executable lies about own existence

Question

Okay, I'm completely baffled on this one. I'm installing a piece of software called InterPro Scan for my superiors, and it is complaining about an executable not existing. Please see below.

root@cpt:/usr/local/lib/iprscan# bin/Linux/seqret 
bash: bin/Linux/seqret: No such file or directory
root@cpt:/usr/local/lib/iprscan# ls bin/Linux/seqret 
bin/Linux/seqret
root@cpt:/usr/local/lib/iprscan# stat bin/Linux/seqret 
  File: `bin/Linux/seqret'
  Size: 949624          Blocks: 1856       IO Block: 4096   regular file
Device: 801h/2049d      Inode: 38541532    Links: 1
Access: (0755/-rwxr-xr-x)  Uid: ( 1257/ UNKNOWN)   Gid: ( 1055/ UNKNOWN)
Access: 2013-06-17 17:28:41.317364148 -0500
Modify: 2009-12-16 05:57:46.000000000 -0600
Change: 2013-06-17 17:28:33.049363860 -0500
 Birth: -
root@cpt:/usr/local/lib/iprscan# md5sum bin/Linux/seqret 
bc08e679fb146bc47e6f41636dcc1f88  bin/Linux/seqret
root@cpt:/usr/local/lib/iprscan# file /usr/local/lib/iprscan/bin/binaries/seqret

/usr/local/lib/iprscan/bin/binaries/seqret: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.2.5, not stripped

It exists! But it says it doesn't? I'm incredibly confused.

root@cpt:/usr/local/lib/iprscan# /usr/local/lib/iprscan/bin/iprscan -cli -i /usr/local/lib/iprscan/test.seq -o /usr/local/lib/iprscan/test.out -format raw -goterms -iprlookup

This calls the wrapper script:

/usr/local/lib/iprscan/conf/seqret.sh: line 18: /usr/local/lib/iprscan/bin/binaries/seqret: No such file or directory
/usr/local/lib/iprscan/bin/iprscan: checkParams: unable to create input files: formatSequences:

This is the original call to the wrapper script:

/usr/local/lib/iprscan/conf/seqret.sh  /usr/local/lib/iprscan/tmp/20130617/iprscan-20130617-17561022/iprscan-20130617-17561022.seqs > /usr/local/lib/iprscan/tmp/20130617/iprscan-20130617-17561022/iprscan-20130617-17561022.input.formatted: exit status 127

All of the input files exist.

The wrapper script itself

root@cpt:/usr/local/lib/iprscan# cat /usr/local/lib/iprscan/conf/seqret.sh
#!/bin/bash

##### NOTE ####
# Should be already set by iprscan_wrapper.pl.
# If not just add the full path to your iprscan installation
#IPRSCAN_HOME=/your/path/here/to/iprscan
###############
IPRSCAN_HOME=/usr/local/lib/iprscan

#Needed for seqret & sixpack emboss applications
EMBOSS_ROOT=$IPRSCAN_HOME/conf
export EMBOSS_ROOT

EMBOSS_ACDROOT=$IPRSCAN_HOME/conf/acd
export EMBOSS_ACDROOT

# "$@" is related to the command line of formatcmd tag in file iprscan.conf.
$IPRSCAN_HOME/bin/binaries/seqret -osf fasta -auto -stdout "$@"

Common mistake, it's probably a script and the first line to the interpretor is missing or something similar, sometimes if the line ends with a ^M you get this too. — EightBitTony, Jun 17 '13 at 22:53
Doesn't look like it... I'm adding the wrapper script for reference. — EricR, Jun 17 '13 at 22:56
@EightBitTony a bad interpreter path error is usually shown as something else. For example — Bratchley, Jun 17 '13 at 22:57
@JoelDavis, a bash script calls an executable, which complains about itself not existing. — EricR, Jun 17 '13 at 23:00
What does file /usr/local/lib/iprscan/bin/binaries/seqret return. — EightBitTony, Jun 17 '13 at 23:01
If my answer on the duplicate question doesn't solve your problem: what does file bin/Linux/seqret say? and uname -m and ldd bin/Linux/seqret? — Gilles 'SO- stop being evil', Jun 17 '13 at 23:01
root@cpt:/usr/local/lib/iprscan/bin# /usr/local/lib/iprscan/bin/binaries/seqret bash: /usr/local/lib/iprscan/bin/binaries/seqret: No such file or directory — EricR, Jun 17 '13 at 23:01

score 1 · Answer 1 · edited Apr 13 '17 at 12:36

1

Based on evidence that stackexhcange poped up with after I'd posted my question, I'm guessing that this will be the cause of the problem. I'm installing 32 bit libraries now.

edited Apr 13 '17 at 12:36

Community

1

answered Jun 17 '13 at 23:04

EricR

171

executable lies about own existence

1 Answers1