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gillet / ulysses

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Error running ulysses #1

Open hangphan opened 9 years ago

hangphan commented 9 years ago

Hi, I tried running the example given in the package but I ran into this error after running ./Ulysses.py

Results written to ulysses/example/example.bamUlysses[NRT/INS/RT]_by[PS/SV].[stats.]csv End of inter-chromosomal SV detection Tue Mar 17 14:46:37 GMT 2015 Traceback (most recent call last): File "./Ulysses.py", line 238, in U.write_VCF(params["out"]+".vcf",dicovcf, params["vcf"], params) File "/gpfs0/users/bsg/hangphan/programs/ulysses/Ulysse_utils.py", line 76, in write_VCF _format_vcffile(dictreader, vcffile, Header, sv, fdr_threshlod, lib, params) File "ulysses/Ulysse_utils.py", line 229, in _format_vcffile QUAL = int(abs(-10*math.log(float(line[_tsv_fields[19]])))) IndexError: tuple index out of range

gillet commented 9 years ago

Hi,

I think this is symptomatic of an issue during the compilation of some R code (probamaxdist.c file). Try to go to ulysses directory and to compile it by hand : cd ulysses rm probamaxdist.so probamaxdist.o R CMD SHLIB probamaxdist.c

If i am right it will not work but the error displayed will help to correct the issue (a library might be missing/out of date...).

Best, Alex

hangphan commented 9 years ago

I recompiled it according to what you suggested, but the cvs files still do not contain the pval column which should be at the end of the row. Thus I still have the same error as before.

Library;(pairof)chromosome(s);ID;nbRP;nbA;nbB;left_borderA;right_borderA;deltaA;cen_posA;left_borderB;right_borderB;deltaB;cen_posB;SV_size_min;SV_size_max;p-balanced;cov;AvrQual

Can you check on your side whether this is happening?

gillet commented 9 years ago

The lack of the pval column is due to R crashing. Usually because compilation went wrong but it might also be due to something else. I will need more information to understand what is happening. Can you please paste here or send me by by email the stdout output of ulysses when you run the detection ?

hangphan commented 9 years ago

I will send it to you tomorrow morning.

Best Hang On 17 Mar 2015, at 16:41, Alexandre GILLET-Markowska notifications@github.com wrote:

The lack of the pval column is due to R crashing. Usually because compilation went wrong but it might also be due to something else. I will need more information to understand what is happening. Can you please paste here or send me by by email the stdout output of ulysses when you run the detection ?

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

hangphan commented 9 years ago

Hi,

below is the log of the run on the example given.

Hope you can figure out what was happening

Best

Hang

Wed Mar 18 12:08:28 GMT 2015

Wed Mar 18 12:10:40 GMT 2015

Wed Mar 18 12:12:57 GMT 2015

Wed Mar 18 12:14:48 GMT 2015

Wed Mar 18 12:18:18 GMT 2015

Wed Mar 18 12:18:18 GMT 2015

Wed Mar 18 12:18:24 GMT 2015

Wed Mar 18 12:21:35 GMT 2015

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

--- ULYSSES v1.0 20141023 ---

Ulysses: Accurate detection of rare structural variations from high coverage genome sequencing

Alexandre Gillet, Hugues Richard, Gilles Fischer and Ingrid Lafontaine

http://www.lcqb.upmc.fr/ulysses

Copyright UPMC - CNRS

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

Parameter file : example_params

All SV type will be detected

Duplications

Inversions

inter chromosomal variants

Deletions

MINPS for a deletion: 2

Processing chr16 - Nb of discordant PS: 5087 - 2015-03-18 12:08:24.555014

Processing chr3 - Nb of discordant PS: 2411 - 2015-03-18 12:08:25.635558

Processing chr5 - Nb of discordant PS: 3108 - 2015-03-18 12:08:28.525889

Detection done

Report file : /gpfs0/users/bsg/hangphan/programs/ulysses/example/example.bam_Ulysses.DEL.report.out

results written to /gpfs0/users/bsg/hangphan/programs/ulysses/example/example.bam_Ulysses_deletions_by[PS/SV].csv

results written to /gpfs0/users/bsg/hangphan/programs/ulysses/example/example.bam_Ulysses_deletions_by[PS/SV].csv

Starting coverage calculation

Added local coverage to /gpfs0/users/bsg/hangphan/programs/ulysses/example/example.bam_Ulysses_deletions_bySV.csv

Statistics done

Execution halted

Starting coverage calculation

Added local coverage to /gpfs0/users/bsg/hangphan/programs/ulysses/example/example.bam_Ulysses_small_insertions_bySV.csv

