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Old 09-04-2015, 05:31 AM   #1
StefanF
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Location: Göteborg, Sweden

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Default gmap_build error

Hey guys,

I am trying to build a custom reference (mm9+ERCC spike-in) to reproduce some single cell RNA-seq results. I appended the mm9 genome (as a fasta file) with the ERCC sequences (also as fasta) and run the following command:

Code:
gmap_build -d mm9_ERCC92 mm9_ERCC92.fa -k 15 -D ~/stefan/scLVM/
All goes well until:

Building suffix array
SACA_K called with n = 2725848238, K = 5, level 0
/usr/local/bin/gmapindex -d mm9_ERCC92 -F /stefan//scLVM//mm9_ERCC92 -D /stefan/scLVM//mm9_ERCC92 -S failed with return code 9 at /usr/local/bin/gmap_build line 375.

Any ideas what could be going on here?
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Old 09-04-2015, 05:43 AM   #2
Michael.Ante
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Location: Vienna

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Hi Stefan,

only a shot in the dark: did you check the fasta's window length? Try fastx-toolkit's fasta_formatter:
Code:
fasta_formatter -w 60 -i mm9_ERCC92.fa -o mm9_ERCC92_w60.fa
diff -s mm9_ERCC92.fa mm9_ERCC92_w60.fa
Cheers,
Michael
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Old 09-04-2015, 06:24 AM   #3
StefanF
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Hi Michael,

I just compared the two files and they are indeed different.
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Old 09-04-2015, 06:32 AM   #4
Michael.Ante
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Thinking about it twice, the two files can differ and still it will not work (if the window-length is constant but not 60 nts).

Just check the line length visually with the first ERCC-transcript (should be ERCC-00002):

Code:
grep -A1 -B1 ERCC-00002 mm9_ERCC92.fa
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Old 09-04-2015, 06:42 AM   #5
StefanF
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Okay, the ERCC sequences are shorter than 60 nts. So gmap_build can't handle that? But it should work with the the corrected file mm9_ERCC92_w60.fa?

Edit: Alright, I get the same error with the formatted file... I really appreciate the help though. Maybe you or someone else has another idea?

Edit 2: The error seems to be in the suffix array construction. Is it really necessary to build that or does it only slow things down later?

Last edited by StefanF; 09-07-2015 at 01:00 AM. Reason: Update
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