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Old 07-14-2011, 08:41 AM   #1
shuang
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Location: IL

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Posts: 100
Default error from SOAPdenovo

When I tried to run SOAPdenovo with a command "./SOAPdenovo all -s SB1.config -K 25 -o output", I received an error message of "-bash: ./SOAPdenovo: No such file or directory".

Why?



This is the content of SB1.config.

#maximal read length
# Lines start with '#' are ignored by the assembler
max_rd_len=50
[LIB]
avg_ins=2000
reverse_seq=1
asm_flags=2
rank=2
# cutoff of pair number for a reliable connection
#(default 5 for large insert size)
pair_num_cutoff=5
#minimal mapped length to contigs for a reliable read location
#(default 35 for large insert size)
map_len=35
q1=/Users/Steve/bin/SOAPdenovo_1.03/SB_short.fastq

Last edited by shuang; 07-14-2011 at 08:43 AM. Reason: wrong title
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Old 07-14-2011, 11:53 AM   #2
nickloman
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Default

Well, er, the obvious question first - is SOAPdenovo in your current directory?

Confirm with ls -l SOAPdenovo

If not you will need to refer to it by the complete path, i.e. /Users/Steve/path/to/SOAPdenovo

Secondly, check the execute permissions are set, e.g. chmod 755 SOAPdenovo

Hope that helps
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Old 07-14-2011, 12:44 PM   #3
shuang
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I tried all 3 things you suggested. But still getting the same error message, cannot execute binary file.

Any other suggestions?
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Old 07-14-2011, 01:04 PM   #4
nickloman
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Make sure you have downloaded the right binary for your system, check uname -a & uname -p to see. If running on Linux make sure you got the correct 32 or 64-bit versions.
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Old 07-14-2011, 04:31 PM   #5
seb567
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The problem is simply that there is no such file or directory.

Otherwise this would happen:

seb@fault:~/software/SOAPdenovo-PPC$ file SOAPdenovo-31mer
SOAPdenovo-31mer: ELF 64-bit MSB executable, 64-bit PowerPC or cisco 7500, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, not stripped

seb@fault:~/software/SOAPdenovo-PPC$ uname -m
i686

seb@fault:~/software/SOAPdenovo-PPC$ ./SOAPdenovo-31mer
bash: ./SOAPdenovo-31mer: cannot execute binary file
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Old 07-15-2011, 12:08 AM   #6
nickloman
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Seb makes a good point.

Can you go into the directory you wish to execute SOAPdenovo from and paste the output of the following commands to this thread:

ls -l

uname -a

uname -m

file SOAPdenovo
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Old 07-15-2011, 07:43 AM   #7
shuang
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I checked my Mac. My Mac is 10.6.3. It seems eligible for the newest release 1.05, which requires Mac OS X, 10.6.5 or later.

Thus, I downloaded Release 1.04 for Mac OS X (64 bit version, above 10.5). However, when I tried to extracted the file with this command:
tar -zxvf SOAPdenovo-v1.04-macos-64.tgz

However, I received this error during the process.

grape_mac_64
tar: A lone zero block at 521


I also tried Mac OS X (32 bit version, above 10.5) and had similar error.

grape_mac_32
tar: A lone zero block at 574

How to I fix this issue? Thanks.
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