bowtie error

[yuliu]

Hi,

I integrate bowtie2 into my pipeline, sometimes I got an error message like:

Warning: Could not open read file "/tmp/2423.unp" for reading; skipping...
Error: Encountered internal Bowtie 2 exception (#1)

then, bowtie will be termintated.

My OS is the latest ubuntu.

Does anyone can help me figure it out?

Thanks

-

[ThePresident]

I know it sound crazy, but it happened to me: have you enough space on your HD?

[yuliu]

space is not an issue. I used my pipeline to analyze 10 datasets. I got the error message when bowtie2 was processing the second dataset, then bowtie2 continued to the third one, and successfully processd all the following dataset.
So space is not an issue.

[westerman]

Just to pound on the space issue some more, what is the size of your /tmp? This can be different that your normal hard drive space.

It is quite possible that if the second dataset was large then when bowtie died on the second dataset because /tmp was full nothing got written to /tmp thus allowing bowtie to process the other datasets.

[yuliu]

good points! Will check my size of /tmp.
Thank you, thePresident & westerman!

Cannot understand why bowtie moves the reads file to /tmp.

[bharat_iyengar]

i got this error while running bowtie (almost near end)

Error while flushing and closing output
terminate called after throwing an instance of 'int'
Aborted (core dumped)

is it because of lack of memory space or anything??

[dlemas]

I am new to bowtie; however when i downloaded the windows version and worked through the tutorial . . everything went well. I have since downloaded the linux source code and compliled it within cygwin and when I start to run the tutorial I get the following error:

$ ./bowtie-build e_coli reads/e_coli_1000.fq
Settings:
Output files: "reads/e_coli_1000.fq.*.ebwt"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 5 (one in 32)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:4, int:4, long:4, size_t:4
Input files DNA, FASTA:
e_coli
Error: could not open e_coli
Total time for call to driver() for forward index: 00:00:00
Command: ./bowtie-build e_coli reads/e_coli_1000.fq

Basically, it does not read the e_coli file? Any thoughts or similar problem?

[westerman]

Command: ./bowtie-build e_coli reads/e_coli_1000.fq

Basically, it does not read the e_coli file? Any thoughts or similar problem?

1) Whenever someone on the forum complains about a program not being able to read a file then the immediate suspicion is that the program is correct and the person made a mistake. In these cases if the person could include a 'ls -l' of the directory in question showing that the file exists, is readable and is of reasonable size then then rest of us could rule out the very likely human error.

2) In your case, if I was to hazard a guess, I suspect that you have your command line parameters turned around. That 'reads/e_coli_1000.fq' should be first since it is the reference and 'e_coli' should be last since it is the base name of your output file.