 3G genome and it seemed works

SDeans0 commented 3 years ago

For future users: I had this problem too and @freshlearner has the right answer. You need both to use a lot of memory and to check through the log file and make sure that all of the steps got to the point where the time taken is reported, as snap seems to fail silently and bs3 continues as though it was successful - there won't be an error message.