bowtie2-build segmentation fault

[willkjh]

Hi, I am trying to build an index using an old reference using rm.fa file downloaded from ftp://ftp.ensembl.org/pub/release-66...toplevel.fa.gz

I keep getting segmentation fault when trying to do
bowtie2-2.2.1/bowtie2-build --large-index mm66.rm.fa mm66out2

Below are the output I get from bowtie2. Can anyone comment on whether I am doing something incorrect here? I do not find similar postings that have this problem. The build works fine when i run it using old version of bowtie.

Settings:
Output files: "mm66bact2.*.bt2l"
Line rate: 7 (line is 128 bytes)
Lines per side: 1 (side is 128 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
mm66bact.rm.fa
Building a LARGE index
Reading reference sizes
Warning: Encountered reference sequence with only gaps
Time reading reference sizes: 00:00:38
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:22
bmax according to bmaxDivN setting: 355766099
Using parameters --bmax 266824575 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 266824575 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:36
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:07
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:20
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Binary sorting into buckets
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Binary sorting into buckets time: 00:01:18
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 2.03295e+08 (target: 266824574)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 7
Reserving size (266824575) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:21
Sorting block of length 150990128
(Using difference cover)
Sorting block time: 00:01:24
Returning block of 150990129
Getting block 2 of 7
Reserving size (266824575) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:27
Sorting block of length 216184660
(Using difference cover)
Sorting block time: 00:02:08
Returning block of 216184661
Getting block 3 of 7
Reserving size (266824575) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:31
Sorting block of length 233641728
(Using difference cover)
Sorting block time: 00:02:19
Returning block of 233641729
Getting block 4 of 7
Reserving size (266824575) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:34
Sorting block of length 216178844
(Using difference cover)
Sorting block time: 00:02:07
Returning block of 216178845
Getting block 5 of 7
Reserving size (266824575) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:36
Sorting block of length 248625690
(Using difference cover)
Sorting block time: 00:02:27
Returning block of 248625691
Getting block 6 of 7
Reserving size (266824575) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:32
Sorting block of length 144796971
(Using difference cover)
Sorting block time: 00:01:22
Returning block of 144796972
Getting block 7 of 7
Reserving size (266824575) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
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Block accumulator loop time: 00:00:23
Sorting block of length 212646372
(Using difference cover)
Sorting block time: 00:02:06
Returning block of 212646373
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 417204348
fchr[G]: 711483392
fchr[T]: 1005808244
fchr[$]: 1423064399
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 591068009 bytes to primary EBWT file: mm66bact2.1.bt2l
Wrote 711532204 bytes to secondary EBWT file: mm66bact2.2.bt2l

[1] Segmentation fault bowtie2-2.2.1/bowtie2-build --large-index mm66.rm.fa mm66out2

[GenoMax]

You are not running out of disk space where the indexes are being written to, correct?

Can you not use the pre-build indexes available here: ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/mm9.zip since the file you are using seems to be mm9?

[willkjh]

Hi,
I do not think so. I also tried using the prebuilt version for bowtie2 using the link from bowtie2 website. (ftp://igenome:[email protected])

This time, i ran into the following problem which I am unsure what it is.

Error while flushing and closing output
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT)

[GenoMax]

Are you running a 64-bit OS? Are you using pre-compiled versions of the programs or did you compile them yourself?

[willkjh]

I am running a 64-bit OS. I am also using pre-compiled versions of the program.
I tried using the mm10 reference online. This time, bowtie2 seem to run but did not display any message when it finishes.

Below is the sh script or command i used to run bowtie2
$fastqFilesR1: all my files separated by "," and in quotes for R1
$fastqFilesR2: all my files separated by "," and in quotes for R2
$2: is my name for the output sam file.
$3: mm10 which is the name for the bowtie2-build files for the mouse reference.

#!/bin/bash
bowtie2-2.2.1/bowtie2 -x $3 -1 $fastqFilesR1 -2 $fastqFilesR2 -S "$2.sam"

Should I anticipate some summary output that this will provide me or is there some indication from the sam file that tells me that the program has finished?

[cliffbeall]

Thread necromancy

bowtie2build gave me a segmentation fault similar to the above, it turned out the fasta file was corrupted. It actually went a bit further in the process, generating a bunch of index files.

You might want to check that if you encounter something like this.