[mira_talk] Problems using sff extract
- From: Ganga Jeena <ganga.jeena@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 14 Dec 2010 12:43:19 +0530
I have tried moving sff_extract file to mira/bin/ /usr/local/bin but I am
still facing error .
How to get it working?
[dc103@hpc orig_data]$ cat flx_linker.fa
>linker_flx
ATAACTTCGTATAATGTATGCTATACGAAGTTAT
[dc103@hpc bin]$ pwd
/home/dc103/apps/mira/bin/
[dc103@hpc bin]$ ls -l
total 62716
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 caf2caf
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 caf2fasta
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 caf2gbf
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 caf2html
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 caf2tcs
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 caf2text
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 convert_project
-rwxr-xr-x 1 dc103 dc103 1340968 Dec 11 13:11 fastatool
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 gbf2caf
-rwxr-xr-x 1 dc103 dc103 4632800 Dec 11 13:11 gbf2fasta
-rwxr-xr-x 1 dc103 dc103 4673800 Dec 11 13:11 mira
-rwxr-xr-x 1 dc103 dc103 4673800 Dec 11 13:11 miraclip
-rwxr-xr-x 1 dc103 dc103 4673800 Dec 11 13:11 miramem
-rwxr-xr-x 1 dc103 dc103 4673800 Dec 11 13:11 miraSearchESTSNPs
-rwxr-xr-x 1 dc103 dc103 1867624 Dec 11 13:11 scftool
-rwxrwxr-x 1 dc103 dc103 52349 Dec 14 09:50 *sff_extract*
-rwxr-xr-x 1 dc103 dc103 227081 Dec 14 11:06 *ssaha2*
-rwxr-xr-x 1 dc103 dc103 104389 Dec 14 11:06 *ssaha2Build*
[dc103@hpc bin]$ cd -
/home/dc103/CP_Data/orig_data
[dc103@hpc orig_data]$ ls
check_for cp_454.fasta cp_454.fasta.qual cp_454.xml flx_linker.fa
linker.fasta out_8k_ONE.fa out_res_check.fa res_check.fa sff_extract
[dc103@hpc orig_data]$ ~/apps/mira/bin/sff_extract -o cp_454 -a -l
flx_linker.fa -i "insert_size:8000, insert_stdev:1000"
/home/dc103/CP_Data/sff_lf/GSMQLLJ01.sff
[Errno 22] Invalid argument
Regards,
Ganga Jeena
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