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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
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chimericReadSearch.py: Error in Calculate Exon/Repeat Interactions #14

Closed ababaian closed 4 years ago

ababaian commented 5 years ago

Hey Richard (@biscuit13161)

I've been helping @dklinkebiel set up LIONS on a local system and ran into an error in the chimericReadSearch.py script. You're quite a bit better at python then me, would you mind trying to get to the bottom of this?

I've tracked the error down to occurring after Line 744, somewhere in the Exon/Repeat Interaction calculations.

LIONS Error Output from Dave.

@dklinkebiel can you post the output of the following commands.

head -n 100 /lustre/work/epigenomics/klinkebiel/parallel/LIONS2/projects/sandbox/DKO_PreTumor/resources/assembly_exons_2

head -n 100 /lustre/work/epigenomics/klinkebiel/parallel/LIONS2/resources/mm10/repeat/forChimericSearch
dklinkebiel commented 5 years ago

Attached is the "First" <head -n 100 *> and "Second" request. This was a different run that had the same error so posting that error. Second.txt First.txt LIONS_ERR.txt

biscuit13161 commented 5 years ago

Hi Dave,

Without having data, I'm having some issues figuring out exactly where the error is occurring.

Could you drop the attached file in place of the chimericReadSearch.py script you have (personally, I'd move the old one to keep it safe before saving this one without the .txt extension), rerun and send me the error log again.

Thanks, Richard

chimericReadSearch.py.txt

dklinkebiel commented 5 years ago

Hi Richard,

Attached is the error log you requested. Thanks LIONS_ERR.txt

Dave

biscuit13161 commented 5 years ago

Apologies Dave,

I'm afraid introduced a typo in that file when I sent it previously. Could you try again with this attached file.

Thanks, Richard

chimericReadSearch.py.txt

dklinkebiel commented 5 years ago

Here is the latest error log.

Dave LIONS_ERR.txt

dklinkebiel commented 5 years ago

Hi Richard,

I was wondering if you got a chance to look at the LIONS error I was encountering. Thanks

David Klinkebiel

From: Richard Thompson [mailto:notifications@github.com] Sent: Wednesday, May 22, 2019 3:58 AM To: ababaian/LIONS Cc: Klinkebiel, David L; Mention Subject: Re: [ababaian/LIONS] chimericReadSearch.py: Error in Calculate Exon/Repeat Interactions (#14)

Non-UNMC email

Apologies Dave,

I'm afraid introduced a typo in that file when I sent it previously. Could you try again with this attached file.

Thanks, Richard

chimericReadSearch.py.txthttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ababaian_LIONS_files_3206523_chimericReadSearch.py.txt&d=DwMCaQ&c=ZukO2fIan9e5E9v43wuy1w&r=vKRPlkEYVk2tW6yg3Wya3TBgZjkiII0bGYp_2yVrE60&m=jhVQV2owEYnJM21Vh57qt3DeGd3-c7z-w2GLduXImMQ&s=_FTeEuRrafW0-wjS3GO1_O19ZqjO5Rn3E9PFGPYWDUs&e=

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biscuit13161 commented 5 years ago

Apologies Dave,

We had a national holiday here and I was caught up finishing things.

It looks like either it's happening after the output loop, which is the last thing in the script, or it's having an issue with a specific piece of data. However I can't see exactly were this error would arise...

Could you try running with this version of the script and let me have the error log again.

chimericReadSearch.py.txt

dklinkebiel commented 5 years ago

Here is the latest error log. Had to give dropbox link since file was to big to insert.

Dave

https://www.dropbox.com/s/89gmn5em2wyd585/LIONS_ERR.txt?dl=0

biscuit13161 commented 5 years ago

Hi Dave,

Thanks, sorry I should have mentioned that I was expecting it to be a large file. Could you send me the stdout log as well?

Thanks, Richard

dklinkebiel commented 5 years ago

Here is the latest stdout log.

Dave LIONS_OUT.txt

biscuit13161 commented 5 years ago

hi Dave,

I suspect we've been looking in the wrong script. Could you revert the chimericReadSearch.py to its original from github and try using chimGroup.R.txt in place of <LIONS_ Root>/scripts/ChimericAnalysis/chimGroup.R Please let me have both the error and stdout logs.

