Solid / Colorspace with bowtie : ERRO -> Extra parameter(s) specified

Question

[essepf]

Hi

I'm trying to map colorspace files with bowtie, with follow command:

bowtie -C -S /mm9IndexColor/m_musculus_ncbi37_c.* -f R_23305011_2011_12_07_1_05_1_3m_F3.csfasta -Q R_23305011_2011_12_07_1_05_1_3m_F3.QV.qual > 3m_bowtie.sam

but constantly get this error:

Extra parameter(s) specified: "/mm9IndexColor/m_musculus_ncbi37_c.4.ebwt", "/mm9IndexColor/m_musculus_ncbi37_c.rev.1.ebwt", "/mm9IndexColor/m_musculus_ncbi37_c.rev.2.ebwt", "R_23305011_2011_12_07_1_05_1_3m_F3.csfasta"
Command: bowtie -C -S -f -Q R_23305011_2011_12_07_1_05_1_3m_F3.QV.qual /mm9IndexColor/m_musculus_ncbi37_c.1.ebwt /mm9IndexColor/m_musculus_ncbi37_c.2.ebwt /mm9IndexColor/m_musculus_ncbi37_c.3.ebwt /mm9IndexColor/m_musculus_ncbi37_c.4.ebwt /mm9IndexColor/m_musculus_ncbi37_c.rev.1.ebwt /mm9IndexColor/m_musculus_ncbi37_c.rev.2.ebwt R_23305011_2011_12_07_1_05_1_3m_F3.csfasta

Someone could give me a little help to understand why I get this error?

Thank you very much for your help

Regards

Answer 1

[Jason]

You might want to try using /mm9IndexColor/m_musculus_ncbi37_c instead, I think bowtie recognizes the other files without the *.

I work in yeast and I have saccer2_R61-1-1.1.ebwt, saccer2_R61-1-1.2.ebwt etc. in my directory but I only use

bowtie -f -C -S saccer2_R61-1-1 in_F3.csfasta > out_F3.sam

as my command

I named the qual file to be similar to the csfasta file so it's not necessary for it to be in the command-line e.g. in_F3_QV.qual

[essepf]

Hi

Thank you for your comment, but doesn't work:

1 OPTION:

bowtie -f -C -S m_musculus_ncbi37_c. R_23305011_2011_12_07_1_05_1_3m_F3.csfasta > out_F3.sam
Could not locate a Bowtie index corresponding to basename "m_musculus_ncbi37_c."
Command: bowtie -f -C -S m_musculus_ncbi37_c. R_23305011_2011_12_07_1_05_1_3m_F3.csfasta

OTHER OPTION:

bowtie -f -C -S m_musculus_ncbi37_c.* R_23305011_2011_12_07_1_05_1_3m_F3.csfasta > out_F3.sam
Extra parameter(s) specified: "m_musculus_ncbi37_c.4.ebwt", "m_musculus_ncbi37_c.rev.1.ebwt", "m_musculus_ncbi37_c.rev.2.ebwt", "R_23305011_2011_12_07_1_05_1_3m_F3.csfasta"
Command: bowtie -f -C -S m_musculus_ncbi37_c.1.ebwt m_musculus_ncbi37_c.2.ebwt m_musculus_ncbi37_c.3.ebwt m_musculus_ncbi37_c.4.ebwt m_musculus_ncbi37_c.rev.1.ebwt m_musculus_ncbi37_c.rev.2.ebwt R_23305011_2011_12_07_1_05_1_3m_F3.csfasta

[Ashutosh Pandey]

Nothing should follow _c. It should look like this:

/mm9IndexColor/m_musculus_ncbi37_c #No . dot, No * wildcharacter

[essepf]

All scripts start run, but after minutes the job finish and return a empty file

So, not get any mapping....

[Ashutosh Pandey]

Check the log file. What does it say?

[essepf]

Just give me the information:

TERMINETED in the erro_file

#################

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
#!/bin/bash
#BSUB -L /bin/bash
#BSUB -n 8

module add UHTS/Aligner/bowtie/0.12.9;
module add UHTS/Analysis/samtools/1.2;



# ------ Color space / Solid Data  --------

#
# ---------------
# RUN Bowtie
# ---------------

bowtie -f -C -S m_musculus_ncbi37_c R_23305011_2011_12_07_1_05_1_3m_F3.csfasta > 3m_mapping.sam



------------------------------------------------------------

TERM_MEMLIMIT: job killed after reaching LSF memory usage limit.
Exited with exit code 143.

Resource usage summary:

    CPU time :               3.15 sec.
    Max Memory :             2321.14 MB
    Average Memory :         1354.40 MB
    Total Requested Memory : -
    Delta Memory :           -
    (Delta: the difference between total requested memory and actual max usage.)
    Max Swap :               2619 MB

    Max Processes :          4
    Max Threads :            5

The output (if any) follows:

Terminated

[Ashutosh Pandey]

You don't have enough memory and that is why job is being terminated for exceeding the memory limit. How much memory you have for each node ? You can change the default memory limit to say 10 Gb by using the following directive in the hedaer: bsub -M 10

[essepf]

I use:

# LSBATCH: User input
#!/bin/bash
#BSUB -L /bin/bash
#BSUB -o out_3m.txt
#BSUB -e erro_3m.txt
#BSUB -M 20 OR 20971520
#BSUB -n 8

And I get the same erro .... I don't know whats happen

I already try:

#!/bin/bash
#BSUB -L /bin/bash
#BSUB -o out_3m.txt
#BSUB -e erro_3m.txt
#BSUB -R "rusage[mem=20480]"
#BSUB -M 20971520
#BSUB -n 8