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MAQ PE issue follow up 

I noticed that I haven't reported in the tracker the MAQ PE issue.

I confirm that I have full permission on all the tree of the output folder, 
that the output has been written correctly in the cache folder and that the 
error (actually not so understandable as you were saying) is:


Unable to copy: 
src=/usr/pl_cache/pipeline/2011August09_14h30m21s353ms/SamToolsmaq2sam-long_1.Ou
tputSAMfile-1.sam, 
dest=projects1/test_pipeline/NEW_ORGANIZATION/Aligners/ALIGNERS_SWITCHED/MAQ_PE/
test.sam

Federica

Original issue reported on code.google.com by [email protected] on 10 Aug 2011 at 7:04

Attachments:

BWA: error in writing the sam 

(1) -BWA-PE: ok the run, but the file is empty:
fgene3 [/projects1/test_pipeline/NEW_ORGANIZATION/BWA_PE] ll total 0
-rw-rw-rw- 1 pipeline pipeline 0 Aug  2 18:09 samfile-0

·       Please not reset the workflow. Copy the command-line executable from 
the (completed) Module-Info tab, paste it on the command line (in a standard 
SSH shell on fgene1/3) and see if there is any additional feedback indicating 
why the result would be null. I think it may be that the result is actually 
written (in some filename/location) but not copied into the user-specified 
partition (permission?) which leaves the impression of an empty result.


..IVO SENT ME A NEW SCRIPT, but:

Hi Ivo,

Unfortunately all the BWA runs failed again in writing the output. As you can 
see when I open up the error window, the samse and sampe process were fine 
(green and not errored). I have used the new script (that is now in: 
/projects1/test_pipeline/NEW_ORGANIZATION/scripts).

I will post also in the issues tracker.

Fed

Original issue reported on code.google.com by [email protected] on 4 Aug 2011 at 9:30

Attachments:

weirdness about renaming of the protocols ;) 

Hi,

I was trying to summarize all the open issues.

Do you remember the weird thing about the renaming of the pipeline? Ivo told me 
you were able to reproduce it and indicate me a zipped jar client verison of 
the pipeline in 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/PipelineWorkflows_
July_2011/others.

I have now the jar file but is doesn't open (see error). I am using the last 
version available on the website now. 

fed

Original issue reported on code.google.com by [email protected] on 18 Aug 2011 at 5:53

Attachments:

BasicQC1-error stream 

Hi Ivo,

I ran  also the BasicQC1. Here the problem is still the script from my 
understanding.  Please find attached the module and the script to double check 
if there is some info missing(I changed the paths and nothing else more).

thanks,

Fed

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 6:49

Attachments:

Variant calling-fai problem 

Hi,

I was trying to test the variant calling pipe. I set up all the input files..I 
am experiencing problem with the index files (fai). The files is there, I also 
try to point to it with the browse funtion and I see it. I added another file 
type (fa.fai) thinking that maybe the extension was the problem but still I 
have the error.

fed

Original issue reported on code.google.com by [email protected] on 20 Oct 2011 at 5:38

Attachments:

some errors in isolated module sol2 fastq conversion 

Hi, I think this issue may be related to the one I have risen few minutes ago. 
I isolated the conversion process between solexa and fastq files as I may need 
to use it separately from  the alignment pipelines. Seems to me that the input 
and the parameters are matching. Also the scripts have always the same 
location, the output folder as well.

Sorry for the naive question, if this is the case.


Fede

Original issue reported on code.google.com by [email protected] on 20 Sep 2011 at 6:32

Attachments:

CNV2 issue still open 

Hi,
I saw the the CNV2(CNVer) issue has been closed but the problem is still there 
(see issue#8).

I have this error:
mkdir /ifs: Permission denied at /applications/CNVer/cnver-0.8.1/src/cnver.pl 
line 100


I have full x permission on the script as you can see. Do tou have the same 
issue?

Federica

Original issue reported on code.google.com by [email protected] on 18 Aug 2011 at 5:23

CNV3 (CNVseq) summary issues 

-CNV3 (CNVseq):

The last discussion we made was:

"(3) CNV3 (CNVseq path): I searched for the Rexe (bc I wanted to avoid bugging 
you anymore but I couldn't find it), so just to keep in mind when you have time.

