where is the error in my input files?

shuang · 08-18-2011, 04:10 PM

When I ran the command below, I received this error. How to know what 's the exact problem from this message in order to fix the issue?

./cross_match 5960.fna retro.fna -screen >> 5960_crossed.txt

min no. words: 0 at 0
max no. words: 111 at 228933
avg no. words: 0.01.008 Mbytes allocated -- total 6.552 Mbytes
Done
Total space allocated: 6.552 Mbytes; currently free: 0.866 Mbytes in 5 blocks
278938 words; after pruning: 187126
Sorting words ... Done

14 146774
Finding subject matches ...
descrip_buffer expanded
descrip_buffer expanded0.504 Mbytes allocated -- total 7.056 Mbytes
0.504 Mbytes allocated -- total 7.560 Mbytes
0.504 Mbytes allocated -- total 8.064 Mbytes
.0.504 Mbytes allocated -- total 8.568 Mbytes
0.504 Mbytes allocated -- total 9.072 Mbytes
. Done
Total space allocated: 9.072 Mbytes; currently free: 2.741 Mbytes in 12 blocks
# pass words: 1587, #fail words: 491
Quickalign: 741 successes, 137 failures
2413 SWAT alignments performed. 867 pairs have score >= 30
Making reversed pairs ... Done
Total space allocated: 9.072 Mbytes; currently free: 7.792 Mbytes in 13 blocks
Printing matches ... Done
Total space allocated: 9.072 Mbytes; currently free: 7.726 Mbytes in 14 blocks
Segmentation fault

sklages · 08-22-2011, 01:46 AM

What kind of hardware(RAM?), linux (32/64bit), which distribution, which version of cross_match, what kind of input data (many seqs? repetitive?).
Have you compiled cross_match on that system?

A bit more info would be helpful :-)

cheers, Sven

shuang · 08-22-2011, 09:53 AM

My server is 4 GB RAM, 64bit Linux, Fedora. I don't know which version of crossmatch I'm using. But I'm sure crossmatch is working because I've used it on other data sets.

The input data is assembled 454 contigs (5960.fna), total about 10 contigs and total length is about 60 KB. The reference is a 4kb sequence (retro.fna).

sklages · 08-23-2011, 02:23 AM

Well, hardware sounds more than enough for the few sequences ... so there's probably sth. wrong with your input data ..
You could try to swap both sequences in the command call just to see if it would run with these two files in general. This should give you a hint wether your files are "corrupted".

If you cannot find any problem in your sequences (also by having a quick look at the file), disk space is enough and hardware is OK, you should probably directly contact Phil Green or David Gordon (or post to their mailing-list 'phui').

I'd be interested to hear were the problem really was ...

hth, Sven

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08-18-2011, 04:10 PM	#1
shuang Senior Member Location: IL Join Date: Jul 2011 Posts: 100	where is the error in my input files? When I ran the command below, I received this error. How to know what 's the exact problem from this message in order to fix the issue? ./cross_match 5960.fna retro.fna -screen >> 5960_crossed.txt min no. words: 0 at 0 max no. words: 111 at 228933 avg no. words: 0.01.008 Mbytes allocated -- total 6.552 Mbytes Done Total space allocated: 6.552 Mbytes; currently free: 0.866 Mbytes in 5 blocks 278938 words; after pruning: 187126 Sorting words ... Done 14 146774 Finding subject matches ... descrip_buffer expanded descrip_buffer expanded0.504 Mbytes allocated -- total 7.056 Mbytes 0.504 Mbytes allocated -- total 7.560 Mbytes 0.504 Mbytes allocated -- total 8.064 Mbytes .0.504 Mbytes allocated -- total 8.568 Mbytes 0.504 Mbytes allocated -- total 9.072 Mbytes . Done Total space allocated: 9.072 Mbytes; currently free: 2.741 Mbytes in 12 blocks # pass words: 1587, #fail words: 491 Quickalign: 741 successes, 137 failures 2413 SWAT alignments performed. 867 pairs have score >= 30 Making reversed pairs ... Done Total space allocated: 9.072 Mbytes; currently free: 7.792 Mbytes in 13 blocks Printing matches ... Done Total space allocated: 9.072 Mbytes; currently free: 7.726 Mbytes in 14 blocks Segmentation fault

08-22-2011, 01:46 AM	#2
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	What kind of hardware(RAM?), linux (32/64bit), which distribution, which version of cross_match, what kind of input data (many seqs? repetitive?). Have you compiled cross_match on that system? A bit more info would be helpful :-) cheers, Sven

08-22-2011, 09:53 AM	#3
shuang Senior Member Location: IL Join Date: Jul 2011 Posts: 100	My server is 4 GB RAM, 64bit Linux, Fedora. I don't know which version of crossmatch I'm using. But I'm sure crossmatch is working because I've used it on other data sets. The input data is assembled 454 contigs (5960.fna), total about 10 contigs and total length is about 60 KB. The reference is a 4kb sequence (retro.fna).

08-23-2011, 02:23 AM	#4
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	Well, hardware sounds more than enough for the few sequences ... so there's probably sth. wrong with your input data .. You could try to swap both sequences in the command call just to see if it would run with these two files in general. This should give you a hint wether your files are "corrupted". If you cannot find any problem in your sequences (also by having a quick look at the file), disk space is enough and hardware is OK, you should probably directly contact Phil Green or David Gordon (or post to their mailing-list 'phui'). I'd be interested to hear were the problem really was ... hth, Sven