Uploading a variable step wig file onto a custom track

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Uploading a variable step wig file onto a custom track

McKiernan, Robert M
Hi everyone,

I'm currently attempting to upload wig files as a custom track onto the following site: http://heptamer.tamu.edu/fgb2/gbrowse/MG1655/ . However, it always returns a processing error, even with example wig files.

I'm wondering whether this is a problem with the format of my files or whether it's a server side problem.
Could someone do me a huge favour and try to upload a variable step wig file which they know is in the correct format for GBrowse please?


You can probably stop reading now but i've included further info below on the files which I've tried to upload, just incase.
I've attempted to upload a few files. The first of which looks like this. I'm only including the start of the files for brevity:

track type=wiggle_0 variableStep chrom=MG1655
43 0.0909090909091
44 0.0909090909091
45 0.0909090909091
46 0.0909090909091

Which gave the following error:
PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f.wig/track000.wig: [Remove Message]

The second file is an example wig file which I'm told has loaded onto GBrowse in the past. The start of it looks like this: 
track type=wiggle_0 name="Reverse Strand Translation Initiation Rates" description="Predicted by RBS Calculator v1.0 (log10 scale)" visibility=full maxHeightPixels=500:500:500 variableStep chrom=MG1655 span=3
3  2.19
11  0.51
22  2.86
29  2.95
70  2.72
125  2.19
141  1.60
150  2.44
157  0.00
159  0.00
163  0.00
176  0.00
183  2.31
185  0.24
.
.
.
and so on. 

This gave the following error:

PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/upload_8214/track000.wig: [Remove Message]


The second file is from the JBrowse tutorial data (found at /JBrowse-1.11.3/docs/tutorial/data_files/volvox_microarray.wig). The start of the file looks like this:

track type=wiggle_0 name="example" description="20 degrees, 2 hr"
fixedStep chrom=ctgA start=1 step=100 span=100
281
183
213
191
288
184
258
173
274
292
227
209
277
.
.
.
etc.

This gives the following error:
PROCESSING ERROR: hashMustFindVal: 'ctgA' not found 

Many thanks,
Rob


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Re: Uploading a variable step wig file onto a custom track

Timothy Parnell
Hi Rob,

The wig file has two special lines, as described in http://genome.ucsc.edu/goldenPath/help/wiggle.html

The track line specifies the type and optionally other parameters, like name
track type=wiggle_0 name=“my data”

The declaration line specifies the type of wiggle. It is repeated for every chromosome. For example
variableStep chrom=chr1
or
fixedStep chrom=chr1 span=100 step=100

In your example, you’ve combined the two, leading to the error.

In the second example from Volvox, the error is regarding the chromosome not being found. Evidently, E coli does not have a chromosome named “ctgA”.  The error is actually a bigWig error, suggesting it is trying to convert your wig file into a bigWig file behind the scenes (default behavior when supported). In this case, you could convert your wig files into bigWigs yourself using utilities available from UCSC and upload those. The advantage there is you can check and fix errors more readily than relying on a remote server.

Hope that helps.
Tim


On Apr 29, 2014, at 4:46 AM, McKiernan, Robert M <[hidden email]<mailto:[hidden email]>> wrote:

Hi everyone,

I'm currently attempting to upload wig files as a custom track onto the following site: http://heptamer.tamu.edu/fgb2/gbrowse/MG1655/ . However, it always returns a processing error, even with example wig files.

I'm wondering whether this is a problem with the format of my files or whether it's a server side problem.
Could someone do me a huge favour and try to upload a variable step wig file which they know is in the correct format for GBrowse please?


You can probably stop reading now but i've included further info below on the files which I've tried to upload, just incase.
I've attempted to upload a few files. The first of which looks like this. I'm only including the start of the files for brevity:

track type=wiggle_0 variableStep chrom=MG1655
43 0.0909090909091
44 0.0909090909091
45 0.0909090909091
46 0.0909090909091

Which gave the following error:
PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f.wig/track000.wig: [Remove Message]

The second file is an example wig file which I'm told has loaded onto GBrowse in the past. The start of it looks like this:
track type=wiggle_0 name="Reverse Strand Translation Initiation Rates" description="Predicted by RBS Calculator v1.0 (log10 scale)" visibility=full maxHeightPixels=500:500:500 variableStep chrom=MG1655 span=3
3  2.19
11  0.51
22  2.86
29  2.95
70  2.72
125  2.19
141  1.60
150  2.44
157  0.00
159  0.00
163  0.00
176  0.00
183  2.31
185  0.24
.
.
.
and so on.