·        I’m sorry I confused you yesterday! I think Rexe is just a pointer 
to the /uci/fgene location of the R executable. I believe (on fgene1) this 
location may be: /raid/programs/linux/R-2.8.1/bin/R"

I run the attached pipe, having an error in the cnvseq module, no error stream 
but if I run the command line I have an error about the Rexe:


/projects1/test_pipeline/NEW_ORGANIZATION/scripts/cnv-seq.pl --test 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_2.OutputHits-1.hi
ts --ref 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_1.OutputHits-1.hi
ts --genome human --Rexe /applications/R-2.11.1/bin/exec/R 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/CNV-Seq_1.OutputCountFile-1.c
ount 
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/CNV-Seq_1.OutputCNVFile-1.cnv
genome size used for calculation is 3253037807
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_2.OutputHits-1.hi
ts: 48477750 reads
/usr/pl_cache/pipeline/2011August04_16h10m56s535ms/ExtractHits_1.OutputHits-1.hi
ts: 34426365 reads
/applications/R-2.11.1/bin/exec/R: error while loading shared libraries: 
libRblas.so: cannot open shared object file: No such file or directory

 Error: can not find program /applications/R-2.11.1/bin/exec/R at /projects1/test_pipeline/NEW_ORGANIZATION/scripts/cnv-seq.pl line 123.

...so the problem is always the path to Rexe, even if I put the path that also 
you suggested and that make more sense also to me.

I don't find any issue about CNV3 on the tracker, so hopefully I anot misisng 
any piece of info.

Original issue reported on code.google.com by [email protected] on 4 Aug 2011 at 11:30

Attachments:

Aligners summary: BOWTIE_PE 

3) BOWTIE_PE: is still running from one day...but until now no errors...is 
strange btw.

IVO: Are you running on fgene1 or fgene3? Is there progress (new printouts) 
reported in the Output or Error Stream tabs?



FED:
fgene3, yes there are printouts both for output and error ...and they are going 
further.

STill running!

Original issue reported on code.google.com by [email protected] on 3 Aug 2011 at 10:35

ANNOVAR 

Hi, I tested the ANNOVAR pipeline you sent me, but it is failing at the first 
step, independently from the .bam file I am choosing as input, here is the 
error stream if I launch it command line:

 /applications/SAMTOOLS/samtools-0.1.16/samtools pileup -vcf /projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa /projects2/USC/canonical-test-data/hg18_ensembl-bwa/full-bam/852603-6191.bam '>'
Floating point exception

Is always the same floating error. :(

Fed

Original issue reported on code.google.com by [email protected] on 4 Oct 2011 at 7:59

Attachments:

a general issue---testing with real data 

Hi all,

as you know I started to  test the aligners both with simulated and real data. 
It comes that the simulation tool is able to generate directly FASTQ files (and 
not solexa.txt). So we have two different kind of data: the original generated 
from the sequencer (.txt) and the FASTQ.

As you know the vast majority of the modules have been developed starting from 
.txt, some of them starting from them starting from the fastq, and the reason 
is that some tools have internal routines that do the conversion, others have 
not.

BTW, with the sim data I started with BOWTIE SE. As the simulated data are 
fastq I have customized my pipeline removing the conversion step and adjusting 
the parameters accordingly. The validation is ok, but the process doesn't work 
and I have got errors with no streams.

I am also attaching the pipe I modified...am I doing something wrong? It is 
important for me as I have to modify many pipes to test those fastq.


Tks,

Fed

Original issue reported on code.google.com by [email protected] on 20 Sep 2011 at 6:22

Attachments:

script missing for CNV2 

Hi Ivo,

this script is missing:

/ifs/ccb/agenco/bioinformatics/scripts/cnver.sh

Last step of CNVER (CNV2 workflow attached).

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 8:57

MOSAIK PE and SE 

Hi,

I ran MOSAIK, and everything went ok other than the MosaikText step. The error 
stream  is empty though in: 

/usr/pl_cache/pipeline/2011August08_17h26m48s975ms/streams

/usr/pl_cache/pipeline/2011August08_17h26m37s881ms/streams/

...and also the output folder is empty as expected. I checked in the cache and 
there is a trunk .sam.gz file:

fgene3 [/usr/pl_cache/pipeline/2011August08_17h26m48s975ms] gunzip 
MosaikText_1.samoutput-1.sam.gz 

gunzip: MosaikText_1.samoutput-1.sam.gz: unexpected end of file.


