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[Staden] assembly problem with 6700 seq

ste.ghi via staden%40net.bio.net (by ste_ghiNOSP At Myshoo.it)
Mon Jan 15 10:44:03 EST 2007


Hi all.
I'm not so new with Staden Package (integrated with
phred/phrap/repeatmasker), but recently I'm facing assembly problems
never found before. At the moment, I'm using Staden v.1.
7 on a FedoraCore3 machine. When trying to assemble about 6700 seqs
(.ab1 and .SCF), stored on a new 80GB HD (97% free space), I'm getting
the following error message (sorry for the length!!):

Mon 15 Jan 16:15:44 2007 sequence_vector_clip::run: couldn't open 
"/mnt/data2/assembly/pregap.tmp": no space left on device
Mon 15 Jan 16:15:44 2007 cross_match_svec::run: couldn't open 
"/mnt/data2/assembly/pregap.fasta": no space left on device
Mon 15 Jan 16:15:44 2007 cloning_vector_clip::run: couldn't open 
"/mnt/data2/assembly/pregap.tmp": no space left on device
Mon 15 Jan 16:15:44 2007 repeat_masker::run: couldn't open 
"/mnt/data2/assembly/pregap.fasta": no space left on device
Mon 15 Jan 16:15:44 2007 phrap_assemble::run: couldn't open 
"/mnt/data2/assembly/pregap.tmp": no space left on device
Mon 15 Jan 16:15:46 2007 Error creating busy file

Mon 15 Jan 16:15:46 2007 No space left on device [28]
Mon 15 Jan 16:15:46 2007 cannot create file [5]
Mon 15 Jan 16:15:46 2007 cannot create database
Mon 15 Jan 16:15:46 2007 gap-create.c:112
Mon 15 Jan 16:15:46 2007 Success [0]
Mon 15 Jan 16:15:46 2007 no error [1000]
Mon 15 Jan 16:15:46 2007 cannot create database
Mon 15 Jan 16:15:46 2007 IO.c:1348
Mon 15 Jan 16:15:46 2007 Continue at own risk!
Mon 15 Jan 16:15:46 2007 open_db:
Mon 15 Jan 16:15:46 2007 shutdown::shutdown: couldn't open 
"/mnt/data2/assembly/pregap.log": no space left on device

..and it's not all.
With Staden 1.7 loaded on a 16 CPU cluster' frontend PC (OS Rocks), with 
the same phred/phrap configuration, I get this error message (sorry for 
the length, again):

[...]

- Report from 'Phrap assembly' -
ERR: Failed to execute phrap.
ERR: "
gcphrap -minmatch 12 -minscore 30 -exp 
/home/users/sghignon/candidatus/p2f10/pregap.assembly 
/home/users/sghignon/candidatus/p2f10/pregap.tmp
gcphrap version 0.990329
Reading parameters ... 1.008 Mbytes allocated -- total 1.008 Mbytes
Run date:time  070115:121704
  Done
Total space allocated: 1.008 Mbytes; currently free: 1.003 Mbytes in 2 
blocks
Reading query file into memory .................... Done
Total space allocated: 1.008 Mbytes; currently free: 0.374 Mbytes in 6 
blocks
Complementing ...1.008 Mbytes allocated -- total 2.016 Mbytes
  Done
Total space allocated: 2.016 Mbytes; currently free: 1.266 Mbytes in 6 
blocks
Allocating align_entries ... Done
Total space allocated: 2.016 Mbytes; currently free: 1.053 Mbytes in 6 
blocks
Reading quality files ...

