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arundurvasula / angsd-wrapper

A project for extending ANGSD
MIT License
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Errors when working through tutorial #99

Closed ChaochihL closed 8 years ago

ChaochihL commented 8 years ago

Comments on Tutorial

Here are some errors that I came across when working through ANGSD-wrapper's tutorial:

$ samtools faidx data/reference.Oryza_sativa.IRGSP-1.0.23.dna.genome_chr.fa.gz

The following error message is outputted:

Cannot index files compressed with gzip, please use bgzip

bgzip is not a command, should mention to users how to unzip the file otherwise they are not able to run through the remainder of the tutorial

bash scripts/SFS.sh scripts/SFS.conf

Error message:

scripts/SFS.sh: line 127: /home/morrellp/liux1299/ANGSD-wrapper_beta_testing/aw_test_iplant1_AD/aw-tutorial/angsd/misc/realSFS: No such file or directory

I will continue testing the remainder of the scripts and see if they are able to run to completion.

rossibarra commented 8 years ago

bgzip is part of HTSLIB and runs just fine on my cluster. Arun are your files bgzip'd? Perhaps we just need to mention people need to have htslib/samtools installed?

$ bgzip

Usage: bgzip [options] [file] ...

Options: -c write on standard output, keep original files unchanged -d decompress -f overwrite files without asking -b INT decompress at virtual file pointer INT -s INT decompress INT bytes in the uncompressed file -h give this help

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Tel: 530-752-1152 @jrossibarra www.rilab.org

On Tue, Nov 3, 2015 at 8:32 AM, ChaochihLiu notifications@github.com wrote:

Comments on Tutorial

  • When calling on samtools, it would be helpful to mention to users they need to load samtools or install samtools if they do not already have samtools installed.

Error messages

Here are some errors that I came across when working through ANGSD-wrapper's tutorial:

  • When running the following command:

$ samtools faidx data/reference.Oryza_sativa.IRGSP-1.0.23.dna.genome_chr.fa.gz

The following error message is outputted:

Cannot index files compressed with gzip, please use bgzip

bgzip is not a command, should mention to users how to unzip the file otherwise they are not able to run through the remainder of the tutorial

  • Solution: use gunzip to decompress fasta files
    • Running the following command:

bash scripts/SFS.sh scripts/SFS.conf

Error message:

scripts/SFS.sh: line 127: /home/morrellp/liux1299/ANGSD-wrapper_beta_testing/aw_test_iplant1_AD/aw-tutorial/angsd/misc/realSFS: No such file or directory

I will continue testing the remainder of the scripts and see if they are able to run to completion.

— Reply to this email directly or view it on GitHub https://github.com/arundurvasula/angsd-wrapper/issues/99.

rossibarra commented 8 years ago

Is /home/morrellp/liux1299/ANGSD-wrapper_beta_testing/awtest iplant1_AD/aw-tutorial/angsd/misc/ a real directory? All line 127 is doing is:

${ANGSD_DIR}/misc/realSFS\ ${RESULTS_DIR}/

It looks like there might be a forward slash missing before ${RESULTS_DIR}, but without knowing what you put in the config file I'm not totally sure.

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Tel: 530-752-1152 @jrossibarra www.rilab.org

On Tue, Nov 3, 2015 at 8:32 AM, ChaochihLiu notifications@github.com wrote:

Comments on Tutorial

  • When calling on samtools, it would be helpful to mention to users they need to load samtools or install samtools if they do not already have samtools installed.

Error messages

Here are some errors that I came across when working through ANGSD-wrapper's tutorial:

  • When running the following command:

$ samtools faidx data/reference.Oryza_sativa.IRGSP-1.0.23.dna.genome_chr.fa.gz

The following error message is outputted:

Cannot index files compressed with gzip, please use bgzip

bgzip is not a command, should mention to users how to unzip the file otherwise they are not able to run through the remainder of the tutorial

  • Solution: use gunzip to decompress fasta files
    • Running the following command:

bash scripts/SFS.sh scripts/SFS.conf

Error message:

scripts/SFS.sh: line 127: /home/morrellp/liux1299/ANGSD-wrapper_beta_testing/aw_test_iplant1_AD/aw-tutorial/angsd/misc/realSFS: No such file or directory

I will continue testing the remainder of the scripts and see if they are able to run to completion.