I ran the same command by command line and I had back this error in the 
conversion of the file:

fgene3 [/usr/pl_cache/pipeline/2011August08_17h26m48s975ms] 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik/Mos
aikText -in /usr/p                                                              

       put-1_bis.sam
------------------------------------------------------------------------------
MosaikText 1.1.0021                                                 2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- converting the alignment archive to the following formats: SAM

Converting alignment archive:
 0% [                                                                                                               ]                                  |ERROR: The base quality is larger than 60.


I found this discussion about this error: 
http://code.google.com/p/mosaik-aligner/issues/detail?id=79

SO I tried to visualize the .dat file 
(/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik/Mo
saikText -in MosaikBuild_2.Outputfileforreads-1.dat -screen) as suggested, and 
I had back:

fgene3 [/usr/pl_cache/pipeline/2011August08_17h26m48s975ms] 
/projects1/idinov/projects/Pipeline_genomics_informatics_2011/scripts/Mosaik/Mos
aikText -in MosaikBuild_2.Outputfileforreads-1.dat -screen
------------------------------------------------------------------------------
MosaikText 1.1.0021                                                 2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

ERROR: It seems that the input file (MosaikBuild_2.Outputfileforreads-1.dat) is 
not in the MOSAIK alignment format.



I remember you told me you ha dto modify some scripts to make it run because 
MOSAIK was not compatible with the PIPELINE environment. I have never 
encountered this kind of error, so I was wondering what may be the reason.

Federica

Original issue reported on code.google.com by [email protected] on 10 Aug 2011 at 6:24

Attachments:

Advanced QC-errors 

Hi Ivo,

I attach here the pipe and the screeshots of the errors. 

(1) GATK_covariate_analysis: seems to me that the flag is correct (I double 
checked on the website). The flag is working well in the previous step 
(covariate calculation). Seems there are problem in the virtual machine 
(?)...memory problem?

(2) There are other errors that I fixed changing the memory allocation of java 
at 2G and not originally to 4G

(3)GATK callability: no error stream

(4)Fix mate is green, went well (a super naive quetsion: in workflow like that 
one where are the outputs? Not in the temp: 

fgene3 [/projects1/test_pipeline/NEW_ORGANIZATION/Advanced_QC/temp] ll
total 0

..and I haven't specified any data sync actually.

(5) for the PICARD modules: it cannot find the temp foder 
/projects1/test_pipeline/NEW_ORGANIZATION/Advanced_QC/temp even if I have full 
permissions on the whole path.

Actually, I don't think it is a problem of samtool version. I can for sure try 
to link the upgraded version of samtools, but I have the feeling this is not 
the reason bc the command lines did work.


Federica

Original issue reported on code.google.com by [email protected] on 21 Jul 2011 at 9:43

Attachments:

BOWTIE PE 

...BOWTIE PE is still running ..from one week! No errors, seems that there are 
no progress in the output stream. I attach it. The input reads are the same I 
used for the other modules: did you have the same strange behavior?

Federica

Original issue reported on code.google.com by [email protected] on 9 Aug 2011 at 11:17

Attachments:

CNV2 (CNVer) 


Hi Ivo,

I have connected the CNVer step to the script. When I validate I have this 
strange message about the output and a path that is clearly on cranium. I 
searched how to change it, but I didn;t fin this output parameter in the data 
source...what does it mean?

Federica

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 11:00

Attachments:

Basic QC2-error stream 


Hi Ivo,

so, I ran overnight the Basic_QC2 module and it stopped (see pics. The Clean 
sam steps had problems, the error says thet the INPUT otpiopn has not been 
recognized. If I run the same command line on the server by itself it 
works..and also the strange thing is that it starts to produce the output 
(OUTPUT=/usr/pl_cache/pipeline/2011July19_18h01m22s328ms/CleanSam_1.Output-1.sam
') that is a perfect partial sam file.

Find attached the module.

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 6:32

Attachments:

PERM single end testing 

Hi,

andy and me we were starting to test also some aligner module even before the 
switch thing. I tested PERM on single end data (see attached). Evrything went 
well, the output is there, the log is correct:

"Options Info:
Reads are processed as in fastq format.
Reads with 'N' or unknown characters will be discarded.
Results for reads that map to more than 200 locations will not be reported.
The effective read length is 101.
2 mismatches are allowed in the length.
Alignments with minimum mismatches will be collected.


