[Bio-Linux] Bowtie 2 and Galaxy
Mallon, Eamonn B. (Dr.)
ebm3 at leicester.ac.uk
Wed May 8 04:56:20 EDT 2013
I found this on the top hat webpage
TopHat 2.0.8 release 2/26/2013
Note (4/12/2013): patched version 2.0.8b was released in order to
provide compatibility with Bowtie v1.0.0
Version 2.0.8 is a quick fix release addressing the following issues:
* This version correctly handles the newest version of Bowtie2 v2.1.0.
* The segment mapping slow-down introduced by some Bowtie2 parameter
changes in version 2.0.7 is now corrected.
Dr Eamonn Mallon
Lecturer in Evolutionary Biology
Adrian 220
Biology Department
University of Leicester
http://www2.le.ac.uk/departments/biology/people/mallon
On 08/05/2013 09:54, "Tim Booth" <tbooth at ceh.ac.uk> wrote:
>Hi Eamonn,
>
>Oh dear - I just tried running the basic example/test dataset on tophat2
>via the command line on my machine and I got the same error, so the
>installation is totally broken. I'm not sure which update caused that
>(it worked before - honest!) but hopefully it will be a simple fix.
>I'll look into it right now.
>
>Cheers,
>
>TIM
>
>On Wed, 2013-05-08 at 07:54 +0100, Mallon, Eamonn B. (Dr.) wrote:
>> 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
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>--
>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
>_______________________________________________
>Bio-Linux mailing list
>Bio-Linux at nebclists.nerc.ac.uk
>http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
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