Thanks, Richard

dklinkebiel commented 5 years ago

Here is the latest error and stdout logs.

Dave LIONS_OUT.txt LIONS_ERR.txt

biscuit13161 commented 5 years ago

Apologies Dave,

I thought I'd sent this to you last week...

as before can you try chimGroup.R.txt and let me have the two log files.

Thanks, Rich

dklinkebiel commented 5 years ago

Latest error and out logs. Thanks

Dave LIONS_ERR.txt LIONS_OUT.txt

biscuit13161 commented 5 years ago

Hi Dave,

I think I understand what's happening but I'd appreciate it if you could run this file - chimGroup.R.txt - to confirm..

... Also would you mind including your input list file (.../parallel/LIONS/controls/input.list)

Thanks Rich

dklinkebiel commented 5 years ago

Latest error and out logs and input.list

. Thanks

Dave LIONS_ERR.txt LIONS_OUT.txt input.list.txt

biscuit13161 commented 5 years ago

Hi Dave,

Can you try again with this file - chimGroup.R.txt

Thanks, Rich

dklinkebiel commented 5 years ago

Here is the latest error and out logs. Thanks

Dave LIONS_OUT.txt LIONS_ERR.txt

biscuit13161 commented 5 years ago

Hi Dave,

Sorry, still investigating but can you try this chimGroup.R.txt

Thanks, Richard

dklinkebiel commented 5 years ago

Here is the latest error and out logs. Dave LIONS_OUT.txt LIONS_ERR.txt

biscuit13161 commented 5 years ago

Hi Dave,

Sorry about all the "To-ing and Fro-ing" but can you run this version .. chimGroup.R.txt

Thanks, Richard

dklinkebiel commented 5 years ago

Here is the latest error and out logs. Thanks

Dave LIONS_OUT.txt LIONS_ERR.txt

biscuit13161 commented 5 years ago

Hi Dave,

I'm sure this back and forth is annoying you as much as it is me ... is there anyway you could let me have an anonymised, minimum dataset that produces the same error? ... then I can do the testing myself

Thanks, Richard

dklinkebiel commented 5 years ago

Here are links to the gzipped fastq files. I hope this works. ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-MT1_S7_R2_001_val_2.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-MT1_S7_R1_001_val_1.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-MT2_S8_R2_001_val_2.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-MT2_S8_R1_001_val_1.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-MT3_S9_R2_001_val_2.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-MT3_S9_R1_001_val_1.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-Ovid1_S1_R2_001_val_2.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-Ovid1_S1_R1_001_val_1.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-Ovid2_S2_R2_001_val_2.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-Ovid2_S2_R1_001_val_1.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-Ovid3_S3_R2_001_val_2.fq.gz ftp://dklinkebiel@webmedia.unmc.edu/BIGDISK/htdocs/public/biochemistry/klinkebiel/GSF1734-D1-Ovid3_S3_R1_001_val_1.fq.gz

Dave

biscuit13161 commented 5 years ago

Sorry Dave,

Those links don't seem to be working for me ... they keep timing out!

I can set up a shared Dropbox folder unless you have any other suggestions

Best, Rich

dklinkebiel commented 5 years ago

Sure – set up a Dropbox folder. Thanks

Dave

From: Richard Thompson [mailto:notifications@github.com] Sent: Tuesday, July 23, 2019 2:12 AM To: ababaian/LIONS Cc: Klinkebiel, David L; Mention Subject: Re: [ababaian/LIONS] chimericReadSearch.py: Error in Calculate Exon/Repeat Interactions (#14)

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Sorry Dave,

Those links don't seem to be working for me ... they keep timing out!

I can set up a shared Dropbox folder unless you have any other suggestions

Best, Rich

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biscuit13161 commented 5 years ago

Hi Dave,

I think I've sorted it... It turns out that this issue occurred when the input.list contains non-unique library names. I've amended the code to allow for this, so if you can re-clone the git repository (I'm assuming you're not using the docker version) and let me know how it runs now.

