Need help in running FAR - The Flexible Adapter Remover' on Mac OS

[weicy]

Hi,

I downloaded "FAR - The Flexible Adapter Remover" from http://sourceforge.net/projects/theflexibleadap/, and installed it in MacOS follwoing the instructions in its "README.TXT" file. The program ran successfully when I used a small fasta sequencing file to test it.

However, when I really applied it to my real sequencing file (in fasta format), It only processed very few read sequences and then stopped, showing "Terminate called throwing an exceptionabort trap 6".

Could anyone help to explain what this sentence mean? How to fix it? Thanks

[GenoMax]

Perhaps you do not have enough memory to process the entire file (you can check on this using a terminal window and "top" while you run FAR). If that is true then you could split your file in pieces and then process the pieces individually.

[weicy]

Perhaps you do not have enough memory to process the entire file (you can check on this using a terminal window and "top" while you run FAR). If that is true then you could split your file in pieces and then process the pieces individually.

Thank you for your reply. I used "top" but I cannot tell which term I should look at. Here is the terms listed:
"PID COMMAND %CPU TIME #TH #WQ #POR #MREG RPRVT RSHRD RSIZE VPRVT VSIZE PGRP PPID STATE UID FAULTS COW MSGSENT MSGRECV SYSBSD SYSMACH CSW PAGEINS KPRVT KSHRD USER"

But based on my observation, I did not see any of them show a significant large number when "Far" was running except "%CPU". Can you tell me what I should look at? Thx!

[GenoMax]

Look for "PhysMem" in the lines that show up above the list you have included below.

Does PhysMem line end up showing "0M free" (or a near zero number) at some point during processing when the error occurs?

How much RAM do you have and how big are your sequence files?

Thank you for your reply. I used "top" but I cannot tell which term I should look at. Here is the terms listed:
"PID COMMAND %CPU TIME #TH #WQ #POR #MREG RPRVT RSHRD RSIZE VPRVT VSIZE PGRP PPID STATE UID FAULTS COW MSGSENT MSGRECV SYSBSD SYSMACH CSW PAGEINS KPRVT KSHRD USER"

But based on my observation, I did not see any of them show a significant large number when "Far" was running except "%CPU". Can you tell me what I should look at? Thx!

[weicy]

Look for "PhysMem" in the lines that show up above the list you have included below.

Does PhysMem line end up showing "0M free" (or a near zero number) at some point during processing when the error occurs?

How much RAM do you have and how big are your sequence files?

No, PhysMem actually did not change too much, and about 450mb is free when FAR is stopped.

I am trying to run FAR in a macbook pro, which has 4G RAM. The sequence files is 13GB and it is in fasta format.

thanks

[JackieBadger]

The fasta is 13GB? That is huge! I have used whole genome in fasta format which are less than 2BG.
Are you sure this file doesn't not include run/quality information also?

Even trying to commit ~2GB of data may cause a stack overflow on a 4GB Macbook (I presume?), and throw a crash. If you do not have access to a Linux machine with much more RAM you have to chop up your fasta file. Still 13BG is very large for such a simple format.

[GenoMax]

I think the best solution is to split the file and then do the adapter removal on the pieces. Use the "split" command (http://www.computerhope.com/unix/usplit.htm).

No, PhysMem actually did not change too much, and about 450mb is free when FAR is stopped.

I am trying to run FAR in a macbook pro, which has 4G RAM. The sequence files is 13GB and it is in fasta format.

thanks

[GenoMax]

Uncompressed HiSeq sample files can be rather large. It is not unusual to have a 13GB fasta file.

The fasta is 13GB? That is huge!. Still 13BG is very large for such a simple format.

[weicy]

I think the best solution is to split the file and then do the adapter removal on the pieces. Use the "split" command (http://www.computerhope.com/unix/usplit.htm).

Thx, I will try

[jimmybee]

The fasta is 13GB? That is huge! I have used whole genome in fasta format which are less than 2BG.
Are you sure this file doesn't not include run/quality information also?

Even trying to commit ~2GB of data may cause a stack overflow on a 4GB Macbook (I presume?), and throw a crash. If you do not have access to a Linux machine with much more RAM you have to chop up your fasta file. Still 13BG is very large for such a simple format.

13Gb is pretty small for what I do. And my macbook pro with 4Gb handles it pretty well.

Can you try a different program other than FAR? Maybe fasta-mcf, cutadapt or the fastx toolkit?

[weicy]

I think the best solution is to split the file and then do the adapter removal on the pieces. Use the "split" command (http://www.computerhope.com/unix/usplit.htm).

I spliced the file and now there is 10m reads per file (around 600mb). The problem still exists. I guess file size is not the key...

but thx anyway