Hello, I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads? If I use bowtie vi comman line I get following output:
bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy. Any idea how I can still access the stats? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341
You can change the bowtie wrapper to save the stderr of the bowtie part. The command line is (bowtie2_wrapper.py): cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - - > %s' Change it to something like: cmd = 'bowtie2 %s -x %s %s %s 2> bowtie_stderr_filename | samtools view -Su - | samtools sort -o - - > %s' Where bowtie_stderr_filename is a temporary filename. And concat this before the stderr afterwards (of the whole command). Hopefully, the official bowtie-wrapper will have this addition too. Hagai On Mon, Feb 25, 2013 at 1:29 PM, Alexander Kurze < alexander.kurze@bioch.ox.ac.uk> wrote: > Hello, > > I am using the bowtie-wrapper on my locally installed galaxy server to > align reads. However I missing the stats read-out. Is there any possibility > to include statistics about unaligned reads? > > If I use bowtie vi comman line I get following output: > > > bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam > End-to-end 2/3-mismatch full-index search: 01:00:21 > # reads processed: 12084153 > # reads with at least one reported alignment: 9391748 (77.72%) > # reads that failed to align: 2692405 (22.28%) > Reported 30293838 alignments to 1 output stream(s) > > > The output should be normally saved in the stderr but unfortunatly the > stderr is somehow deleted after the alignment job is done in bowtie under > galaxy. > > Any idea how I can still access the stats? > > Thanks, > > Alex > > -- > Alexander Kurze, DPhil > University of Oxford > Department of Biochemistry > South Parks Road > Oxford, OX1 3QU > United Kingdom > > Tel: +44 1865 613 230 > Fax:+44 1865 613 341 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >
Hello Alexander I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool). I've attached patches to the tool in case they're any use to you. (As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?) HTH, best wishes, Peter On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads?
If I use bowtie vi comman line I get following output:
bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Thanks it is working now. Best wishes, Alex On Wed, Feb 27, 2013 at 9:35 AM, Peter Briggs <peter.briggs@manchester.ac.uk
wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool).
I've attached patches to the tool in case they're any use to you.
(As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads?
If I use bowtie vi comman line I get following output:
bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam
End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
-- Alexander Kurze 70 Sunningwell Road Oxford, OX1 4SX Tel: +44 1865-243-609 Mobile: +44 7962-425-865
Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper: https://trello.com/c/TdYxdbkm Best, J. On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool).
I've attached patches to the tool in case they're any use to you.
(As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads?
If I use bowtie vi comman line I get following output:
bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
<bowtie_wrapper.xml.patch>
Hi Jeremy - that's awesome, thanks! One thing: not sure if I read this right (I'm a Trello newbie) however it looks like only the patch to the tool XML has was attached to the card. This change also requires a patch to the python wrapper script (should have been attached to my earlier message). Apologies if I missed something, thanks again Best wishes, Peter On 27/02/13 18:33, Jeremy Goecks wrote:
Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper:
Best, J.
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool).
I've attached patches to the tool in case they're any use to you.
(As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads?
If I use bowtie vi comman line I get following output:
bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
<bowtie_wrapper.xml.patch>
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hmm, I don't see a patch for your changes to the wrapper script. Can you please bundle up and send along your tool definition + wrapper script changes and I'll add it to the card? Thanks, J. On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote:
Hi Jeremy - that's awesome, thanks!
One thing: not sure if I read this right (I'm a Trello newbie) however it looks like only the patch to the tool XML has was attached to the card. This change also requires a patch to the python wrapper script (should have been attached to my earlier message).
Apologies if I missed something, thanks again
Best wishes, Peter
On 27/02/13 18:33, Jeremy Goecks wrote:
Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper:
Best, J.
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool).
I've attached patches to the tool in case they're any use to you.
(As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads?
If I use bowtie vi comman line I get following output:
bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
<bowtie_wrapper.xml.patch>
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Hi Jeremy No problem - zip file with the two patches is attached, please let me know if there's a problem. Best wishes Peter On 28/02/13 15:07, Jeremy Goecks wrote:
Hmm, I don't see a patch for your changes to the wrapper script. Can you please bundle up and send along your tool definition + wrapper script changes and I'll add it to the card?
Thanks, J.
On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote:
Hi Jeremy - that's awesome, thanks!
One thing: not sure if I read this right (I'm a Trello newbie) however it looks like only the patch to the tool XML has was attached to the card. This change also requires a patch to the python wrapper script (should have been attached to my earlier message).
Apologies if I missed something, thanks again
Best wishes, Peter
On 27/02/13 18:33, Jeremy Goecks wrote:
Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper:
Best, J.
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool).
I've attached patches to the tool in case they're any use to you.
(As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads?
If I use bowtie vi comman line I get following output:
bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
<bowtie_wrapper.xml.patch>
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
Attached to the card, thanks Peter. J. On Feb 28, 2013, at 11:14 AM, Peter Briggs wrote:
Hi Jeremy No problem - zip file with the two patches is attached, please let me know if there's a problem. Best wishes Peter
On 28/02/13 15:07, Jeremy Goecks wrote:
Hmm, I don't see a patch for your changes to the wrapper script. Can you please bundle up and send along your tool definition + wrapper script changes and I'll add it to the card?
Thanks, J.
On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote:
Hi Jeremy - that's awesome, thanks!
One thing: not sure if I read this right (I'm a Trello newbie) however it looks like only the patch to the tool XML has was attached to the card. This change also requires a patch to the python wrapper script (should have been attached to my earlier message).
Apologies if I missed something, thanks again
Best wishes, Peter
On 27/02/13 18:33, Jeremy Goecks wrote:
Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper:
Best, J.
On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote:
Hello Alexander
I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool).
I've attached patches to the tool in case they're any use to you.
(As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?)
HTH, best wishes, Peter
On 25/02/13 11:29, Alexander Kurze wrote:
Hello,
I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads?
If I use bowtie vi comman line I get following output:
> bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s)
The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy.
Any idea how I can still access the stats?
Thanks,
Alex
-- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom
Tel: +44 1865 613 230 Fax:+44 1865 613 341
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
<bowtie_wrapper.xml.patch>
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
<bowtie_wrapper_patches_pjbriggs.zip>
participants (6)
-
Alexander Kurze -
Alexander Kurze -
Hagai Cohen -
Jeremy Goecks -
Jeremy Goecks
-
Peter Briggs