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Old 08-24-2008, 07:13 PM   #1
lemon027
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Location: HongKong

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Posts: 9
Question what is wrong with my MAQ?

[lemon@localhost Desktop]$ maq map flc_N.map flc.bfa /var/SEQ/Ningyou7_solexa.bfq
-- maq-0.6.8
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 35.
[ma_load_reads] 21952885*2 reads loaded.
[ma_longread2read] encoding reads... 43905770 sequences processed.
[ma_match] set the minimum insert size as 36.
[match_core] round 1/3...
[match_core] making index...
[match_core] processing sequence sjh (1100 bp)...
[match_core] round 2/3...
[match_core] making index...
[match_core] processing sequence sjh (1100 bp)...
[match_core] round 3/3...
[match_core] making index...
[match_core] processing sequence sjh (1100 bp)...
[match_core] sorting the hits and dumping the results...
[ma_load_reads] loading reads...
[ma_load_reads] 21952885*2 reads loaded.
[mapping_count_single] 16, 16, 16, 16
已杀死
??

Last edited by lemon027; 09-11-2008 at 06:17 PM. Reason: sloved
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Old 08-25-2008, 03:28 AM   #2
lh3
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Maq man page will suggest you put 2 million (instead of 20 million) reads in a batch to run maq map. Probably the process gets killed due to insufficient memory.

You can also use maq.pl easyrun if you works with small genomes. It will split the input for you.
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Old 08-25-2008, 11:39 AM   #3
ECO
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lemon:

To follow up on lh3's comment, use the fastq2bfq command with the -n option (say -n 2000000, or 10000000) to automatically split the reads.

Then run a map command on each file, then use mapmerge.
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Old 08-25-2008, 05:17 PM   #4
lemon027
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Question my data is too large? but for anther maq, it had done well

maq map /home/lemon/Desktop/flc_T.map /home/lemon/Desktop/flc.bfa Tapidor_solexa.bfq
-- maq-0.6.8
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 35.
[ma_load_reads] 19002103*2 reads loaded.
[ma_longread2read] encoding reads... 38004206 sequences processed.
[ma_match] set the minimum insert size as 36.
[match_core] round 1/3...
[match_core] making index...
[match_core] processing sequence sjh (1100 bp)...
[match_core] round 2/3...
[match_core] making index...
[match_core] processing sequence sjh (1100 bp)...
[match_core] round 3/3...
[match_core] making index...
[match_core] processing sequence sjh (1100 bp)...
[match_core] sorting the hits and dumping the results...
[ma_load_reads] loading reads...
[ma_load_reads] 19002103*2 reads loaded.
[mapping_count_single] 16, 16, 16, 16
[maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
[match_data2mapping] 62 out of 38004206 raw reads are mapped with 0 in pairs.
-- (total, isPE, mapped, paired) = (19002103, 0, 62, 0)
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Old 08-25-2008, 05:18 PM   #5
lemon027
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thank you I am trying your suggestion
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Old 08-25-2008, 05:25 PM   #6
lemon027
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Yes ,
your right~
the error never come out again!
but I had to merge the results together?
can i use one line command to get the all the result?
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Old 08-25-2008, 07:10 PM   #7
ECO
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Yes, once you issue the maq mapmerge command (with all the proper filenames of course...see the man page)...you will have one .map file that is all of your data combined!
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