Empty depth file

[jillcasey]

I can get ExonDel running at the beginning but then it throws an error in R.

The rlog file gives the following error:

Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: read.bigFile -> read.delim -> read.table
Execution halted

I downloaded the gtf file from the link in an earlier post (thankyou as this was also causing a problem!) so i dont think that is the issue.

Plus none of my reference files have chr in them so ive excluded that possibility also.

My depth file is empty so im guessing thats where the problem lies. I just cant figure out what needs to be fixed.

Any help appreciated. Thanks

[slzhao]

Hello Jill,

Have you tested the example in README of ExonDel? It will work as all files
including gtf were provided there.
If the example works, would you please check the log file to see if there
is a warning message like "The format in GTF file may not be supported.
Please check the descriptions for GTF in README file"?
If there is no warning, the gtf file should be fine. As you said depth file
is empty, then would you please send me the content in "genesPassQCwithGC.bed"
file?

Thank you!

Best,
Shilin

2015-06-02 11:18 GMT-05:00 jillcasey notifications@github.com:

I can get ExonDel running at the beginning but then it throws an error in
R.

The rlog file gives the following error:

Error in read.table(file = file, header = header, sep = sep, quote =
quote, :
no lines available in input
Calls: read.bigFile -> read.delim -> read.table
Execution halted

I downloaded the gtf file from the link in an earlier post (thankyou as
this was also causing a problem!) so i dont think that is the issue.

Plus none of my reference files have chr in them so ive excluded that
possibility also.

My depth file is empty so im guessing thats where the problem lies. I just
cant figure out what needs to be fixed.

Any help appreciated. Thanks

—
Reply to this email directly or view it on GitHub
#5.

[jillcasey]

Hi Shilin,

1. Yes it does give that warning that the gtf may not be supported. I downloaded the gtf from the link you provided in a previous thread and it looks like the same format as the example. But maybe thats an issue. I clicked on the link, changed it to RefSeq genes, hg19 and downloaded it. It has the bin in the first column. Is there another setting that i need to change?

2. Yes the example works perfectly so i think that i have all the necessary programmes installed in the right places. So it must be something to do with one or more of my files.

3. I solved one problem last night - there was empty white space in the Bams.list file and that was causing a problem. I fixed that and had 2 bams listed for it to run overnight. When i checked this morning, there was no depth file generated at all (not even an empty one) and the terminal said "killed." So it must be running out of memory or something. It gets as far as "thread 4 stared" and then no further. I have set it running there again now but just with one bam file to see if that runs. But maybe this relates to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed server limit.

Thanks for your help. Im eager to get it up and running because its a tool that will be really useful to me.

[slzhao]

Hi Jill,

I've checked the "genesPassQCwithGC.bed" file you send to me, I think it is
fine. Then the problem should be in depth file as you said it was empty.
ExonDel is getting depth from bam file with following command:
"samtools depth -q $baseQ -Q $mapQ -b $resultDir/genesPassQCwithGC.bed
bamfile"

$baseQ and $mapQ were set as 20 based on the ExonDel.cfg file,
genesPassQCwithGC.bed
file is the file you send to me.

So would you please run the command in your system to see if it works?
If it works, would you please send the result from the command to me so
that I can see if it can be loaded into ExonDel?

Thank you!

Best,
Shilin

2015-06-03 2:40 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

1. Yes it does give that warning that the gtf may not be supported. I
   downloaded the gtf from the link you provided in a previous thread and it
   looks like the same format as the example. But maybe thats an issue. I
   clicked on the link, changed it to RefSeq genes, hg19 and downloaded it. It
   has the bin in the first column. Is there another setting that i need to
   change?

2. Yes the example works perfectly so i think that i have all the
   necessary programmes installed in the right places. So it must be something
   to do with one or more of my files.

3. I solved one problem last night - there was empty white space in the
   Bams.list file and that was causing a problem. I fixed that and had 2 bams
   listed for it to run overnight. When i checked this morning, there was no
   depth file generated at all (not even an empty one) and the terminal said
   "killed." So it must be running out of memory or something. It gets as far
   as "thread 4 stared" and then no further. I have set it running there again
   now but just with one bam file to see if that runs. But maybe this relates
   to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed server limit.

