Bowtie 2 error

Question

[Azhar]

Bowtie 2 error warnning that you run bowtei2 dircltly you shuold run wrapper script. need help

[GouthamAtla]

post your command and error message.

[Azhar]

*** Warning ***
'bowtie2-align' was run directly. It is recommended that you run the wrapper script 'bowtie2' instead.

Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-align -x /home/caojun/Hg/hg19.fasta -u /home/caojun/Hg/ID0003.clean.fq -s /home/caojun/Hg/SAMfiles/output.sam

[Devon Ryan]

Read my answer below.

[Azhar]

need soultion

[Devon Ryan]

"need soultion" (sp) isn't a meaningful reply to anyone.

[Azhar]

Dear

Nice for your advice but can you tell me some solution or wrapper script for this problem, or can you give me your email so that I am going to do some NGS analysis might be needing your help in future as well

Regards

[Devon Ryan]

I already told you the solution. Use bowtie2 rather than bowtie2-align. The bowtie2 package already comes with the bowtie2 program, there isn't any other wrapper script you need.

[Azhar]

Now this error

bowtie2 -x /home/caojun/Hg/hg19 -u /home/caojun/Hg/ID0003.clean.f
q -s /home/caojun/Hg/SAMfiles/output.sam
-u/--qupto arg must be at least 1

[Devon Ryan]

Reread the bowtie2 usage page. You want -U rather than -u.

[Azhar]

Thanks Sir,

Command runs, can I know how much time it takes because I have given it more than 7to 8 hours and then last night whole night and then this error comes

Bowtie2 return internal error 1
invalid input files

This error is when botwie runs for whole night and in morning this error comes and I am using ssh server

[Devon Ryan]

The internal error suggests that maybe something is wrong with one of the fastq files. Be sure to use multiple threads (the -p options).

Answer 1

[Devon Ryan]

Don't use the bowtie2-align-s or bowtie2-align-l program directly unless you really know what you're doing. That's what the bowtie2 wrapper perl script is for.

[Azhar]

I run Bowtie2 omitting one of the input file that was creating problem successfully with one file, but there is no output.sam file in the given directory path

[Devon Ryan]

Did you specify that there should be? Bowtie2 prints to the screen unless you redirect the output or give it the -S some_file.sam option.

[Azhar]

Yes I gave like /home/caojun/hg/SAMfiles/output.sam

[Devon Ryan]

Assuming that path exists, then that file should exist.

[Azhar]

Yes that's what I am thinking but their is not, if path would have not exit command mind have not run

But it runs and there is no file in SAMfile director

[Devon Ryan]

Then you have some other problem going on and are likely getting an error or warning message elsewhere. This isn't something that anyone can help you with. You need to simply figure this out yourself.

[Azhar]

Dear do you know how to work with Homer and can u guide me