Statistics done

Execution halted

End of deletion detection

MINPS for duplications: 1

Processing chr16 - Nb of discordant PS: 69 - 2015-03-18 12:04

Processing chr3 - Nb of discordant PS: 259 - 2015-03-18 12:04

Processing chr5 - Nb of discordant PS: 29 - 2015-03-18 12:04

Detection done

Statistics done

Execution halted

End of duplication detection

MINPS for inversions: 1

Processing chr16 - Nb of discordant PS: 213 - 2015-03-18 12:13

Processing chr3 - Nb of discordant PS: 42 - 2015-03-18 12:13

Processing chr5 - Nb of discordant PS: 103 - 2015-03-18 12:13

Detection done

Statistics done

Execution halted

End of inversions detection

**** Detection of Inter chromosomal SV

Centromeres positions not given. Distinction between INS and RT will not be optimal

PS loaded from BAM file

Execution halted

Execution halted

Execution halted

* Processing chr16-chr3 205 *

Starting Etape 1: PS sorting by orientation 2015-03-18 12:18:18.518520

Starting Detection 2015-03-18 12:18:18.519870

Orientation "--"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:18.519886

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:18.528243

Starting Etape 4: Makes the list of potential SVs from 49 left groups

2015-03-18 12:18:18.531445

Starting Etape 5: Classification of SVs 2015-03-18 12:18:18.532193

Orientation "++"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:18.533593

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:18.542706

Starting Etape 4: Makes the list of potential SVs from 47 left groups

2015-03-18 12:18:18.546367

Starting Etape 5: Classification of SVs 2015-03-18 12:18:18.547116

Orientation "-+"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:18.548530

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:18.555534

Starting Etape 4: Makes the list of potential SVs from 45 left groups

2015-03-18 12:18:18.558028

Starting Etape 5: Classification of SVs 2015-03-18 12:18:18.558551

Orientation "+-"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:18.559583

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:18.565427

Starting Etape 4: Makes the list of potential SVs from 42 left groups

2015-03-18 12:18:18.567710

Starting Etape 5: Classification of SVs 2015-03-18 12:18:18.568150

Starting Etape 6: Remove SV duplicates 2015-03-18 12:18:18.569032

Start affichage 2015-03-18 12:18:18.569184

* Processing chr16-chr5 846 *

Starting Etape 1: PS sorting by orientation 2015-03-18 12:18:18.883893

Starting Detection 2015-03-18 12:18:18.887935

Orientation "--"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:18.887951

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:18.908138

Starting Etape 4: Makes the list of potential SVs from 82 left groups

2015-03-18 12:18:18.912358

Starting Etape 5: Classification of SVs 2015-03-18 12:18:18.913203

Orientation "++"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:18.914801

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:18.928657

Starting Etape 4: Makes the list of potential SVs from 69 left groups

2015-03-18 12:18:18.932351

Starting Etape 5: Classification of SVs 2015-03-18 12:18:18.933058

50 / 69 / 0 / 1

Orientation "-+"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:18.934431

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:19.127027

Starting Etape 4: Makes the list of potential SVs from 85 left groups

2015-03-18 12:18:19.468097

Starting Etape 5: Classification of SVs 2015-03-18 12:18:21.316059

Orientation "+-"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:21.351162

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:21.581484

Starting Etape 4: Makes the list of potential SVs from 92 left groups

2015-03-18 12:18:21.929184

Starting Etape 5: Classification of SVs 2015-03-18 12:18:23.463195

Starting Etape 6: Remove SV duplicates 2015-03-18 12:18:23.495387

Start affichage 2015-03-18 12:18:23.498835

* Processing chr3-chr5 110 *

Starting Etape 1: PS sorting by orientation 2015-03-18 12:18:24.050903

Starting Detection 2015-03-18 12:18:24.053141

Orientation "--"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:24.053157

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:24.055327

Starting Etape 4: Makes the list of potential SVs from 25 left groups

2015-03-18 12:18:24.059097

Starting Etape 5: Classification of SVs 2015-03-18 12:18:24.059512

Orientation "++"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:24.060118

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:24.063244

Starting Etape 4: Makes the list of potential SVs from 31 left groups

2015-03-18 12:18:24.064617

Starting Etape 5: Classification of SVs 2015-03-18 12:18:24.064975

Orientation "-+"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:24.065669

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:24.067598

Starting Etape 4: Makes the list of potential SVs from 24 left groups

2015-03-18 12:18:24.068716

Starting Etape 5: Classification of SVs 2015-03-18 12:18:24.068986

Orientation "+-"

Starting Etape 2: Making groups of PS in the same orientation

2015-03-18 12:18:24.069468

Starting Etape 3: Individual opposite PS collection 2015-03-18

12:18:24.072194

Starting Etape 4: Makes the list of potential SVs from 29 left groups

2015-03-18 12:18:24.073347

Starting Etape 5: Classification of SVs 2015-03-18 12:18:24.073619

Starting Etape 6: Remove SV duplicates 2015-03-18 12:18:24.074184

Start affichage 2015-03-18 12:18:24.074324

Statistics done

Execution halted

Statistics done

Execution halted

Statistics done

Execution halted

Detection done

Report file : /gpfs0/users/bsg/hangphan/programs/ulysses/example/example.bam_Ulysses.INTER.report.out

