Groups
Groups
Sign in
Groups
Groups
SMufin
Conversations
Labels
About
Send feedback
Help
SMufin
1–30 of 52
Mark all as read
Report group
0 selected
ricch...@gmail.com
, …
edev...@gmail.com
4
5/15/20
Q&A
Unable to install Smufin on cluster
I had similar problem with smufin, due to the fact that we host centralised bwa index that are non
unread,
Q&A
Unable to install Smufin on cluster
I had similar problem with smufin, due to the fact that we host centralised bwa index that are non
5/15/20
rchi...@gmail.com
,
SMuFin
2
3/25/19
Q&A
mpic++: Command not found
Hello, It seems your environment is not properly exported. A fast way to fix it is adding the
unread,
Q&A
mpic++: Command not found
Hello, It seems your environment is not properly exported. A fast way to fix it is adding the
3/25/19
Zen
,
SMuFin
2
8/30/17
Q&A
can we use de novo transcriptomes as reference?
If you do not have a reference genome the results can not be mapped neither you will get the
unread,
Q&A
can we use de novo transcriptomes as reference?
If you do not have a reference genome the results can not be mapped neither you will get the
8/30/17
Andrew
,
SMuFin
2
8/30/17
Q&A
Expected Runtime for Test File
Dear Andrew, In the error file you should see some lines like this ones: idl 14:2 [bam_header_parse]
unread,
all-questions
Q&A
Expected Runtime for Test File
Dear Andrew, In the error file you should see some lines like this ones: idl 14:2 [bam_header_parse]
8/30/17
renat...@gmail.com
7/18/17
Q&A
Annotation output
How to annotate the results (smal and large)? What program would you recommend? Best. Renato
unread,
Q&A
Annotation output
How to annotate the results (smal and large)? What program would you recommend? Best. Renato
7/18/17
huic...@gmail.com
, …
hamz...@gmail.com
3
3/3/17
Q&A
running SMuFin problems，can not read file?
Hi, I have a similar issue where the input sequence can't be read. The permissions for the
unread,
Q&A
running SMuFin problems，can not read file?
Hi, I have a similar issue where the input sequence can't be read. The permissions for the
3/3/17
davewin...@gmail.com
2
11/20/16
Q&A
Repeat Sequences and false positives
In regards to the curiosities with the process. I fail to find a call to BWA for alignment. Indeed, I
unread,
Q&A
Repeat Sequences and false positives
In regards to the curiosities with the process. I fail to find a call to BWA for alignment. Indeed, I
11/20/16
thename...@gmail.com
7/18/16
Q&A
How are consensus sequences generated, after breakpoint groups extracted?
Dear SMuFin team, I am wondering how consensus sequences are generated after extraction of the
unread,
Q&A
How are consensus sequences generated, after breakpoint groups extracted?
Dear SMuFin team, I am wondering how consensus sequences are generated after extraction of the
7/18/16
xiongl...@gmail.com
,
SMuFin
3
7/4/16
Q&A
Question about running time of 30x WGS
Hi Thanks for the reply. The human reference folder is in my own path, and everything is fine when I
unread,
Q&A
Question about running time of 30x WGS
Hi Thanks for the reply. The human reference folder is in my own path, and everything is fine when I
7/4/16
huic...@gmail.com
,
SMuFin
3
7/4/16
Q&A
running mpirun, mpirun noticed that process rank 0 with PID 5835 on node localhost exited on signal 11 (Segmentation fault).
Hi, You should change your mpi. To run SMuFin is required the OpenMPI >= 1.5.X. Regards
unread,
Q&A
running mpirun, mpirun noticed that process rank 0 with PID 5835 on node localhost exited on signal 11 (Segmentation fault).
Hi, You should change your mpi. To run SMuFin is required the OpenMPI >= 1.5.X. Regards
7/4/16
izaak.c...@gmail.com
5/23/16
Q&A
FPGA hardware acceleration of SMuFiN
Dear SmuFin team, We are interested in exploring the application of FPGA's to the SMuFiN
unread,
Q&A
FPGA hardware acceleration of SMuFiN
Dear SmuFin team, We are interested in exploring the application of FPGA's to the SMuFiN
5/23/16
izaak.c...@gmail.com
2
5/22/16
Q&A
SMuFin development documentation
Also, in the current version. Is array8.c or array.c used as default. I see #ifdef
unread,
Q&A
SMuFin development documentation
Also, in the current version. Is array8.c or array.c used as default. I see #ifdef
5/22/16
izaak.c...@gmail.com
,
SMuFin
3
5/22/16
Q&A
Running SMuin on smaller dataset
Thankyou for the help!
unread,
Q&A
Running SMuin on smaller dataset
Thankyou for the help!