Thanks for your help. Im eager to get it up and running because its a tool
that will be really useful to me.

—
Reply to this email directly or view it on GitHub
#5 (comment).

[jillcasey]

Hi Shilin,

Sure, i will run the samtools command on one of the bams and see what
happens.

Thanks
Jill

On 3 June 2015 at 18:18, slzhao notifications@github.com wrote:

Hi Jill,

I've checked the "genesPassQCwithGC.bed" file you send to me, I think it is
fine. Then the problem should be in depth file as you said it was empty.
ExonDel is getting depth from bam file with following command:
"samtools depth -q $baseQ -Q $mapQ -b $resultDir/genesPassQCwithGC.bed
bamfile"

$baseQ and $mapQ were set as 20 based on the ExonDel.cfg file,
genesPassQCwithGC.bed
file is the file you send to me.

So would you please run the command in your system to see if it works?
If it works, would you please send the result from the command to me so
that I can see if it can be loaded into ExonDel?

Thank you!

Best,
Shilin

2015-06-03 2:40 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

1. Yes it does give that warning that the gtf may not be supported. I
   downloaded the gtf from the link you provided in a previous thread and it
   looks like the same format as the example. But maybe thats an issue. I
   clicked on the link, changed it to RefSeq genes, hg19 and downloaded it.
   It
   has the bin in the first column. Is there another setting that i need to
   change?

2. Yes the example works perfectly so i think that i have all the
   necessary programmes installed in the right places. So it must be
   something
   to do with one or more of my files.

3. I solved one problem last night - there was empty white space in the
   Bams.list file and that was causing a problem. I fixed that and had 2
   bams
   listed for it to run overnight. When i checked this morning, there was no
   depth file generated at all (not even an empty one) and the terminal said
   "killed." So it must be running out of memory or something. It gets as
   far
   as "thread 4 stared" and then no further. I have set it running there
   again
   now but just with one bam file to see if that runs. But maybe this
   relates
   to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed server limit.

Thanks for your help. Im eager to get it up and running because its a
tool
that will be really useful to me.

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

[jillcasey]

Hi Shilin,

Ive run that command butit doesnt generate an output file? Everything
happens in the terminal itself. Am i missing a piece of the command?

samtools depth -q 20 -Q 20 -b results/genesPassQCwithGC.bed Test.bam

Thanks
Jill

On 3 June 2015 at 18:18, slzhao notifications@github.com wrote:

Hi Jill,

I've checked the "genesPassQCwithGC.bed" file you send to me, I think it is
fine. Then the problem should be in depth file as you said it was empty.
ExonDel is getting depth from bam file with following command:
"samtools depth -q $baseQ -Q $mapQ -b $resultDir/genesPassQCwithGC.bed
bamfile"

$baseQ and $mapQ were set as 20 based on the ExonDel.cfg file,
genesPassQCwithGC.bed
file is the file you send to me.

So would you please run the command in your system to see if it works?
If it works, would you please send the result from the command to me so
that I can see if it can be loaded into ExonDel?

Thank you!

Best,
Shilin

2015-06-03 2:40 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

1. Yes it does give that warning that the gtf may not be supported. I
   downloaded the gtf from the link you provided in a previous thread and it
   looks like the same format as the example. But maybe thats an issue. I
   clicked on the link, changed it to RefSeq genes, hg19 and downloaded it.
   It
   has the bin in the first column. Is there another setting that i need to
   change?

2. Yes the example works perfectly so i think that i have all the
   necessary programmes installed in the right places. So it must be
   something
   to do with one or more of my files.

3. I solved one problem last night - there was empty white space in the
   Bams.list file and that was causing a problem. I fixed that and had 2
   bams
   listed for it to run overnight. When i checked this morning, there was no
   depth file generated at all (not even an empty one) and the terminal said
   "killed." So it must be running out of memory or something. It gets as
   far
   as "thread 4 stared" and then no further. I have set it running there
   again
   now but just with one bam file to see if that runs. But maybe this
   relates
   to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed server limit.

Thanks for your help. Im eager to get it up and running because its a
tool
that will be really useful to me.

