[susanklein]

No,

its dynamically allocated on a cluster. Unlimited space.

I can't get on another linux machine atm to test it again. Other files are doing it too, but all about the same size.

Thanks,

S.

[dpryan]

Contact your cluster admin.

[susanklein]

Unfortunately, they wont' know anything about bowtie or attempt to fix a software issue.

[dpryan]

It's not a bowtie problem.

[susanklein]

Eveything else ont the cluster and my machine is fine. So it is something to do with bowtie. So they won't take it on. I'll have to try something else.

[GenoMax]

I also tried your file on a Mac with bowtie2 v.2.2.3. No problems creating the indexes. Use the indexes Devon posted if you had posted the complete file.

[susanklein]

ok, thanks. I have been using bowtie2 version 2.2.4.

I have many indices to make so that's not really a solution, thanks anyway.

[susanklein]

just tried 2.2.3 same error. And again larger and smaller files are fine.

[susanklein]

2.0.1 same

[GenoMax]

This is making no sense. What OS are you using?

[susanklein]

Linux version 3.10-3-amd64 ([email protected]) (gcc version 4.7.2 (Debian 4.7.2-5) ) #1 SMP Debian 3.10.11-1 (2013-09-10)

[susanklein]

but if you look at the log (posted above) it makes the indexes.. then decides there is no fasta file and exits. Its very strange.

[susanklein]

tried bowtie-build and get the same error. I even copied the text, pasted it into word, copied it out into notepad++, changed line returns to unix. Agan if I make the file half as long or twice a long, everything works fine.

Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4252970 bytes to primary EBWT file: plasmids.1.ebwt
Wrote 25544 bytes to secondary EBWT file: plasmids.2.ebwt
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 204308
bwtLen: 204309
sz: 51077
bwtSz: 51078
lineRate: 6
linesPerSide: 1
offRate: 5
offMask: 0xffffffe0
isaRate: -1
isaMask: 0xffffffff
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 6385
offsSz: 25540
isaLen: 0
isaSz: 0
lineSz: 64
sideSz: 64
sideBwtSz: 56
sideBwtLen: 224
numSidePairs: 457
numSides: 914
numLines: 914
ebwtTotLen: 58496
ebwtTotSz: 58496
reverse: 0
Total time for call to driver() for forward index: 00:00:01
Reading reference sizes
Warning: Empty input file
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Reference file does not seem to be a FASTA file
Time to join reference sequences: 00:00:00
Total time for backward call to driver() for mirror index: 00:00:00
Command: bowtie-build --wrapper basic-0 /OSM/HOME-MEL/all29c/plasmids.fna plasmids
all29c@aahl-02-mel:~/bin/bowtie-1.1.1$

[GenoMax]

You are using bowtie v.1? Or is this happening with both v.1 and v.2?

[susanklein]

its happening with 1 and 2