NO QUALITY FILE /home/users/sghignon/candidatus/p2f10/pregap.tmp.qual 
WAS FOUND. REMAINING INPUT QUALITIES SET TO 15. Done
Total space allocated: 2.016 Mbytes; currently free: 1.053 Mbytes in 6 
blocks
5.040 Mbytes allocated -- total 7.056 Mbytes
Finding words ...
  0  961779
  10  86573
  20  170
  30  35
  40  12
  50  3
  60  1
  110  1
  160  1
  170  1
min no. words: 0 at 24
max no. words: 161 at 0
avg no. words: 0.0 Done
Total space allocated: 7.056 Mbytes; currently free: 1.070 Mbytes in 7 
blocks
186214 words; after pruning: 165396
Sorting words ... Done

12  101555
13  11
14  11
15  7
16  3
17  1
18  1
19  2
Finding complement word matches ... Done
Total space allocated: 7.056 Mbytes; currently free: 0.943 Mbytes in 8 
blocks
n_cross_matches: 1706
# pass words: 3482, #fail words: 12406
num_cand_pairs: 1145, num_dups: 561
Finding internal word matches ...  n_same_matches: 2010
, #pass words: 2010, #fail words: 7179 num_cand_pairs: 2351, num_dups: 1365
  Done
Total space allocated: 7.056 Mbytes; currently free: 0.919 Mbytes in 8 
blocks
Finding duplicates ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.941 Mbytes in 7 
blocks
SWATTING ...... Done
Total space allocated: 7.056 Mbytes; currently free: 5.756 Mbytes in 8 
blocks
Quickalign: 466 successes, 104 failures
3564 SWAT alignments performed. 562 pairs have score >= 30
Making reversed pairs ... Done
Total space allocated: 7.056 Mbytes; currently free: 5.824 Mbytes in 8 
blocks
Finding starts/ends ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.824 Mbytes in 8 
blocks
Total # pairs: 2000, size: 0.112 Mbytes
Finding segments ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding more vector ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding mean offsets ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding near duplicates ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding self matches ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding node rejects ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding truncated pairs ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding multi-segment reads ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding starts/ends ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding deletions ...  Done
Total space allocated: 7.056 Mbytes; currently free: 5.744 Mbytes in 8 
blocks
Finding extents ...  Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Printing qualities ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Computing LLR scores ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Finding extents ...  Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Computing LLR scores ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Printing qualities ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Printing coverage ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Finding blocked reads ...  Done
Total space allocated: 7.056 Mbytes; currently free: 4.886 Mbytes in 8 
blocks
Merging ...

Pass: 1
#reads  #contigs (not counting singlets)
     1     34
     7      1
     9      1
    10      1
    13      1
    16      1
    23      1
    38      1

Pass: 3
#reads  #contigs (not counting singlets)
     1      9
     2      6
     9      1
    10      1
    11      1
    15      1
    19      1
    25      1
    40      1

Pass: 4
#reads  #contigs (not counting singlets)
     3      1
     9      1
    13      1
    14      1
    19      2
    25      1
    48      1

Read equivalence class histogram:
     1   24
     3    1
     9    1
    13    1
    14    1
    19    2
    25    1
    48    1
  Done
Total space allocated: 7.056 Mbytes; currently free: 4.855 Mbytes in 8 
blocks
Merging chimeras ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.855 Mbytes in 8 
blocks
Merging other singletons ...
LLR_join_cutoff: -60
  Done
Total space allocated: 7.056 Mbytes; currently free: 4.855 Mbytes in 8 
blocks
Finding extents ...  Done
Total space allocated: 7.056 Mbytes; currently free: 4.859 Mbytes in 9 
blocks
Making contig sequences ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.713 Mbytes in 18 
blocks
Aligning reads to contigs ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.687 Mbytes in 23 
blocks
Revising contigs ... Done
Total space allocated: 7.056 Mbytes; currently free: 4.518 Mbytes in 23 
blocks
  289 old base segments, 0.009 Mb
  3826 new base segments, 0.122 Mb
  total old contig length 33053, 0.099 Mb
  total new contig length 32782, 0.098 Mb
Aligning reads to contigs ..."
ERR: Aborting assembly.

- Report from 'Enter assembly (into Gap4)' -
ERR: Could not open file 
/home/users/sghignon/candidatus/p2f10/pregap.assembly/fofn.
ERR: "couldn't open "fofn": no such file or directory"
ERR: Aborting enter assembly.



                        ***   Processing finished   ***

How can I solve those issues? are both related to memory resources?
Is there someone aware oh this?
Thanks in advance

stefano



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