[Bio-Linux] Bowtie 2 and Galaxy
Mallon, Eamonn B. (Dr.)
ebm3 at leicester.ac.uk
Wed May 8 02:54:58 EDT 2013
Hi Tim,
I really appreciate you getting back to me so quickly and generally for all the work you've done on BioLinux.
I tried your suggestion. Bowtie2 now works but neither tophat nor tophat2 do. See error report below. Version 2.1.0 of bowtie2 is installed
Thanks
Eamonn
Dataset 73: Tophat2 on data 4 and data 6: deletions
Tool execution generated the following error message:
Error in tophat:
[2013-05-08 07:47:45] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-05-08 07:47:45] Checking for Bowtie
Error: TopHat requires Bowtie 2.0.5 or later
The tool produced the following additional output:
Settings:
Output files: "/tmp/tmphaTcDz/dataset_6.*.bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 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:
/usr/lib/galaxy-server/database/files/000/dataset_6.dat
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 12804
Using parameters --bmax 9603 --dcv 1024
Doing ahead-of-time memory usage test
TopHat v2.0.7
Passed! Constructing with these parameters: --bmax 9603 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
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
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 1; iterating...
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 6401.5 (target: 9602)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 7826
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 7827
Getting block 2 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 8958
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 8959
Getting block 3 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 926
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 927
Getting block 4 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 9019
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 9020
Getting block 5 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 9538
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 9539
Getting block 6 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 1983
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 1984
Getting block 7 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 7919
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 7920
Getting block 8 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 5043
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 5044
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 12811
fchr[G]: 25322
fchr[T]: 37448
fchr[$]: 51219
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.1.bt2
Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 51219
bwtLen: 51220
sz: 12805
bwtSz: 12805
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 3202
offsSz: 12808
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 267
numLines: 267
ebwtTotLen: 17088
ebwtTotSz: 17088
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:00
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 12804
Using parameters --bmax 9603 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 9603 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
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
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 7; iterating...
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 1; iterating...
Binary sorting into buckets
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Binary sorting into buckets time: 00:00:00
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 6401.5 (target: 9602)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 7682
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 7683
Getting block 2 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 6747
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 6748
Getting block 3 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 4689
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 4690
Getting block 4 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 7452
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 7453
Getting block 5 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 6415
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 6416
Getting block 6 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 7731
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 7732
Getting block 7 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 8264
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 8265
Getting block 8 of 8
Reserving size (9603) for bucket
Calculating Z arrays
Calculating Z arrays time: 00:00:00
Entering block accumulator loop:
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Block accumulator loop time: 00:00:00
Sorting block of length 2232
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 2233
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 12811
fchr[G]: 25322
fchr[T]: 37448
fchr[$]: 51219
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.1.bt2
Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 51219
bwtLen: 51220
sz: 12805
bwtSz: 12805
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 3202
offsSz: 12808
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 267
numLines: 267
ebwtTotLen: 17088
ebwtTotSz: 17088
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00
tophat2 -p 4 /tmp/tmphaTcDz/dataset_6 /usr/lib/galaxy-server/database/files/000/dataset_4.dat
________________________________________
From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth [tbooth at ceh.ac.uk]
Sent: Tuesday, May 07, 2013 3:39 PM
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Bowtie 2 and Galaxy
Hi Eamonn,
It seems there is an omission in the update script, so it could well be
that you are missing bowtie2 and you just have bowtie on there. Please
try:
sudo apt-get install bowtie2 bowtie2-examples
Hopefully this will be enough to get Galaxy working, but please be aware
that the Galaxy configuration is badly in need of maintenance and it may
still not work. If so, please send the full error message and I'll see
what I can do.
Cheers,
TIM
On Tue, 2013-05-07 at 15:07 +0100, Mallon, Eamonn B. (Dr.) wrote:
> Hi
> I've just installed biolinux 7. I tried to run top hat through galaxy
> and I keep getting an error. It seems to be because bowtie2 doesn't
> exist. Has anyone had a similar experience. Any tips?
>
>
> Eamonn
>
>
>
>
> Dr Eamonn Mallon
> Lecturer in Evolutionary Biology
> Adrian 220
> Biology Department
> University of Leicester
>
>
> http://www2.le.ac.uk/departments/biology/people/mallon
>
>
--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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