This gave the following error:

PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/upload_8214/track000.wig: [Remove Message]


The second file is from the JBrowse tutorial data (found at /JBrowse-1.11.3/docs/tutorial/data_files/volvox_microarray.wig). The start of the file looks like this:

track type=wiggle_0 name="example" description="20 degrees, 2 hr"
fixedStep chrom=ctgA start=1 step=100 span=100
281
183
213
191
288
184
258
173
274
292
227
209
277
.
.
.
etc.

This gives the following error:
PROCESSING ERROR: hashMustFindVal: 'ctgA' not found

Many thanks,
Rob

------------------------------------------------------------------------------
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unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Uploading a variable step wig file onto a custom track

McKiernan, Robert M
Hi Tim,

Thanks for the help. I fixed the beginning lines and copy and pasted the file into the text box and it worked fine. However, uploading the file via the file uploader still gave this error:

PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f_copy.wig/track000.wig

I've got my data to be uploaded now, so I'm happy, but I thought I should flag this up anyway.

Thanks,
Rob
________________________________________
From: Timothy Parnell [[hidden email]]
Sent: 30 April 2014 04:34
To: McKiernan, Robert M
Cc: [hidden email]; Ellis, Tom
Subject: Re: [Gmod-gbrowse] Uploading a variable step wig file onto a custom    track

Hi Rob,

The wig file has two special lines, as described in http://genome.ucsc.edu/goldenPath/help/wiggle.html

The track line specifies the type and optionally other parameters, like name
track type=wiggle_0 name=“my data”

The declaration line specifies the type of wiggle. It is repeated for every chromosome. For example
variableStep chrom=chr1
or
fixedStep chrom=chr1 span=100 step=100

In your example, you’ve combined the two, leading to the error.

In the second example from Volvox, the error is regarding the chromosome not being found. Evidently, E coli does not have a chromosome named “ctgA”.  The error is actually a bigWig error, suggesting it is trying to convert your wig file into a bigWig file behind the scenes (default behavior when supported). In this case, you could convert your wig files into bigWigs yourself using utilities available from UCSC and upload those. The advantage there is you can check and fix errors more readily than relying on a remote server.

Hope that helps.
Tim


On Apr 29, 2014, at 4:46 AM, McKiernan, Robert M <[hidden email]<mailto:[hidden email]>> wrote:

Hi everyone,

I'm currently attempting to upload wig files as a custom track onto the following site: http://heptamer.tamu.edu/fgb2/gbrowse/MG1655/ . However, it always returns a processing error, even with example wig files.

I'm wondering whether this is a problem with the format of my files or whether it's a server side problem.
Could someone do me a huge favour and try to upload a variable step wig file which they know is in the correct format for GBrowse please?


You can probably stop reading now but i've included further info below on the files which I've tried to upload, just incase.
I've attempted to upload a few files. The first of which looks like this. I'm only including the start of the files for brevity:

track type=wiggle_0 variableStep chrom=MG1655
43 0.0909090909091
44 0.0909090909091
45 0.0909090909091
46 0.0909090909091

Which gave the following error:
PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f.wig/track000.wig: [Remove Message]

The second file is an example wig file which I'm told has loaded onto GBrowse in the past. The start of it looks like this:
track type=wiggle_0 name="Reverse Strand Translation Initiation Rates" description="Predicted by RBS Calculator v1.0 (log10 scale)" visibility=full maxHeightPixels=500:500:500 variableStep chrom=MG1655 span=3
3  2.19
11  0.51
22  2.86
29  2.95
70  2.72
125  2.19
141  1.60
150  2.44
157  0.00
159  0.00
163  0.00
176  0.00
183  2.31
185  0.24
.
.
.
and so on.

This gave the following error:

PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/upload_8214/track000.wig: [Remove Message]


The second file is from the JBrowse tutorial data (found at /JBrowse-1.11.3/docs/tutorial/data_files/volvox_microarray.wig). The start of the file looks like this:

track type=wiggle_0 name="example" description="20 degrees, 2 hr"
fixedStep chrom=ctgA start=1 step=100 span=100
281
183
213
191
288
184
258
173
274
292
227
209
277
.
.
.
etc.

This gives the following error:
PROCESSING ERROR: hashMustFindVal: 'ctgA' not found

Many thanks,
Rob

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs_______________________________________________
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------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Uploading a variable step wig file onto a custom track

Timothy Parnell
That’s curious. If the file has anything but unix line endings, then I’m pretty sure it will fail. So if the file has gone through a Windows machine or some Mac applications (Excel on Mac, for example), that will explain it.

Otherwise, I’m at a loss.