Thanks, Richard

dklinkebiel commented 5 years ago

Hi Richard,

I seem to be getting this message in my out log. Thanks

---------- Set-up Project Workspace ---------- Initializing sandbox Directory: /lustre/work/epigenomics/klinkebiel/parallel/LIONS/projects/sandbox /lustre/work/epigenomics/klinkebiel/parallel/LIONS/controls/input.list /lustre/work/epigenomics/klinkebiel/parallel/LIONS/controls/parameter.ctrl ERROR 7B: Input File Not Accesible (Fastq) files: /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid1_S1_R1_001_val_1.fq ; /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid1_S1_R2_001_val_2.fq a) The non-bam input file (.fq_1 & .fq_2) isnt found b) If youre using FASTQ; make sure youre listing two files in the input.list file seperated by a comma

Dave

ababaian commented 5 years ago

might the spaces between the semi colons?

dklinkebiel commented 5 years ago

This is my input.list

DKO_Ovid /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid1_S1_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid1_S1_R2_001_val_2.fq 1 DKO_Ovid /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid2_S2_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid2_S2_R2_001_val_2.fq 1 DKO_Ovid /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid3_S3_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid3_S3_R2_001_val_2.fq 1 DKO_MatureTumor /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT1_S7_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT1_S7_R2_001_val_2.fq 2 DKO_MatureTumor /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT2_S8_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT2_S8_R2_001_val_2.fq 2 DKO_MatureTumor /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT3_S9_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT3_S9_R2_001_val_2.fq 2

biscuit13161 commented 5 years ago

Hi Dave,

I had that come up too... I think that's an issue with the file paths ...

For me, it was because the files were gzipped but the input.list defined non-gzipped files, so LIONS couldn/t find them

@Artem Babaian ababaian@bccrc.ca do you think it's worth adding a file check to allow this gzip/non-gzip difference without erroring?

thanks, Richard

On Wed, 7 Aug 2019 at 23:12, dklinkebiel notifications@github.com wrote:

This is my input.list

DKO_Ovid /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid1_S1_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid1_S1_R2_001_val_2.fq 1 DKO_Ovid /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid2_S2_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid2_S2_R2_001_val_2.fq 1 DKO_Ovid /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid3_S3_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-Ovid3_S3_R2_001_val_2.fq 1 DKO_MatureTumor /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT1_S7_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT1_S7_R2_001_val_2.fq 2 DKO_MatureTumor /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT2_S8_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT2_S8_R2_001_val_2.fq 2 DKO_MatureTumor /lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT3_S9_R1_001_val_1.fq,/lustre/work/epigenomics/klinkebiel/parallel/LIONS/data/GSF1734-D1-MT3_S9_R2_001_val_2.fq 2

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dklinkebiel commented 5 years ago

How could I correct for this issue with current LIONS. Would unzipping files work. Thanks Dave

biscuit13161 commented 5 years ago

Hi Dave,

Sorry for the late reply, I'm on holiday at the moment.

It's just a mismatch between input.list and the file names. As the files are already gzipped, i'd just modify the input.list to match. Especially as one of the first steps is to gzip the files if they aren't!

Best, Richard

On Mon, 12 Aug 2019, 23:15 dklinkebiel, notifications@github.com wrote:

How could I correct for this issue with current LIONS. Would unzipping files work. Thanks Dave

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dklinkebiel commented 5 years ago

Hi Richard,

Seem to have run into another error. Attached are the error and out logs. Thanks

Dave LIONS_OUT.txt LIONS_ERR.txt

dklinkebiel commented 5 years ago

Hi Richard,

Have you had a chance to look at my last LIONS error. Thanks

Dave

biscuit13161 commented 5 years ago

Hi Dave,

Apologies for not getting back to you earlier, I've been away and I realised that I'd been testing against the wrong species reference.

I'm running some tests at the moment and I'll get back to you soon.

Best, Richard

On Tue, 17 Sep 2019 at 17:27, dklinkebiel notifications@github.com wrote:

Hi Richard,

Have you had a chance to look at my last LIONS error. Thanks

Dave

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dklinkebiel commented 5 years ago

Thanks !!