Info 3: Reference 
/projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa 
has 3080436076 bases.
Info 3: There are 225075736 N in the genome.
Build genome in bits  in 34 seconds.                                         
Count bucket size  in 852 seconds.                                         
Hash record  in 1303 seconds.                                         
Sort table  in 2751 seconds.                                         
Check masked loci  in 34 seconds.                                         
Info 3: Successfully made the index
Mapping 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1_F (101-bp reads) with F1 seed.
Deal read no. 37347 in 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1.fastq.
Mapping no 0 reads.
Deal read no. 37347 in 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1.fastq.
/applications/PERM/PerM0.3.3Source/perm 
/projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1.fastq -o 
/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/PERM_1.Outputs-1

/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1_F, Reads:, Filtered#, 153, Kept#, 37347, Mapped#, 32989, 
Multimapped#, 1184, Multimapped>200#, 88                                        

/usr/pl_cache/pipeline/2011July19_16h33m37s028ms/MAQSol2SangerConverter_1.Output
fastqfie-1_F,_ Sub0, 25662, Sub1, 5942, Sub2, 1385, 
Mapping takes in 17 seconds.                                         
Mapped single-ended long reads in 18 seconds."    

..I dont' really understand why it gives an error on the Output bc the two jobs 
9MAQSol to sanger and PERM are green and no errors, and the output have been 
written). There are no error streams.

Fed

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 6:56

Attachments:

Aligners run, summary of the problems and updates: BWA SE and PE 


1) -BWA-PE: ok the run, but the file is empty:
fgene3 [/projects1/test_pipeline/NEW_ORGANIZATION/BWA_PE] ll total 0
-rw-rw-rw- 1 pipeline pipeline 0 Aug  2 18:09 samfile-0

IVO:

Please not reset the workflow. Copy the command-line executable from the 
(completed) Module-Info tab, paste it on the command line (in a standard SSH 
shell on fgene1/3) and see if there is any additional feedback indicating why 
the result would be null. I think it may be that the result is actually written 
(in some filename/location) but not copied into the user-specified partition 
(permission?) which leaves the impression of an empty result.

FED:

Done it (both for single and paired end alignment), this is what I got FOR SE:

  /projects1/test_pipeline/NEW_ORGANIZATION/scripts/bwa_sam.sh samse samfile /usr/pl_cache/pipeline/2011August03_12h07m39s584ms/Link_1.Destination-1.fasta /usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAsamsesampe_1.Output-1 /usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai -fastq /projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k.fq -
/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai
/projects1/test_pipeline/NEW_ORGANIZATION/scripts/bwa_sam.sh: line 23: [: !=: 
unary operator expected
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k
.fq -

/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k
.fq
mkdir: cannot create directory 
`/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAsamsesampe_1.Output-1': 
File exists
[bwa_sai2sam_se_core] fail to open file 
'/usr/pl_cache/pipeline/2011August03_12h07m39s584ms/BWAaln_1.Outputsaifile-1.sai
[0]'. Abort!
/projects1/test_pipeline/NEW_ORGANIZATION/scripts/bwa_sam.sh: line 47: 16258 
Aborted                 /applications/BWA/bwa-0.5.9rc1/bwa $routine $options 
$ref $sai[0] $fastq[0] > ${outdir}/${outbase}-$i


..seems to be a writing problem?!?!?

For PE, I noticed that I haven't changed samse with sampe..I am surpr
ised that the run didn't give any error! I am running it again.

Fed

Original issue reported on code.google.com by [email protected] on 3 Aug 2011 at 10:34

REAL HUMAN HIGH COVERAGE DATA-BOWTIE SE 

Hi, yesterday I started the testing with real human data (input: 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/full_patient_fastq/941603/94
1603_fwd.txt) but I had an error (see pic). The error stream BTW is empty:


[ftorri@fgene3 streams]$ ll
total 12
-rw-rw-rw- 1 pipeline pipeline     0 Sep 20 08:58 BowtieAlignment_1_1.error
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 20:23 BowtieAlignment_1_1.out
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 17:57 Bowtieindexing_1_1.error
-rw-rw-rw- 1 pipeline pipeline 12271 Sep 19 20:23 Bowtieindexing_1_1.out
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 17:57 
MAQSol2SangerConverter_1_1.error
-rw-rw-rw- 1 pipeline pipeline     0 Sep 19 17:57 MAQSol2SangerConverter_1_1.out


..but the process partially ran because there is a .sam file with a proper 
format:

[ftorri@fgene3 BOWTIE_SE_results]$ vi bowtie_se.sam 

I attach here the pipe. How can I diagnose the reason why the process quits? 
The other processes that were running on fgene3 are all still running...