— Reply to this email directly or view it on GitHub https://github.com/arundurvasula/angsd-wrapper/issues/99.

tvkent commented 8 years ago

can you not just do something like zless data/reference.Oryza_sativa.IRGSP-1.0.23.dna.genome_chr.fa.gz | samtools faidx - ? I always gzip and constantly gzipping and gunzipping is a bad idea.

ChaochihL commented 8 years ago

Yes, /home/morrellp/liux1299/ANGSD-wrapper_beta_testing/aw_test_ iplant1_AD/aw-tutorial/angsd/misc/ is a real directory. I checked in the directory but did not find realSFS in it. I think the issue might be an error with installating angsd.

When running make in angsd directory, I get the following error:

g++ -O3 -D_USE_KNETFILE  -o angsd.static *.o -lz -lpthread --static                                             
/usr/bin/ld: cannot find -lz                                                                                    
collect2: ld returned 1 exit status                                                                             
make: *** [angsd.static] Error 1
rossibarra commented 8 years ago

That's the lib error you guys have on your system. Make a note in the wiki/tutorial that you need zlib installed, and that should be the end of that issue.

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Tel: 530-752-1152 @jrossibarra www.rilab.org

On Tue, Nov 3, 2015 at 1:39 PM, ChaochihLiu notifications@github.com wrote:

Yes, /home/morrellp/liux1299/ANGSD-wrapper_beta_testing/awtest iplant1_AD/aw-tutorial/angsd/misc/ is a real directory. I checked in the directory but did not find realSFS in it. I think the issue might be an error with installating angsd.

When running make in angsd directory, I get the following error:

g++ -O3 -D_USEKNETFILE -o angsd.static .o -lz -lpthread --static /usr/bin/ld: cannot find -lz collect2: ld returned 1 exit status make: _\ [angsd.static] Error 1

— Reply to this email directly or view it on GitHub https://github.com/arundurvasula/angsd-wrapper/issues/99#issuecomment-153497773 .

rossibarra commented 8 years ago

Yes, this is a better solution.

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Tel: 530-752-1152 @jrossibarra www.rilab.org

On Tue, Nov 3, 2015 at 12:44 PM, Tyler Kent notifications@github.com wrote:

can you not just do something like zless data/reference.Oryza_sativa.IRGSP-1.0.23.dna.genome_chr.fa.gz | samtools faidx - ? I always gzip and constantly gzipping and gunzipping is a bad idea.

— Reply to this email directly or view it on GitHub https://github.com/arundurvasula/angsd-wrapper/issues/99#issuecomment-153482372 .

pmorrell commented 8 years ago

Just ask yourself, "What would Vince Buffalo do?". He would use a pipe.

Sent from my iPhone

On Nov 3, 2015, at 15:53, Jeffrey Ross-Ibarra notifications@github.com wrote:

Yes, this is a better solution.

Jeffrey Ross-Ibarra

Dept. of Plant Sciences 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616

Tel: 530-752-1152 @jrossibarra www.rilab.org

On Tue, Nov 3, 2015 at 12:44 PM, Tyler Kent notifications@github.com wrote:

can you not just do something like zless data/reference.Oryza_sativa.IRGSP-1.0.23.dna.genome_chr.fa.gz | samtools faidx - ? I always gzip and constantly gzipping and gunzipping is a bad idea.

— Reply to this email directly or view it on GitHub < https://github.com/arundurvasula/angsd-wrapper/issues/99#issuecomment-153482372

.

— Reply to this email directly or view it on GitHub https://github.com/arundurvasula/angsd-wrapper/issues/99#issuecomment-153500993 .

arundurvasula commented 8 years ago

Put the zlib thing in the installation instructions, FAQ, and tutorial. Will close issue.