5/22/16
corleo
,
SMuFin
2
3/16/16
Q&A
SMUFIN OUTPUT
Dear Corleo, Do you have the --patient_id option to running SMuFin? Regards,
unread,
Q&A
SMUFIN OUTPUT
Dear Corleo, Do you have the --patient_id option to running SMuFin? Regards,
3/16/16
corleo
,
SMuFin
3
3/8/16
Q&A
building SMuFin problems
Thank you for the reply, the version is openmpi-1.5.5
unread,
Q&A
building SMuFin problems
Thank you for the reply, the version is openmpi-1.5.5
3/8/16
hongen xu
,
SMuFin
2
2/8/16
Q&A
running smufin on older openMPI
Hello Hongen, The openMPI version must be 1.5.X (or higher). About memory problem it should be solved
unread,
Q&A
running smufin on older openMPI
Hello Hongen, The openMPI version must be 1.5.X (or higher). About memory problem it should be solved
2/8/16
giaco...@gmail.com
,
SMufin
2
11/6/15
Q&A
main.cpp:110:54: error: 'open_memstream' was not declared in this scope
Dear Giacomo, The open_memstream function is a POSIX function which is not available for MAC OSX. (
unread,
Q&A
main.cpp:110:54: error: 'open_memstream' was not declared in this scope
Dear Giacomo, The open_memstream function is a POSIX function which is not available for MAC OSX. (
11/6/15
zxf...@gmail.com
,
montse
2
11/5/15
Q&A
terminated with signal 11
Hello, Can you provide more information about your data? Human whole genome sequencing? Which
unread,
Q&A
terminated with signal 11
Hello, Can you provide more information about your data? Human whole genome sequencing? Which
11/5/15
zxf...@gmail.com
, …
SMufin
5
11/5/15
Q&A
Qs about running time of Smufin
Hi, Did you use the MPI enviroment? If so, which one did you use? Thank you,
unread,
Q&A
Qs about running time of Smufin
Hi, Did you use the MPI enviroment? If so, which one did you use? Thank you,
11/5/15
emelie....@scilifelab.se
, …
giaco...@gmail.com
3
11/2/15
Q&A
Problem during installation
Hi, I had the same problem. SOLVED updating GCC version to the last one.] Thanks
unread,
Q&A
Problem during installation
Hi, I had the same problem. SOLVED updating GCC version to the last one.] Thanks
11/2/15
Peter Waltman
,
SMufin
3
10/23/15
Q&A
"missing colon in auxiliary data" error when working with fastq's
Ok, well, I can easily generate a sam file since I have bam files for this data, but things that I
unread,
Q&A
"missing colon in auxiliary data" error when working with fastq's
Ok, well, I can easily generate a sam file since I have bam files for this data, but things that I
10/23/15
han...@gmail.com
,
SMufin
2
10/22/15
Q&A
How are paired ends handled?
Hello Qazhus, SMuFin do not use paired end information. So, currently, out method cannot take
unread,
Q&A
How are paired ends handled?
Hello Qazhus, SMuFin do not use paired end information. So, currently, out method cannot take
10/22/15
jinyan...@gmail.com
10/20/15
Q&A
It seems that smufin still cannot support bam input.
When will smufin support bam input?
unread,
Q&A
It seems that smufin still cannot support bam input.
When will smufin support bam input?
10/20/15
Sofia P
, …
chris....@gmail.com
10
10/6/15
Q&A
Fatal error in MPI_Send
Hi all, Ran into the same problem, at the same MPI_Send call. It doesn't matter whether your
unread,
Q&A
Fatal error in MPI_Send
Hi all, Ran into the same problem, at the same MPI_Send call. It doesn't matter whether your
10/6/15
chris....@gmail.com
,
montse
2
10/5/15
Q&A
Warn if no slaves appear!
Hi Chris, Thank you for your suggestion. We will take a look. Regards, SMuFin
unread,
Q&A
Warn if no slaves appear!
Hi Chris, Thank you for your suggestion. We will take a look. Regards, SMuFin
10/5/15
Clark Lee
, …
Joel Martin
7
7/28/15
Q&A
mpirun exited due to process rank 1 exiting improperly
fwiw, this turned out to be a formatting issue with the reference and the odd exit message. Issue is
unread,
Q&A
mpirun exited due to process rank 1 exiting improperly
fwiw, this turned out to be a formatting issue with the reference and the odd exit message. Issue is
7/28/15
Courtney Leisner
,
montse
4
7/9/15
Q&A
Segmentation Fault
Hi Courtney, SMuFin has been designed to analyse samples in human, so we do not know what could be
unread,
Q&A
Segmentation Fault
Hi Courtney, SMuFin has been designed to analyse samples in human, so we do not know what could be
7/9/15
skill...@gmail.com
, …
montse
5
7/8/15
Q&A
Any temporary output files?
SMuFin, at the moment, only provide this information using a redirection of the error on the cluster.
unread,
Q&A
Any temporary output files?
SMuFin, at the moment, only provide this information using a redirection of the error on the cluster.
7/8/15
skill...@gmail.com
,
montse
3
7/7/15
Q&A
Runtime & cluster size
We've now run it in two different contexts. In the first we have 20 nodes from a heterogeneous
unread,
Q&A
Runtime & cluster size
We've now run it in two different contexts. In the first we have 20 nodes from a heterogeneous
7/7/15
chris....@gmail.com
, …
SMufin
3
7/7/15
Q&A
Disable normal_bam and cancer_bam options?
Dear Chris, You are right, the normal_bam and cancer_bam options are not fully implemented on the
unread,
Q&A
Disable normal_bam and cancer_bam options?
Dear Chris, You are right, the normal_bam and cancer_bam options are not fully implemented on the
7/7/15