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

[slzhao]

Hello Jill,
I've tested your bed file with my bam file, and it worked.

samtools depth -q 20 -Q 20 -b /scratch/cqs/zhaos/temp/genesPassQCwithGC.bed
test.bam >testResult.txt
more testResult.txt
1 761586 0
1 761587 0
1 761588 0
1 761589 0
1 761590 0
1 761591 0
1 761592 0
1 761593 2
1 761594 4
1 761595 4
1 761596 4
1 761597 4
1 761598 4

Would you please try again or change another bam to try?

Best,
Shilin

2015-06-04 8:52 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

Ive run that command butit doesnt generate an output file? Everything
happens in the terminal itself. Am i missing a piece of the command?

samtools depth -q 20 -Q 20 -b results/genesPassQCwithGC.bed Test.bam

Thanks
Jill

On 3 June 2015 at 18:18, slzhao notifications@github.com wrote:

Hi Jill,

I've checked the "genesPassQCwithGC.bed" file you send to me, I think it
is
fine. Then the problem should be in depth file as you said it was empty.
ExonDel is getting depth from bam file with following command:
"samtools depth -q $baseQ -Q $mapQ -b $resultDir/genesPassQCwithGC.bed
bamfile"

$baseQ and $mapQ were set as 20 based on the ExonDel.cfg file,
genesPassQCwithGC.bed
file is the file you send to me.

So would you please run the command in your system to see if it works?
If it works, would you please send the result from the command to me so
that I can see if it can be loaded into ExonDel?

Thank you!

Best,
Shilin

2015-06-03 2:40 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

1. Yes it does give that warning that the gtf may not be supported. I
   downloaded the gtf from the link you provided in a previous thread and
   it
   looks like the same format as the example. But maybe thats an issue. I
   clicked on the link, changed it to RefSeq genes, hg19 and downloaded
   it.
   It
   has the bin in the first column. Is there another setting that i need
   to
   change?

2. Yes the example works perfectly so i think that i have all the
   necessary programmes installed in the right places. So it must be
   something
   to do with one or more of my files.

3. I solved one problem last night - there was empty white space in the
   Bams.list file and that was causing a problem. I fixed that and had 2
   bams
   listed for it to run overnight. When i checked this morning, there was
   no
   depth file generated at all (not even an empty one) and the terminal
   said
   "killed." So it must be running out of memory or something. It gets as
   far
   as "thread 4 stared" and then no further. I have set it running there
   again
   now but just with one bam file to see if that runs. But maybe this
   relates
   to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed server
   limit.

Thanks for your help. Im eager to get it up and running because its a
tool
that will be really useful to me.

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

[jillcasey]

​
testResult.txt.tar.gz
https://docs.google.com/a/ucd.ie/file/d/0B0i1fcyHS86VTzZtZXFGVmhLcWM/edit?usp=drive_web
​Hi Shilin,

Attached is the samtools output file.

Thanks
Jill

On 5 June 2015 at 03:59, slzhao notifications@github.com wrote:

Hello Jill,
I've tested your bed file with my bam file, and it worked.

samtools depth -q 20 -Q 20 -b /scratch/cqs/zhaos/temp/genesPassQCwithGC.bed
test.bam >testResult.txt
more testResult.txt
1 761586 0
1 761587 0
1 761588 0
1 761589 0
1 761590 0
1 761591 0
1 761592 0
1 761593 2
1 761594 4
1 761595 4
1 761596 4
1 761597 4
1 761598 4

Would you please try again or change another bam to try?

Best,
Shilin

2015-06-04 8:52 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

Ive run that command butit doesnt generate an output file? Everything
happens in the terminal itself. Am i missing a piece of the command?

samtools depth -q 20 -Q 20 -b results/genesPassQCwithGC.bed Test.bam

Thanks
Jill

On 3 June 2015 at 18:18, slzhao notifications@github.com wrote:

Hi Jill,

I've checked the "genesPassQCwithGC.bed" file you send to me, I think
it
is
fine. Then the problem should be in depth file as you said it was
empty.
ExonDel is getting depth from bam file with following command:
"samtools depth -q $baseQ -Q $mapQ -b $resultDir/genesPassQCwithGC.bed
bamfile"

$baseQ and $mapQ were set as 20 based on the ExonDel.cfg file,
genesPassQCwithGC.bed
file is the file you send to me.

