extract extra info (logs) from history
Hi, I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f Is it possible to access these logs? Cheers Jochen
There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options". Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi,
I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f
Is it possible to access these logs?
Cheers Jochen ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Hi Devon, do you mean Alignment Summary? How can I access that information and use it for an other tool. Cheers Jochen On 26.04.2018 14:14, Devon Ryan wrote:
There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options".
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi,
I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f
Is it possible to access these logs?
Cheers Jochen ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Flagstat might be a good choice here… Brad
On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi Devon,
do you mean Alignment Summary? How can I access that information and use it for an other tool.
Cheers Jochen
On 26.04.2018 14:14, Devon Ryan wrote:
There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options".
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi,
I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f
Is it possible to access these logs?
Cheers Jochen ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
That's also an interesting tool. Which gives almost the same result as in the log file of at HISAT output. I'm not sure why the number of mapped reads are not 100% identical... but anyway can someone tell me, or maybe Devon did already, where is the log info of HISAT saved? Cheers Jochen On 02.05.2018 12:37, Langhorst, Brad wrote:
Flagstat might be a good choice here…
Brad
On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi Devon,
do you mean Alignment Summary? How can I access that information and use it for an other tool.
Cheers Jochen
On 26.04.2018 14:14, Devon Ryan wrote:
There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options".
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi,
I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f
Is it possible to access these logs?
Cheers Jochen ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
By default the logs are just to stdout. You need to use one of the options (under "Summary Options" on the version on our instance) if you want things saved as a history item. Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
That's also an interesting tool. Which gives almost the same result as in the log file of at HISAT output. I'm not sure why the number of mapped reads are not 100% identical...
but anyway can someone tell me, or maybe Devon did already, where is the log info of HISAT saved?
Cheers Jochen
On 02.05.2018 12:37, Langhorst, Brad wrote:
Flagstat might be a good choice here…
Brad
On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi Devon,
do you mean Alignment Summary? How can I access that information and use it for an other tool.
Cheers Jochen
On 26.04.2018 14:14, Devon Ryan wrote:
There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options".
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi,
I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f
Is it possible to access these logs?
Cheers Jochen ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Thanks Devon, I think now I got it ;-). We are running 17.05 I might not have the "Summary Options" ? I cannot find them... But maybe I can use the flagstat tool for now. Cheers Jochen On 02.05.2018 16:34, Devon Ryan wrote:
By default the logs are just to stdout. You need to use one of the options (under "Summary Options" on the version on our instance) if you want things saved as a history item.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
That's also an interesting tool. Which gives almost the same result as in the log file of at HISAT output. I'm not sure why the number of mapped reads are not 100% identical...
but anyway can someone tell me, or maybe Devon did already, where is the log info of HISAT saved?
Cheers Jochen
On 02.05.2018 12:37, Langhorst, Brad wrote:
Flagstat might be a good choice here…
Brad
On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi Devon,
do you mean Alignment Summary? How can I access that information and use it for an other tool.
Cheers Jochen
On 26.04.2018 14:14, Devon Ryan wrote:
There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options".
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi,
I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f
Is it possible to access these logs?
Cheers Jochen ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Sounds like a good excuse to upgrade :) Sent from my iPhone
On 2. May 2018, at 16:40, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Thanks Devon,
I think now I got it ;-). We are running 17.05 I might not have the "Summary Options" ? I cannot find them...
But maybe I can use the flagstat tool for now.
Cheers Jochen
On 02.05.2018 16:34, Devon Ryan wrote: By default the logs are just to stdout. You need to use one of the options (under "Summary Options" on the version on our instance) if you want things saved as a history item.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Wed, May 2, 2018 at 4:32 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote: That's also an interesting tool. Which gives almost the same result as in the log file of at HISAT output. I'm not sure why the number of mapped reads are not 100% identical...
but anyway can someone tell me, or maybe Devon did already, where is the log info of HISAT saved?
Cheers Jochen
On 02.05.2018 12:37, Langhorst, Brad wrote: Flagstat might be a good choice here…
Brad
On May 2, 2018, at 1:48 AM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi Devon,
do you mean Alignment Summary? How can I access that information and use it for an other tool.
Cheers Jochen
On 26.04.2018 14:14, Devon Ryan wrote: There are two alignment summary options in the wrapper that will cause most/all of that to be written to a history item. They're under "Summary Options".
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Thu, Apr 26, 2018 at 2:11 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote: > Hi, > > I would like to use the info (log) HISAT is showing, for another tool. > e.g.: > 26781724 reads; of these: > 26781724 (100.00%) were unpaired; of these: > 2445411 (9.13%) aligned 0 times > 20399099 (76.17%) aligned exactly 1 time > 3937214 (14.70%) aligned >1 times > 90.87% overall alignment rate > [bam_sort_core] merging from 21 f > > > Is it possible to access these logs? > > Cheers Jochen > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
participants (4)
-
Devon Ryan -
Devon Ryan -
Jochen Bick -
Langhorst, Brad