MAQ error

jyli · 09-01-2009, 05:40 AM

I am using MAQ 0.7.1 and I recently encountered a weird errors:

-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 35.
[ma_load_reads] 17547636*2 reads loaded.
[ma_longread2read] encoding reads... maq: read.cc:106: match_info_t* ma_longread2read(const longreads_t*): Assertion `matches' failed.

I double checked that both query data and database data were OK. Any insight is appreciated.

johnwhitaker · 10-12-2009, 04:01 AM

I also got this error. Did you ever work out what was going wrong?

gcarbajosa · 10-12-2009, 11:27 AM

from the maq's user manual:

"The best way to run this command is to provide about 1 to 3 million reads as input. More reads consume more memory"

I suggest that you split the file in smaller sets of 1 to 3 million reads as suggested. I've done it and it works faster and safer.

http://maq.sourceforge.net/maq-manpage.shtml

johnwhitaker · 10-12-2009, 11:57 AM

I got around the problem by increasing the memory to 16 Gigs.

jyli · 10-12-2009, 12:20 PM

So, it is memory usage problem then? Interesting though as the developer claimed that we do NOT need to split file, which I always did in the past.

erichpowell · 04-29-2010, 10:09 AM

Quote:

I got around the problem by increasing the memory to 16 Gigs.

How did you increase the memory? I don't see any parameters to modify that?

I am very interested in this solution because I have encountered this error before and in past times I was able to get past this error by reducing the number of reads I was aligning, say, from 2M to 1M. In this case, I have dropped the number of reads as low as 750,000 and still the error persists.

johnwhitaker · 04-29-2010, 10:29 AM

I think I just specified that the job should be allowed more memory when submitting to our cluster.

Brajbio · 06-26-2010, 06:19 AM

I too got the similar error.

But surprisingly when i am feeding the single read input file (.bfq) of size 2.9 GB of each read 75 bp, its running sucessfully with MAQ but when i am giving the input file (.bfq) of size 3.0 GB (each read 75 bp), i am getting the error:

-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 75.
[ma_load_reads] 82785673*2 reads loaded.
[ma_longread2read] encoding reads... maq: read.cc:106: match_info_t* ma_longread2read(const longreads_t*): Assertion `matches' failed.
Aborted

I am pretty sure there is no memory problem , as i am using 64 GB RAM

I will greatly appreciate if someone can help me out to tackle this.

Brajbio · 06-26-2010, 07:24 AM

To my previous post i would like to add that......i had already successfully match this big size reads data once before with MAQ and even i have got the output as .map files, so i am pretty sure, size of reads and the memory is not the constrain to be pointed out. Still i am running the Maq with input of 2.9 GB of reads files (.bfq) having length read 75 bp each, which is processing perfectly.

qiuyongquan · 04-16-2012, 03:20 AM

What does the following sentence mean?
"Over all the raw reads, the average Phred-like quality value at base 80 was Q26.6 and the average base position at which this declined below Q30 was 69.7."

How can I use maq to get Phred-like quality value?

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09-01-2009, 05:40 AM	#1
jyli Member Location: North Carolina Join Date: Nov 2008 Posts: 21	MAQ error I am using MAQ 0.7.1 and I recently encountered a weird errors: -- maq-0.7.1 [ma_load_reads] loading reads... [ma_load_reads] set length of the first read as 35. [ma_load_reads] 175476362 reads loaded. [ma_longread2read] encoding reads... maq: read.cc:106: match_info_t ma_longread2read(const longreads_t*): Assertion `matches' failed. I double checked that both query data and database data were OK. Any insight is appreciated.

10-12-2009, 11:27 AM	#3
gcarbajosa Junior Member Location: London Join Date: May 2009 Posts: 4	maybe you are loading too many reads at the same time? from the maq's user manual: "The best way to run this command is to provide about 1 to 3 million reads as input. More reads consume more memory" I suggest that you split the file in smaller sets of 1 to 3 million reads as suggested. I've done it and it works faster and safer. http://maq.sourceforge.net/maq-manpage.shtml

04-16-2012, 03:20 AM	#10
qiuyongquan Junior Member Location: China Join Date: Feb 2012 Posts: 1	Phred-like quality value What does the following sentence mean? "Over all the raw reads, the average Phred-like quality value at base 80 was Q26.6 and the average base position at which this declined below Q30 was 69.7." How can I use maq to get Phred-like quality value?

10-12-2009, 04:01 AM	#2
johnwhitaker Junior Member Location: leeds Join Date: Jan 2009 Posts: 6	I also got this error. Did you ever work out what was going wrong?

10-12-2009, 11:57 AM	#4
johnwhitaker Junior Member Location: leeds Join Date: Jan 2009 Posts: 6	I got around the problem by increasing the memory to 16 Gigs.

10-12-2009, 12:20 PM	#5
jyli Member Location: North Carolina Join Date: Nov 2008 Posts: 21	So, it is memory usage problem then? Interesting though as the developer claimed that we do NOT need to split file, which I always did in the past.

04-29-2010, 10:29 AM	#7
johnwhitaker Junior Member Location: leeds Join Date: Jan 2009 Posts: 6	I think I just specified that the job should be allowed more memory when submitting to our cluster.

06-26-2010, 06:19 AM	#8
Brajbio Member Location: India Join Date: Jun 2010 Posts: 20	I too got the similar error. But surprisingly when i am feeding the single read input file (.bfq) of size 2.9 GB of each read 75 bp, its running sucessfully with MAQ but when i am giving the input file (.bfq) of size 3.0 GB (each read 75 bp), i am getting the error: -- maq-0.7.1 [ma_load_reads] loading reads... [ma_load_reads] set length of the first read as 75. [ma_load_reads] 827856732 reads loaded. [ma_longread2read] encoding reads... maq: read.cc:106: match_info_t ma_longread2read(const longreads_t*): Assertion `matches' failed. Aborted I am pretty sure there is no memory problem , as i am using 64 GB RAM I will greatly appreciate if someone can help me out to tackle this.

06-26-2010, 07:24 AM	#9
Brajbio Member Location: India Join Date: Jun 2010 Posts: 20	To my previous post i would like to add that......i had already successfully match this big size reads data once before with MAQ and even i have got the output as .map files, so i am pretty sure, size of reads and the memory is not the constrain to be pointed out. Still i am running the Maq with input of 2.9 GB of reads files (.bfq) having length read 75 bp each, which is processing perfectly.