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Old 09-06-2009, 11:38 AM   #1
sasignor
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Default MAQ problems

I'm having some issues with MAQ running correctly and I'm not sure what the problem is. I'm just starting out, with quite limited knowledge of programming. Basically MAQ compiles without any errors (I do have to use the correction for a 32 bit processor by modifying the makefile and then use make -f Makefile.generic to compile).

I need to apply the patch which converts the new illumina pipeline scores to ones that MAQ knows how to use to I downloaded the maq-ill2sanger.patch file and tried to use the patch with

cd maq-0.7.1; patch -p1 < ../maq-ill2sanger.patch

which does not generate any errors. However, for one thing I'm not sure how the patch works in general, but ill2sanger doesn't come up as a valid command.

Using the following string of commands:

./maq sol2sanger s_7_sequence.txt reads.fastq
./maq fastq2bfq reads.fastq reads.bfq
(then do the same thing to my reference genome but with fasta and bfa)
./maq map in_out.map reference.bfa reads.bfq
./maq pileup reference.bfa in_out.map > in_out.pileup

The pileup file is about 5 gigs bigger than I think it is supposed to be (it is 6 G in total) and it won't open. My computer gives me an error message saying the file cannot be opened. All of the commands go through without any errors, but that doesn't mean much.

I have no idea what could be going wrong, or how to fix this. If anybody has any idea, I would appreciate it very much.
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Old 09-06-2009, 01:05 PM   #2
maubp
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Default

Quote:
Originally Posted by sasignor View Post
I need to apply the patch which converts the new illumina pipeline scores to ones that MAQ knows how to use to I downloaded the maq-ill2sanger.patch file and tried to use the patch with

cd maq-0.7.1; patch -p1 < ../maq-ill2sanger.patch

which does not generate any errors. However, for one thing I'm not sure how the patch works in general, but ill2sanger doesn't come up as a valid command.
Where did you get the patch from? Are you using Davide Cittaro's patch?

What do you mean by "doesn't come up as a valid command"?

It could be the patch is out of date, or didn't apply properly, and has messed up the perl script.

P.S. I was going to suggest you try the maq mailing list, but you already have:
http://sourceforge.net/mailarchive/f..._name=maq-help

Last edited by maubp; 09-06-2009 at 01:18 PM.
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Old 09-07-2009, 12:31 AM   #3
dawe
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Quote:
Originally Posted by maubp View Post
It could be the patch is out of date, or didn't apply properly, and has messed up the perl script.
The patch doesn't modify any per script... It has been written for v0.7.1 (latest available on maq repository).
Have you recompiled and reinstalled maq after patching?

d
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Old 09-07-2009, 02:51 AM   #4
maubp
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Quote:
Originally Posted by dawe View Post
The patch doesn't modify any perl script...
Sorry, my mistake (memory at fault). Its C code:
http://sourceforge.net/tracker/?func...15&atid=938895

The current version of the patch doesn't update main.c to list the new ill2sanger option. This may be what sasignor was confused by? i.e. I would change this:

Code:
fprintf(stderr, "         sol2sanger  convert Solexa FASTQ to standard/Sanger FASTQ\n");
to:

Code:
fprintf(stderr, "         sol2sanger  convert early Solexa/Illumina FASTQ to standard/Sanger FASTQ\n");
fprintf(stderr, "         ill2sanger  convert Illumina 1.3+ FASTQ to standard/Sanger FASTQ\n");
Peter
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Old 09-07-2009, 02:59 AM   #5
dawe
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Hi Peter,
Actually it does (starting at line 64 of the patch file):
Code:
diff -Naur maq-0.7.1/main.c maq-0.7.1.new/main.c
--- maq-0.7.1/main.c	2008-09-22 10:54:10.000000000 +0200
+++ maq-0.7.1.new/main.c	2009-08-25 18:56:45.000000000 +0200
@@ -28,6 +28,7 @@
 	fprintf(stderr, "         glfgen      generate .glz consensus\n\n");
 	fprintf(stderr, "Format converting:\n");
 	fprintf(stderr, "         sol2sanger  convert Solexa FASTQ to standard/Sanger FASTQ\n");
+	fprintf(stderr, "         ill2sanger  convert Illumina (GA 1.3+) FASTQ to standard/Sanger FASTQ\n");
 	fprintf(stderr, "         mapass2maq  convert mapass2's map format to maq's map format\n");
 	fprintf(stderr, "         bfq2fastq   convert BFQ to FASTQ format\n\n");
 	fprintf(stderr, "Information extracting:\n");
@@ -80,6 +81,7 @@
 	else if (strcmp(argv[1], "assemble") == 0) return ma_assemble(argc-1, argv+1);
 	else if (strcmp(argv[1], "glfgen") == 0) return maq_glfgen(argc-1, argv+1);
 	else if (strcmp(argv[1], "sol2sanger") == 0) return ma_sol2sanger(argc-1, argv+1);
+	else if (strcmp(argv[1], "ill2sanger") == 0) return ma_ill2sanger(argc-1, argv+1);
 	else if (strcmp(argv[1], "mapass2maq") == 0) return ma_mapass2maq(argc-1, argv+1);
 	else if (strcmp(argv[1], "bfq2fastq") == 0) return ma_bfq2fastq(argc-1, argv+1);
 	else if (strcmp(argv[1], "mapview") == 0) return ma_mapview(argc-1, argv+1);
diff -Naur maq-0.7.1/main.h maq-0.7.1.new/main.h
--- maq-0.7.1/main.h	2008-09-22 10:54:10.000000000 +0200
+++ maq-0.7.1.new/main.h	2009-08-25 18:56:45.000000000 +0200
@@ -25,6 +25,7 @@
 	int ma_rbcc(int argc, char *argv[]);
 	int ma_subpos(int argc, char *argv[]);
 	int ma_sol2sanger(int argc, char *argv[]);
+	int ma_ill2sanger(int argc, char *argv[]);
 	int ma_bfq2fastq(int argc, char *argv[]);
 	int ma_fakemut(int argc, char *argv[]);     /* in fasta2bfa.c */
 	int ma_abpair(int argc, char *argv[]);      /* in pair_stat.cc */
My patched version of maq output:

