Maq problem: 0 raw reads mapped

[pparg]

Dear all,
I tried Maq recently on some RNA-seq short read data. I kept getting none of the reads mapped.

Here is my code:
maq fasta2bfa chr1.fa chr1.bfa
maq fastq2bfq Control-6S.HWI-E4_8_3003J.fastq Control-6S.HWI-E4_8_3003J.bfq
#so far so good
maq match Control-6S.HWI-E4_8_3003J.map chr1.bfa Control-6S.HWI-E4_8_3003J.bfq

output for the last line:
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
ras:SRA002355 luow$ head -n 20 nohup.out
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
[match_search] 1% processed in 271.364 sec: 0 / 0 = 0.000
...(output truncated)
[match_search] 99% processed in 573.003 sec: 0 / 0 = 0.000
[match_search] 100% processed in 573.304 sec: 0 / 0 = 0.000
[match_core] sorting the hits and dumping the results...
[ma_load_reads] loading reads...
[ma_load_reads] 24347196*2 reads loaded.
[mapping_count_single] 0, 0, 0, 0
[maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
[match_data2mapping] 0 out of 48694392 raw reads are mapped with 0 in pairs.
-- (total, isPE, mapped, paired) = (24347196, 0, 0, 0)

If you are interested in trying this out, the raw short read data (you may want to use only part of the data for a quick trial) and reference genome can be downloaded by typing:
curl -O ftp://hgdownload.cse.ucsc.edu/golden...ps/chromFa.zip
curl -O ftp://ftp.ncbi.nlm.nih.gov/sra/stati...3003J.fastq.gz

I got similar results when I used ‘maq.pl easyrun’. align reported similar results before here: http://seqanswers.com/forums/showthread.php?t=902, but no soluatoin has been posted. I used a Mac OSX 10.5 system, Maq built from the platform independent version maq-0.7.1.tar.bz2. Any suggestions/thoughts would be greatly appreciated.

[zee]

I dont see your BFA file in the "maq match" step, so no genome to search against

it is :

maq map [options] <out.map> <chr.bfa> <reads_1.bfq> [reads_2.bfq]

[pparg]

Thanks Zee,
Good call. This turns out to be a typo in my post, sorry about that and I corrected it now.
I actually had chr1.bfa in my maq match line originally, otherwise there would just be an error message without any output.
Any other thoughts/suggestions?

[zee]

It does appear to be a strange error. Perhaps try a much smaller chunk of your dataset. You might want to check whether your reads match another chromosome e.g. chr22 or chrX - make a BFA file of that.
I would also look at trying another aligner altogether e.g. Novoalign (www.novocraft.com) and Bowtie (bowtie-bio.sourceforge.net) that export MAQ's .map format.

[pparg]

I built the same maq from the platform independent version maq-0.7.1.tar.bz2 on a linux machine. And repeated the same job in my original post. It works fine this time. This makes me doubt that maq does not work for Mac machines with powerpc architecture (common for Mac systems) somehow. And this may explain why the other people got the same strange problem as me here: http://seqanswers.com/forums/showthread.php?t=902.

[kaixinsjtu]

Hi, where did you get the sra002355? I can not find it on sra. Did they deleted it?? need help, thanks!!

Dear all,
I tried Maq recently on some RNA-seq short read data. I kept getting none of the reads mapped.

Here is my code:
maq fasta2bfa chr1.fa chr1.bfa
maq fastq2bfq Control-6S.HWI-E4_8_3003J.fastq Control-6S.HWI-E4_8_3003J.bfq
#so far so good
maq match Control-6S.HWI-E4_8_3003J.map chr1.bfa Control-6S.HWI-E4_8_3003J.bfq

output for the last line:
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
ras:SRA002355 luow$ head -n 20 nohup.out
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
[match_search] 1% processed in 271.364 sec: 0 / 0 = 0.000
...(output truncated)
[match_search] 99% processed in 573.003 sec: 0 / 0 = 0.000
[match_search] 100% processed in 573.304 sec: 0 / 0 = 0.000
[match_core] sorting the hits and dumping the results...
[ma_load_reads] loading reads...
[ma_load_reads] 24347196*2 reads loaded.
[mapping_count_single] 0, 0, 0, 0
[maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
[match_data2mapping] 0 out of 48694392 raw reads are mapped with 0 in pairs.
-- (total, isPE, mapped, paired) = (24347196, 0, 0, 0)

If you are interested in trying this out, the raw short read data (you may want to use only part of the data for a quick trial) and reference genome can be downloaded by typing:
curl -O ftp://hgdownload.cse.ucsc.edu/golden...ps/chromFa.zip
curl -O ftp://ftp.ncbi.nlm.nih.gov/sra/stati...3003J.fastq.gz

I got similar results when I used ‘maq.pl easyrun’. align reported similar results before here: http://seqanswers.com/forums/showthread.php?t=902, but no soluatoin has been posted. I used a Mac OSX 10.5 system, Maq built from the platform independent version maq-0.7.1.tar.bz2. Any suggestions/thoughts would be greatly appreciated.

[tsp]

Has anybody succeeded in solving this problem with "0 raw reads mapped"?
I have exactly the same problem on the ia64 (Altix) machine. Using the same Typhi data with the same command line arguments as in this thread fails on the ia64 but succeeds on my i586 desktop. (using maq-0.7.1). It looks like that there is an architecture problem in the match_search function (match.cc) ...
The first differences when comparing the different runs show up after following command:
maq map -n 2 -e 70 -u [email protected] [email protected] ref.bfa [email protected]

[rlan]

MAQ does not work correctly on Ia64 linux

MAQ code seems architecture dependent. I have the same problem. zero mapped reads on a Ia64 linux machine. I tried it on a x86 linux machine. it worked fine. It might have something to do with 64 bit compiling. I can't use m64 or mlp64 option even though it's a 64 bit machine.

There is another strange problem. I only have 3 reads in the test file. However MAQ map tells me 3*2 reads
[ma_load_reads] 3*2 reads loaded.
[mapping_count_single] 4, 4, 4, 4
[maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
[match_data2mapping] 3 out of 6 raw reads are mapped with 0 in pairs.

Has any one encounted the same problem? I checked the map file etc. It seems nothing wrong apart from above incorrect reporting.

[Jonathan]

Yes, maq does that 2*(#reads) for single-ended reads -
don't know why - maybe it is hardcoded in the message-print?
Haven't bothered to look yet;

Best
-Jonathan