Federica

Original issue reported on code.google.com by [email protected] on 20 Sep 2011 at 5:36

Attachments:

NOVOALIGN 


Hi Sam,

a conceptual  question as I have never used Novoalign before. WHat is the Index 
file name? Because The moidule is validated ok, but I have these errors:

-NOVO INDEX

===Pipeline Errors===
Error encountered while trying to execute 
/projects1/Alignment/Novoalign/novoindex.sh 
/projects1/test_pipeline/NEW_ORGANIZATION/Aligners/NOVOALIGN/SE indexfile 
/projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa 
instance 1      

-NOVO ALIGN

# novoalign (V2.07.13 - Build Jul 18 2011 @ 09:03:08 - A short read aligner 
with qualities.
# (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
# novoalign.lic file not found.
# Licensed for evaluation, educational, and not-for-profit use only.
#  novoalign -d indexfile -f 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k
.txt 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_2_sequence.150k
.txt -F ILMFQ -o SAM 
# Starting at Fri Sep  9 14:52:03 2011
# Interpreting input files as Illumina FASTQ, Casava Pipeline 1.3 to 1.7.
Bad file descriptor
Error opening file indexfile


I attach the pipe I have mosified to use if from my local client.

Fed

Original issue reported on code.google.com by [email protected] on 9 Sep 2011 at 10:01

Attachments:

Need wrapper scripts for BWA PE and SE module 

I'm beginning to test the BWA PE & SE Aligner modules on fgene1. First I'm 
converting them to fgene1-specific paths. 

To complete this step, Ivo, could I have a copy of these wrapper scripts from 
the CRANIUM-based pipeline?

/ifshome/shobel/scripts/BWA_aln.sh
/ifshome/shobel/scripts/bwa_sampe.sh

Also, as luck would have it, the very next version of BWA released after we 
wrote up the pipeline documents includes a new '-f' option to define an output 
file (eliminating the need for shell redirectors ">" in a wrapper script). 
There is also another essential new parameter, -I (an upper case 'i'), that 
eliminates the need for the MAQ sol2sanger step.

So I think it would be worthwhile to update our BWA module to include these 
nice features in the new version. I'll update the pipeline documentation first, 
though and follow up on that soon.

Original issue reported on code.google.com by [email protected] on 20 Jul 2011 at 2:22

ABYSS 

Hi,

I have this error stream:

/usr/pl_cache/pipeline/2011September09_11h41m34s438ms/streams/ABYSS_1_1.error

/projects1/Alignment/Abyss/bin/ABYSS: /usr/lib64/libstdc++.so.6: version 
`GLIBCXX_3.4.9' not found (required by /projects1/Alignment/Abyss/bin/ABYSS

Is something related to Linux right? DO you have this library?

Fed

Original issue reported on code.google.com by [email protected] on 9 Sep 2011 at 10:16

Advanced QC module: failing in finding the tmp folder 

Hi,

I am running now the pipeline through my local client.  I ran the dvanced QC 
module overnight. It ran for 15 hours  and everything went well for the 
Interval creation step. But it stopped at the second step (realigning) and the 
error states that it cannot access to te temp directory in 
/projects1/test_pipeline/NEW_ORGANIZATION/Advanced_QC/temp/ .

the WHOLE path is owned by me, and also I can browse this folder from the 
pipeline GUI.

What do you think may be the problem?

I also attach the window with the Temp Dir parameters. As you can see as u 
suggested I de-ticked the directory source. The path is correct but seems to be 
on the local host, but to change the server address I have to tick again the 
directory source square and it gives me tons of errors. All the oaths of the 
workflows are on fgene1 and I am working on fgene1. I am running the same 
workflow on fgene3.

Fed

Original issue reported on code.google.com by [email protected] on 19 Jul 2011 at 6:00

Visualization 

Hi Federica,

I want to setup a module that will launch the visualization tool remotely and 
display the GUI to the user via X11. Can you please point me to the tool(s) 
that run(s) the visualization component?

Thanks,
Alen

Original issue reported on code.google.com by [email protected] on 14 Sep 2011 at 3:07

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