From: Richard Thompson [mailto:notifications@github.com] Sent: Wednesday, September 18, 2019 12:13 AM To: ababaian/LIONS Cc: Klinkebiel, David L; Mention Subject: Re: [ababaian/LIONS] chimericReadSearch.py: Error in Calculate Exon/Repeat Interactions (#14)

Non-UNMC email Hi Dave,

Apologies for not getting back to you earlier, I've been away and I realised that I'd been testing against the wrong species reference.

I'm running some tests at the moment and I'll get back to you soon.

Best, Richard

On Tue, 17 Sep 2019 at 17:27, dklinkebiel notifications@github.com wrote:

Hi Richard,

Have you had a chance to look at my last LIONS error. Thanks

Dave

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biscuit13161 commented 5 years ago

Hi Dave,

Apologies for how long this has taken, but I think I've sorted it now...

It appears one of the steps got confused when there's more than one entry with the same starting coordinates in the Repeat Masker DB. I've amended and committed the script, but let me know if you're still having issues.

Best, Richard

dklinkebiel commented 5 years ago

Hi Richard,

The folders are not downloading complete.

Dave

biscuit13161 commented 5 years ago

Hi Dave,

I'm afraid I've re-downloaded the folders (using git clone) on a couple of different computers without issue...🤔 How are you getting the files? ... git clone? ... or downloading the zip file? ... or Github Desktop?

Artem,

Are you aware of any issues with this?

Best, Richard

On Mon, 28 Oct 2019 at 17:16, dklinkebiel notifications@github.com wrote:

Hi Richard,

The folders are not downloading complete.

Dave

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dklinkebiel commented 5 years ago

If I download the zipped file via Clone with HTTPS and un-zip the folders are empty with the files outside. I was able to open it in desktop and the format was intact. Program is running now so will see. Thanks

Dave

dklinkebiel commented 5 years ago

Hi Richard,

Do the attached error and out logs suggest that LIONS completed. Thanks Now to determine what the out put means. Any clues about that.

Dave LIONS_ERR.txt LIONS_OUT.txt

biscuit13161 commented 5 years ago

Hi Dave,

That's pretty much what I had expected ... unless Artem sees something I don't.

Artem, do you have any comments about interpreting the output?

Best, Richard

On Sat, 2 Nov 2019 at 00:46, dklinkebiel notifications@github.com wrote:

Hi Richard,

Do the attached error and out logs suggest that LIONS completed. Thanks Now to determine what the out put means. Any clues about that.

Dave LIONS_ERR.txt https://github.com/ababaian/LIONS/files/3799732/LIONS_ERR.txt LIONS_OUT.txt https://github.com/ababaian/LIONS/files/3799733/LIONS_OUT.txt

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ababaian commented 4 years ago

This looks like it completed? I don't see anything either that's out of the ordinary.

dklinkebiel commented 4 years ago

Hi Artem,

I was looking at the LIONS output and in the *.lions output there is a category “Contribution An estimate of the promoter contribution of this Repeat TSS to the ex- pression of gene in total. Calculated with ExonMax and UpExonMax.” Is this value the percent of contribution? For example a value of 0.5 would be 0.05 percent of total or is it 50 percent of total. Thanks

Dave

From: Artem Babaian [mailto:notifications@github.com] Sent: Wednesday, August 07, 2019 2:13 PM To: ababaian/LIONS Cc: Klinkebiel, David L; Mention Subject: Re: [ababaian/LIONS] chimericReadSearch.py: Error in Calculate Exon/Repeat Interactions (#14)

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might the spaces between the semi colons?

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ababaian commented 4 years ago

0.5 would be 50% of total expression. Keep in mind this is an estimate but it's pretty spot on a lot of the time.

dklinkebiel commented 4 years ago

How do you account for value such as 1.89 ? Thanks

Dave

From: Artem Babaian [mailto:notifications@github.com] Sent: Monday, December 09, 2019 4:04 PM To: ababaian/LIONS Cc: Klinkebiel, David L; Mention Subject: Re: [ababaian/LIONS] chimericReadSearch.py: Error in Calculate Exon/Repeat Interactions (#14)

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0.5 would be 50% of total expression. Keep in mind this is an estimate but it's pretty spot on a lot of the time.

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ababaian commented 4 years ago

The expression of the TE portion is higher then the gene with which it fuses.