Results written to /gpfs0/users/bsg/hangphan/programs/ulysses/example/example.bamUlysses[NRT/INS/RT]_by[PS/SV].[stats.]csv

End of inter-chromosomal SV detection

Traceback (most recent call last):

File "./Ulysses.py", line 238, in 

U.write_VCF(params["out"]+".vcf",dicovcf, params["vcf"], params)

File "/gpfs0/users/bsg/hangphan/programs/ulysses/Ulysse_utils.py", line 76, in write_VCF

_format_vcffile(dictreader, vcffile, Header, sv, fdr_threshlod, lib,

params)

File "/gpfs0/users/bsg/hangphan/programs/ulysses/Ulysse_utils.py", line 229, in _format_vcffile

QUAL = int(abs(-10*math.log(float(line[_tsv_fields[19]]))))

IndexError: tuple index out of range

On Tue, Mar 17, 2015 at 4:42 PM, Hang Phan hangphan@gmail.com wrote:

I will send it to you tomorrow morning.

Best Hang On 17 Mar 2015, at 16:41, Alexandre GILLET-Markowska < notifications@github.com> wrote:

The lack of the pval column is due to R crashing. Usually because compilation went wrong but it might also be due to something else. I will need more information to understand what is happening. Can you please paste here or send me by by email the stdout output of ulysses when you run the detection ?

— Reply to this email directly or view it on GitHub https://github.com/gillet/ulysses/issues/1#issuecomment-82464043.

gillet commented 9 years ago

Hi Hang, R is crashing for an unknown reason. Can you send me the output of the R c code compilation: cd ulysses rm probamaxdist.so probamaxdist.o R CMD SHLIB probamaxdist.c

Also, can you send me the same output as before after removing probamaxdist.so and probamaxdist.o files. cd ulysses rm probamaxdist.so probamaxdist.o cd example ../Ulysses.py

Alex

hangphan commented 9 years ago

Hi Alex,

I recompiled the R code, but there’s nothing abnormal about it

-bash-4.1$ R CMD SHLIB probamaxdist.c gcc -std=gnu99 -I/apps/well/R/3.1.2/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c probamaxdist.c -o probamaxdist.o gcc -std=gnu99 -shared -L/apps/well/R/3.1.2/lib64/R/lib -L/usr/local/lib64 -o probamaxdist.so probamaxdist.o -L/apps/well/R/3.1.2/lib64/R/lib -lR -bash-4.1$

Best regards, Hang On 18 Mar 2015, at 13:24, Alexandre GILLET-Markowska notifications@github.com wrote:

Hi Hang, R is crashing for an unknown reason. Can you send me the output of the R c code compilation: cd ulysses rm probamaxdist.so probamaxdist.o R CMD SHLIB probamaxdist.c

Also, can you send me the same output as before after removing probamaxdist.so and probamaxdist.o files. cd ulysses rm probamaxdist.so probamaxdist.o cd example ../Ulysses.py

Alex

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

gillet commented 9 years ago

I cannot manage to reproduce the bug. What OS you are using ? What is your R version ? You can also re-run the detection in debug mode (you need to replace 2 files in the ulysses directory: https://dl.dropboxusercontent.com/u/52471317/scriptRClusterSize.R https://dl.dropboxusercontent.com/u/52471317/Ulysse_stats.py ) and send me the output. Best, Alex

hangphan commented 9 years ago

I use a Linux system, not sure which version of Linux, and the R version is R/3.1.2 Does this ring any bell?

On Wed, Mar 18, 2015 at 2:20 PM, Alexandre GILLET-Markowska < notifications@github.com> wrote:

I cannot manage to reproduce the bug. What OS you are using ? What is your R version ? You can also re-run the detection in debug mode (you need to replace 2 files in the ulysses directory: https://dl.dropboxusercontent.com/u/52471317/Rfunctions.R https://dl.dropboxusercontent.com/u/52471317/Ulysse_stats.py ) and send me the output. Best, Alex

— Reply to this email directly or view it on GitHub https://github.com/gillet/ulysses/issues/1#issuecomment-82993729.

gillet commented 9 years ago

I've edited the links in the previous message, one was wrong sorry

hangphan commented 9 years ago

Which link was wrong?

On Wed, Mar 18, 2015 at 2:24 PM, Alexandre GILLET-Markowska < notifications@github.com> wrote:

I've edited the links in the previous message, one was wrong sorry

— Reply to this email directly or view it on GitHub https://github.com/gillet/ulysses/issues/1#issuecomment-82994744.

gillet commented 9 years ago

the first one

gillet commented 9 years ago

Your R version looks alright to me (we use the same version). Linux should not be faulty here (some users have had some problems compiling the R code with mac os 10.10).

In you case, R seems to crash only when it writes down some files. There might be something with file permissions. We might have more details with the debug mode.