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chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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minor bugs when making index #11

Closed antonkulaga closed 5 years ago

antonkulaga commented 5 years ago

When I make an index I have some minor bugs like:

rm: cannot remove 'tmp_ref.tmp.sa5': No such file or directory

Also, sometimes I get:

sh: 1: ./psascan: not found

when it is run inside of the bash script changes the current working folder. Unfortunately: I can only reproduce "psascan not found" with cromwell, cannot give a cromwell-independent example.

chhylp123 commented 5 years ago

As for "sh: 1: ./psascan: not found", this problem is caused by bitmapperBS cannot find "psascan" binary. bitmapperBS utilizes "psascan" binary to build index, so the binary of "psascan" and the binary of "bitmapperBS" must be saved in the same folder. So you need to check if these two binaries are saved together.

As for the first problem, don't worry about this. Actually, this is not a bug. It just an output information.

antonkulaga commented 5 years ago

The problem is that psascan is indeed in thr same folder as bitmapperbs, at east in docker container. But for some reason if the working folder is changed (automatically by cromwell in my case)d it sometimes cannot find it. I suggest the following solution: if it cannot find psascan in the same folder, can it run it as a command ( I can add psascsn to the system path in docker container)

chhylp123 commented 5 years ago

The problem is that psascan is indeed in thr same folder as bitmapperbs, at east in docker container. But for some reason if the working folder is changed (automatically by cromwell in my case)d it sometimes cannot find it. I suggest the following solution: if it cannot find psascan in the same folder, can it run it as a command ( I can add psascsn to the system path in docker container)

ok, i will do it as you said.

chhylp123 commented 5 years ago

The problem is that psascan is indeed in thr same folder as bitmapperbs, at east in docker container. But for some reason if the working folder is changed (automatically by cromwell in my case)d it sometimes cannot find it. I suggest the following solution: if it cannot find psascan in the same folder, can it run it as a command ( I can add psascsn to the system path in docker container)

The problem has been solved. Please try the new version from github.