On May 1, 2014, at 3:51 AM, McKiernan, Robert M <[hidden email]> wrote:

> Hi Tim,
>
> Thanks for the help. I fixed the beginning lines and copy and pasted the file into the text box and it worked fine. However, uploading the file via the file uploader still gave this error:
>
> PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f_copy.wig/track000.wig
>
> I've got my data to be uploaded now, so I'm happy, but I thought I should flag this up anyway.
>
> Thanks,
> Rob
> ________________________________________
> From: Timothy Parnell [[hidden email]]
> Sent: 30 April 2014 04:34
> To: McKiernan, Robert M
> Cc: [hidden email]; Ellis, Tom
> Subject: Re: [Gmod-gbrowse] Uploading a variable step wig file onto a custom    track
>
> Hi Rob,
>
> The wig file has two special lines, as described in http://genome.ucsc.edu/goldenPath/help/wiggle.html
>
> The track line specifies the type and optionally other parameters, like name
> track type=wiggle_0 name=“my data”
>
> The declaration line specifies the type of wiggle. It is repeated for every chromosome. For example
> variableStep chrom=chr1
> or
> fixedStep chrom=chr1 span=100 step=100
>
> In your example, you’ve combined the two, leading to the error.
>
> In the second example from Volvox, the error is regarding the chromosome not being found. Evidently, E coli does not have a chromosome named “ctgA”.  The error is actually a bigWig error, suggesting it is trying to convert your wig file into a bigWig file behind the scenes (default behavior when supported). In this case, you could convert your wig files into bigWigs yourself using utilities available from UCSC and upload those. The advantage there is you can check and fix errors more readily than relying on a remote server.
>
> Hope that helps.
> Tim
>
>
> On Apr 29, 2014, at 4:46 AM, McKiernan, Robert M <[hidden email]<mailto:[hidden email]>> wrote:
>
> Hi everyone,
>
> I'm currently attempting to upload wig files as a custom track onto the following site: http://heptamer.tamu.edu/fgb2/gbrowse/MG1655/ . However, it always returns a processing error, even with example wig files.
>
> I'm wondering whether this is a problem with the format of my files or whether it's a server side problem.
> Could someone do me a huge favour and try to upload a variable step wig file which they know is in the correct format for GBrowse please?
>
>
> You can probably stop reading now but i've included further info below on the files which I've tried to upload, just incase.
> I've attempted to upload a few files. The first of which looks like this. I'm only including the start of the files for brevity:
>
> track type=wiggle_0 variableStep chrom=MG1655
> 43 0.0909090909091
> 44 0.0909090909091
> 45 0.0909090909091
> 46 0.0909090909091
>
> Which gave the following error:
> PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f.wig/track000.wig: [Remove Message]
>
> The second file is an example wig file which I'm told has loaded onto GBrowse in the past. The start of it looks like this:
> track type=wiggle_0 name="Reverse Strand Translation Initiation Rates" description="Predicted by RBS Calculator v1.0 (log10 scale)" visibility=full maxHeightPixels=500:500:500 variableStep chrom=MG1655 span=3
> 3  2.19
> 11  0.51
> 22  2.86
> 29  2.95
> 70  2.72
> 125  2.19
> 141  1.60
> 150  2.44
> 157  0.00
> 159  0.00
> 163  0.00
> 176  0.00
> 183  2.31
> 185  0.24
> .
> .
> .
> and so on.
>
> This gave the following error:
>
> PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/upload_8214/track000.wig: [Remove Message]
>
>
> The second file is from the JBrowse tutorial data (found at /JBrowse-1.11.3/docs/tutorial/data_files/volvox_microarray.wig). The start of the file looks like this:
>
> track type=wiggle_0 name="example" description="20 degrees, 2 hr"
> fixedStep chrom=ctgA start=1 step=100 span=100
> 281
> 183
> 213
> 191
> 288
> 184
> 258
> 173
> 274
> 292
> 227
> 209
> 277
> .
> .
> .
> etc.
>
> This gives the following error:
> PROCESSING ERROR: hashMustFindVal: 'ctgA' not found
>
> Many thanks,
> Rob
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>


------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
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Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: Uploading a variable step wig file onto a custom track

McKiernan, Robert M
Hi Tim,

Sorry I forgot to reply to this. Yes, it had windows line endings. I've got it displaying correctly now.

Cheers for the help,
Rob
________________________________________
From: Timothy Parnell [[hidden email]]
Sent: 01 May 2014 18:52
To: McKiernan, Robert M
Cc: [hidden email]; Ellis, Tom
Subject: Re: [Gmod-gbrowse] Uploading a variable step wig file onto a custom    track

That’s curious. If the file has anything but unix line endings, then I’m pretty sure it will fail. So if the file has gone through a Windows machine or some Mac applications (Excel on Mac, for example), that will explain it.