Code:
$ maq

Program: maq (Mapping and Assembly with Qualities)
Version: 0.7.1
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   maq <command> [options]



Format converting:
         sol2sanger  convert Solexa FASTQ to standard/Sanger FASTQ
         ill2sanger  convert Illumina (GA 1.3+) FASTQ to standard/Sanger FASTQ
         mapass2maq  convert mapass2's map format to maq's map format
         bfq2fastq   convert BFQ to FASTQ format
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Old 09-07-2009, 03:09 AM   #6
maubp
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Quote:
Originally Posted by dawe View Post
Hi Peter,
Actually it does (starting at line 64 of the patch file):
Sorry - quite right, I didn't double check that before posting (I must have missed it at the end of the patch file). Whoops.

So what has gone wrong with sasignor's attempt to apply the patch?
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Old 09-07-2009, 03:13 AM   #7
dawe
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Quote:
Originally Posted by maubp View Post
Sorry - quite right, I didn't double check that before posting (I must have missed it at the end of the patch file). Whoops.
:-) Nevermind! It also happens every day to me!

Quote:
Originally Posted by maubp View Post
So what has gone wrong with sasignor's attempt to apply the patch?
Actually I don't know... I only guess that sasignor patched the source but didn't reinstall the binary...
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Old 09-07-2009, 11:03 AM   #8
sasignor
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Default Thanks!

You were write about needing to recompile and reinstall the binary - the ill2sanger command is working now.

I'm still having the same problem with the pileup file, but I have no idea why. It looks like none of the reads are mapping to the reference, which doesn't make much sense. I'll have to do more investigation to find out why.

Thank you for all your responses!!
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Old 09-07-2009, 02:08 PM   #9
sasignor
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Default Additional problem

The patch now seems to be working. However, I am currently reproducing an alignment performed by somebody else using the exact same input files. So it should work at least to the extent that it worked previously. However using the commands I listed in my original post I consistently get zero mapped reads after entering the map command, and a pileup file that won't open.

Can anybody imagine why that might happen?
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Old 10-28-2009, 01:34 PM   #10
prk
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Default having the same problem with the ill2sanger patch

Hi

having the same problem. installation went fine with the patch - recompiled and reinstalled binary but getting "zero mapped reads"!??

and i know these reads should map!
Whats going on?
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Old 10-29-2009, 01:34 AM   #11
dawe
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@prk @sasignor: can you post at least 10 reads that are supposed to map? In the orignial form and with the maq command line you are using...
I had no problems so far in aligning converted reads...
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Old 02-11-2011, 07:38 AM   #12
Seq84
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Quote:
Originally Posted by prk View Post
Hi

having the same problem. installation went fine with the patch - recompiled and reinstalled binary but getting "zero mapped reads"!??

and i know these reads should map!
Whats going on?
Hi all,

Me too i've the same problem!! Can anyone suggest a solution?
Thanks in advance
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Old 06-17-2011, 11:21 AM   #13
jiltysequence
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Seq,

Do you have the exact same thing going on? If you can give me a little detail I might be able to help you out. First I would recommend cleaning out your system and re-reading this thread, then go ahead and let us know what's up. Also, what is the purpose of you running sequencing programs? As I student, i have been instructed to use sequencing to get behind the science in creating a rapid prototype involving casting or molding. I'm trying to figure out other ways this can be beneficial.

Last edited by jiltysequence; 06-23-2011 at 11:11 AM.
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