So would you please run the command in your system to see if it works?
If it works, would you please send the result from the command to me so
that I can see if it can be loaded into ExonDel?

Thank you!

Best,
Shilin

2015-06-03 2:40 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

1. Yes it does give that warning that the gtf may not be supported. I
   downloaded the gtf from the link you provided in a previous thread
   and
   it
   looks like the same format as the example. But maybe thats an issue.
   I
   clicked on the link, changed it to RefSeq genes, hg19 and downloaded
   it.
   It
   has the bin in the first column. Is there another setting that i need
   to
   change?

2. Yes the example works perfectly so i think that i have all the
   necessary programmes installed in the right places. So it must be
   something
   to do with one or more of my files.

3. I solved one problem last night - there was empty white space in
   the
   Bams.list file and that was causing a problem. I fixed that and had 2
   bams
   listed for it to run overnight. When i checked this morning, there
   was
   no
   depth file generated at all (not even an empty one) and the terminal
   said
   "killed." So it must be running out of memory or something. It gets
   as
   far
   as "thread 4 stared" and then no further. I have set it running there
   again
   now but just with one bam file to see if that runs. But maybe this
   relates
   to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed server
   limit.

Thanks for your help. Im eager to get it up and running because its a
tool
that will be really useful to me.

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

[slzhao]

Hello Jill,

the file is too large. Would you please send me some lines from it. I think
it is enough.

Best,
Shilin

2015-06-11 2:18 GMT-05:00 jillcasey notifications@github.com:

​
testResult.txt.tar.gz
<
https://docs.google.com/a/ucd.ie/file/d/0B0i1fcyHS86VTzZtZXFGVmhLcWM/edit?usp=drive_web

​Hi Shilin,

Attached is the samtools output file.

Thanks
Jill

On 5 June 2015 at 03:59, slzhao notifications@github.com wrote:

Hello Jill,
I've tested your bed file with my bam file, and it worked.

samtools depth -q 20 -Q 20 -b
/scratch/cqs/zhaos/temp/genesPassQCwithGC.bed
test.bam >testResult.txt
more testResult.txt
1 761586 0
1 761587 0
1 761588 0
1 761589 0
1 761590 0
1 761591 0
1 761592 0
1 761593 2
1 761594 4
1 761595 4
1 761596 4
1 761597 4
1 761598 4

Would you please try again or change another bam to try?

Best,
Shilin

2015-06-04 8:52 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

Ive run that command butit doesnt generate an output file? Everything
happens in the terminal itself. Am i missing a piece of the command?

samtools depth -q 20 -Q 20 -b results/genesPassQCwithGC.bed Test.bam

Thanks
Jill

On 3 June 2015 at 18:18, slzhao notifications@github.com wrote:

Hi Jill,

I've checked the "genesPassQCwithGC.bed" file you send to me, I think
it
is
fine. Then the problem should be in depth file as you said it was
empty.
ExonDel is getting depth from bam file with following command:
"samtools depth -q $baseQ -Q $mapQ -b
$resultDir/genesPassQCwithGC.bed
bamfile"

$baseQ and $mapQ were set as 20 based on the ExonDel.cfg file,
genesPassQCwithGC.bed
file is the file you send to me.

So would you please run the command in your system to see if it
works?
If it works, would you please send the result from the command to me
so
that I can see if it can be loaded into ExonDel?

Thank you!

Best,
Shilin

2015-06-03 2:40 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

1. Yes it does give that warning that the gtf may not be
   supported. I
   downloaded the gtf from the link you provided in a previous thread
   and
   it
   looks like the same format as the example. But maybe thats an
   issue.
   I
   clicked on the link, changed it to RefSeq genes, hg19 and
   downloaded
   it.
   It
   has the bin in the first column. Is there another setting that i
   need
   to
   change?

2. Yes the example works perfectly so i think that i have all the
   necessary programmes installed in the right places. So it must be
   something
   to do with one or more of my files.

3. I solved one problem last night - there was empty white space in
   the
   Bams.list file and that was causing a problem. I fixed that and
   had 2
   bams
   listed for it to run overnight. When i checked this morning, there
   was
   no
   depth file generated at all (not even an empty one) and the
   terminal
   said
   "killed." So it must be running out of memory or something. It gets
   as
   far
   as "thread 4 stared" and then no further. I have set it running
   there
   again
   now but just with one bam file to see if that runs. But maybe this
   relates
   to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed server
   limit.