Otherwise, I’m at a loss.


On May 1, 2014, at 3:51 AM, McKiernan, Robert M <[hidden email]> wrote:

> Hi Tim,
>
> Thanks for the help. I fixed the beginning lines and copy and pasted the file into the text box and it worked fine. However, uploading the file via the file uploader still gave this error:
>
> PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f_copy.wig/track000.wig
>
> I've got my data to be uploaded now, so I'm happy, but I thought I should flag this up anyway.
>
> Thanks,
> Rob
> ________________________________________
> From: Timothy Parnell [[hidden email]]
> Sent: 30 April 2014 04:34
> To: McKiernan, Robert M
> Cc: [hidden email]; Ellis, Tom
> Subject: Re: [Gmod-gbrowse] Uploading a variable step wig file onto a custom    track
>
> Hi Rob,
>
> The wig file has two special lines, as described in http://genome.ucsc.edu/goldenPath/help/wiggle.html
>
> The track line specifies the type and optionally other parameters, like name
> track type=wiggle_0 name=“my data”
>
> The declaration line specifies the type of wiggle. It is repeated for every chromosome. For example
> variableStep chrom=chr1
> or
> fixedStep chrom=chr1 span=100 step=100
>
> In your example, you’ve combined the two, leading to the error.
>
> In the second example from Volvox, the error is regarding the chromosome not being found. Evidently, E coli does not have a chromosome named “ctgA”.  The error is actually a bigWig error, suggesting it is trying to convert your wig file into a bigWig file behind the scenes (default behavior when supported). In this case, you could convert your wig files into bigWigs yourself using utilities available from UCSC and upload those. The advantage there is you can check and fix errors more readily than relying on a remote server.
>
> Hope that helps.
> Tim
>
>
> On Apr 29, 2014, at 4:46 AM, McKiernan, Robert M <[hidden email]<mailto:[hidden email]>> wrote:
>
> Hi everyone,
>
> I'm currently attempting to upload wig files as a custom track onto the following site: http://heptamer.tamu.edu/fgb2/gbrowse/MG1655/ . However, it always returns a processing error, even with example wig files.
>
> I'm wondering whether this is a problem with the format of my files or whether it's a server side problem.
> Could someone do me a huge favour and try to upload a variable step wig file which they know is in the correct format for GBrowse please?
>
>
> You can probably stop reading now but i've included further info below on the files which I've tried to upload, just incase.
> I've attempted to upload a few files. The first of which looks like this. I'm only including the start of the files for brevity:
>
> track type=wiggle_0 variableStep chrom=MG1655
> 43 0.0909090909091
> 44 0.0909090909091
> 45 0.0909090909091
> 46 0.0909090909091
>
> Which gave the following error:
> PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/GSE53767_fp_rdm_pooled_f.wig/track000.wig: [Remove Message]
>
> The second file is an example wig file which I'm told has loaded onto GBrowse in the past. The start of it looks like this:
> track type=wiggle_0 name="Reverse Strand Translation Initiation Rates" description="Predicted by RBS Calculator v1.0 (log10 scale)" visibility=full maxHeightPixels=500:500:500 variableStep chrom=MG1655 span=3
> 3  2.19
> 11  0.51
> 22  2.86
> 29  2.95
> 70  2.72
> 125  2.19
> 141  1.60
> 150  2.44
> 157  0.00
> 159  0.00
> 163  0.00
> 176  0.00
> 183  2.31
> 185  0.24
> .
> .
> .
> and so on.
>
> This gave the following error:
>
> PROCESSING ERROR: Unrecognized line 1 of /var/lib/gbrowse2/userdata/MG1655/a3740f0315fa24da7dba53937f0f82c6/upload_8214/track000.wig: [Remove Message]
>
>
> The second file is from the JBrowse tutorial data (found at /JBrowse-1.11.3/docs/tutorial/data_files/volvox_microarray.wig). The start of the file looks like this:
>
> track type=wiggle_0 name="example" description="20 degrees, 2 hr"
> fixedStep chrom=ctgA start=1 step=100 span=100
> 281
> 183
> 213
> 191
> 288
> 184
> 258
> 173
> 274
> 292
> 227
> 209
> 277
> .
> .
> .
> etc.
>
> This gives the following error:
> PROCESSING ERROR: hashMustFindVal: 'ctgA' not found
>
> Many thanks,
> Rob
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>


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