[zhuyan]

What ditribution are you using?

My linux system is "Ubuntu 10.04".

This morning, I successfully run TGICL on another machine with "Ubuntu 11.04":

$ ldd cdbfasta
linux-gate.so.1 => (0xf774d000)
libm.so.6 => /lib32/libm.so.6 (0xf7704000)
libc.so.6 => /lib32/libc.so.6 (0xf75a6000)
/lib/ld-linux.so.2 (0xf774e000)

At the previous machine with "Ubuntu 10.04", there are only 64-bit edition library file - "ld-linux-x86-64.so.2", but the compilation of cdbfasta needs 32-bit edition library file - "ld-linux.so.2". I think maybe this is the cause.

[sklages]

My linux system is "Ubuntu 10.04".

This morning, I successfully run TGICL on another machine with "Ubuntu 11.04":

At the previous machine with "Ubuntu 10.04", there are only 64-bit edition library file - "ld-linux-x86-64.so.2", but the compilation of cdbfasta needs 32-bit edition library file - "ld-linux.so.2". I think maybe this is the cause.

Yes, the linux loader has not been found (because not present) ..
nevertheless, 'ldd' should have reported that ...

Please report back if you have solved the problem this way on your "Ubuntu 10.04" machine.

[chris_s]

Hi, I know that this comes much much later and that the issue must have been overcome since, but in case someone else ever encounters such a problem, I just wanted to provide some tips based on what my experience.

I just had exactly the same issue with an error saying "tgicl encountered an error at step Initialization" though it had been working for weeks on my ubuntu 14.04. I suspected that the issue may be to the length of the input file name and, at least in my case this has proven to be the case. I moved the input file to the home directory and ran TGICL from there, thereby significantly reducing the length of the path to my input file (I guess I try to sort my data into a few too many sub-folder levels), and TGICL ran like a charm again. So if anyone else encounters the same issue, there is a chance that this might be the cause.

Cheers,

Chris

[sklages]

Is there any more info with that error message or have you checked the log file(s)?
Maybe you had a whitespace in the previous folder structure that caused TGICL to fail?

best,
Sven

[chris_s]

Yes, I checked the error log, but there didn't seem to be any blank spaces or bad characters in the file path (see below).

>>> --- Initialization [/home/chris/Bioinformatics/Data_Analysis/Guam_2013/RNA-seq/4_Assembly/merged_assemblies/Assembly_CAT_So21-121_Oa35-115_Tr25_merged.fasta] started at Oct 9 18:14:29 2014
tgicl running options:
tgicl /home/chris/Bioinformatics/Data_Analysis/Guam_2013/RNA-seq/4_Assembly/merged_assemblies/Assembly_CAT_So21-121_Oa35-115_Tr25_merged.fasta -c 8 -p 99 -l 40 -v 100
Standard log file: tgicl_Assembly_CAT_So21-121_Oa35-115_Tr25_merged.fasta.log
Error log file: err_tgicl_Assembly_CAT_So21-121_Oa35-115_Tr25_merged.fasta.log
Using 8 CPUs for clustering and assembly
-= Rebuilding /home/chris/Bioinformatics/Data_Analysis/Guam_2013/RNA-seq/4_Assembly/merged_assemblies/Assembly_CAT_So21-121_Oa35-115_Tr25_merged.fasta indices =-
Error at 'formatdb -p F -o F -i /home/chris/Bioinformatics/Data_Analysis/Guam_2013/RNA-seq/4_Assembly/merged_assemblies/Assembly_CAT_So21-121_Oa35-115_Tr25_merged.fasta'

Process terminated with an error, at step 'Initialization'!
tgicl (/home/chris/Bioinformatics/Data_Analysis/Guam_2013/RNA-seq/4_Assembly/merged_assemblies/Assembly_CAT_So21-121_Oa35-115_Tr25_merged.fasta) encountered an error at step Initialization
Working directory was /home/chris/Bioinformatics/Data_Analysis/Guam_2013/RNA-seq/4_Assembly/merged_assemblies/1_TGICL.

[sklages]

Ah, ok, I see .. formatdb died .. probably an old 32bit binary as well.
You could try to see if you get a more meaningful message when you start the formatdb command on its own.

And, well, it's a really ancient peace of software ;-)

[huan]

@chris_s I have met the same error and have solved by your sollution. Thanks a lot!
BTW, have you found the reason why this error occours in the formatdb? Thanks a lot.