Thanks for your help. Im eager to get it up and running because
its a
tool
that will be really useful to me.

—
Reply to this email directly or view it on GitHub
<#5 (comment)
.

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

[jillcasey]

Hi Shilin,

Yes will do. Im beginning to think that perhaps the depth file could be
empty because my computer is running out of memory. But i will send you
some lines tomorrow from the samtools output to see if thats in order.

Thanks
Jill

On 11 June 2015 at 20:28, slzhao notifications@github.com wrote:

Hello Jill,

the file is too large. Would you please send me some lines from it. I think
it is enough.

Best,
Shilin

2015-06-11 2:18 GMT-05:00 jillcasey notifications@github.com:

​
testResult.txt.tar.gz
<

https://docs.google.com/a/ucd.ie/file/d/0B0i1fcyHS86VTzZtZXFGVmhLcWM/edit?usp=drive_web

​Hi Shilin,

Attached is the samtools output file.

Thanks
Jill

On 5 June 2015 at 03:59, slzhao notifications@github.com wrote:

Hello Jill,
I've tested your bed file with my bam file, and it worked.

samtools depth -q 20 -Q 20 -b
/scratch/cqs/zhaos/temp/genesPassQCwithGC.bed
test.bam >testResult.txt
more testResult.txt
1 761586 0
1 761587 0
1 761588 0
1 761589 0
1 761590 0
1 761591 0
1 761592 0
1 761593 2
1 761594 4
1 761595 4
1 761596 4
1 761597 4
1 761598 4

Would you please try again or change another bam to try?

Best,
Shilin

2015-06-04 8:52 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

Ive run that command butit doesnt generate an output file? Everything
happens in the terminal itself. Am i missing a piece of the command?

samtools depth -q 20 -Q 20 -b results/genesPassQCwithGC.bed Test.bam

Thanks
Jill

On 3 June 2015 at 18:18, slzhao notifications@github.com wrote:

Hi Jill,

I've checked the "genesPassQCwithGC.bed" file you send to me, I
think
it
is
fine. Then the problem should be in depth file as you said it was
empty.
ExonDel is getting depth from bam file with following command:
"samtools depth -q $baseQ -Q $mapQ -b
$resultDir/genesPassQCwithGC.bed
bamfile"

$baseQ and $mapQ were set as 20 based on the ExonDel.cfg file,
genesPassQCwithGC.bed
file is the file you send to me.

So would you please run the command in your system to see if it
works?
If it works, would you please send the result from the command to
me
so
that I can see if it can be loaded into ExonDel?

Thank you!

Best,
Shilin

2015-06-03 2:40 GMT-05:00 jillcasey notifications@github.com:

Hi Shilin,

1. Yes it does give that warning that the gtf may not be
   supported. I
   downloaded the gtf from the link you provided in a previous
   thread
   and
   it
   looks like the same format as the example. But maybe thats an
   issue.
   I
   clicked on the link, changed it to RefSeq genes, hg19 and
   downloaded
   it.
   It
   has the bin in the first column. Is there another setting that i
   need
   to
   change?

2. Yes the example works perfectly so i think that i have all the
   necessary programmes installed in the right places. So it must be
   something
   to do with one or more of my files.

3. I solved one problem last night - there was empty white space
   in
   the
   Bams.list file and that was causing a problem. I fixed that and
   had 2
   bams
   listed for it to run overnight. When i checked this morning,
   there
   was
   no
   depth file generated at all (not even an empty one) and the
   terminal
   said
   "killed." So it must be running out of memory or something. It
   gets
   as
   far
   as "thread 4 stared" and then no further. I have set it running
   there
   again
   now but just with one bam file to see if that runs. But maybe
   this
   relates
   to the gtf file?

4. I've emailed you the bed file as it exceeded the allowed
   server
   limit.

Thanks for your help. Im eager to get it up and running because
its a
tool
that will be really useful to me.

—
Reply to this email directly or view it on GitHub
<
#5 (comment)
.

—
Reply to this email directly or view it on GitHub
<#5 (comment)
.

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).

—
Reply to this email directly or view it on GitHub
#5 (comment).