Can't locate File/Which.pm in @INC

[juliannichol...@gmail.com]

Hello, I am trying to run V2beta, just the .pl script with no other commands to test the installation and am getting this error:

Can't locate File/Which.pm in @INC (you may need to install the File::Which module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.24.1 /usr/local/share/perl/5.24.1 /usr/lib/x86_64-linux-gnu/perl5/5.24 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.24 /usr/share/perl/5.24 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/bin/denovo_map.pl line 34.

BEGIN failed--compilation aborted at /usr/local/bin/denovo_map.pl line 34.

Any help would be greatly appreciated. 

[Julian Catchen]

Hi Julian,

You can safely delete that line from the script (line 34). I have
removed it in the source.

julian

[juliannichol...@gmail.com]

Julian, I deleted line 34 and am now getting this is the error:

'/usr/local/bin/denovo_map.pl' 

String found where operator expected at /usr/local/bin/denovo_map.pl line 80, near "which "samtools""

(Do you need to predeclare which?)

syntax error at /usr/local/bin/denovo_map.pl line 80, near "which "samtools""

Execution of /usr/local/bin/denovo_map.pl aborted due to compilation errors.

[Julian Catchen]

Hi Julian, make sure you are working with Beta2; we have removed that
module in Beta2.

[juliannichol...@gmail.com]

Julian, i went ahead and deleted all of the stacks files from usr/local/bin then downloaded the most recent file from http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0Beta1.tar.gz, ran ./ configure, make, sudo make install, then ran /usr/local/bin/denovo_map.pl and got the same line 34 error. So I deleted: use File::Which; and got the same error:

/usr/local/bin/denovo_map.plString found where operator expected at /usr/local/bin/denovo_map.pl line 80, near "which "samtools""

(Do you need to predeclare which?)

syntax error at /usr/local/bin/denovo_map.pl line 80, near "which "samtools""

Execution of /usr/local/bin/denovo_map.pl aborted due to compilation errors.

Any ideas? 

[Julian Catchen]

The file you are downloading is beta1:

http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0Beta1.tar.gz

I'm not sure where you are getting the link, but you want Beta2.

[juliannichol...@gmail.com]

Thank you it is now working with beta2, though I would like to turn off database interactions and it seems "  Database options (currently disabled in beta):"

is there a way to disable the database?

[Julian Fiorentino]

Julian, I was able to get denovo_map.pl to run, it follows the script to:

/usr/local/bin/tsv2bam -P /some/path/stacks  -t 7 -M /some/path/_pop_map.txt

Logging to '/some/path/stacks/tsv2bam.log'.

Then I get this error:

tsv2bam: src/tsv2bam.cc:265: void run(const std::vector<int>&, const string&, const std::unordered_map<int, long unsigned int>&, std::size_t, std::ostream&): Assertion `l->len == cloc_lengths.at(m->cat_id)' failed.

denovo_map.pl: Aborted because the last command failed. (134)

it is not a resource issue as I watched my system monitor while running the above command alone and it only used about 10% of my available ram before aborting. 

On Fri, Oct 20, 2017 at 10:36 PM, Julian Catchen <jcat...@illinois.edu> wrote:

The file you are downloading is beta1:

http://catchenlab.life.illinois.edu/stacks/source/stacks-2.0Beta1.tar.gz

I'm not sure where you are getting the link, but you want Beta2.

[Nicolas Rochette]

Hi Julian,

This may be a problem on our side. Could you send me the denovo_map.log file so I can look into it? Thanks.

Best,

Nicolas

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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[Julian Fiorentino]

Julian, when I run denovo in fixed mode:

/usr/local/bin/denovo_map.pl -m 3 -M 2 -n 1 -T 7 -X "ustacks:--model_type fixed" -X "ustacks:--bc_err_freq 0.01" -o /./stacks --popmap /./Combined_pop_map.txt --samples /./stacks I get the above error, 

when I run:

/usr/local/bin/denovo_map.pl -m 3 -M 2 -n 1 -T 7 -o /./SNP --popmap /./Combined_pop_map.txt --samples /./stacks

the pipeline runs fine. 

[juliannichol...@gmail.com]

Attached is the log file. 

Additionally the pipeline is not producing a output fasta file.  

[Tom Harrop]

Hi all,

I'm also running into this problem with Stacks 2.0Beta4.

Here's my denovo_map call:

bin/denovo_map.pl --samples data/radtags --popmap output/filtering/replicate_1_popmap.txt -T 50 -o output/stacks/m3/M7/n1/rep1 -m 3 -M 7 -n 1

Here's the `tsv2bam` section of denovo_map.log

tsv2bam
==========
/path/to/tsv2bam -P output/stacks/m3/M7/n1/rep1  -M output/filtering/replicate_1_popmap.txt -t 50
Logging to 'output/stacks/m3/M7/n1/rep1/tsv2bam.log'.
Configuration for this run:
  Stacks directory: 'output/stacks/m3/M7/n1/rep1/'
  Batch ID: 1
  Population map: 'output/filtering/replicate_1_popmap.txt'
  Num. samples: 8
  Multithreaded.

Loading the catalog...
Processing sample 'Tangihanga-Station9'...
Processing sample 'Greymouth47'...
Processing sample 'Lincoln20'...
Processing sample 'Tangihanga-Station12'...
Processing sample 'Terakaka-DairyFarm7'...
Processing sample 'Terakaka-DairyFarm5'...
Processing sample 'Opotiki4'...
Processing sample 'Ruakura14'...

tsv2bam: src/tsv2bam.cc:265: void run(const std::vector<int>&, const string&, const std::unordered_map<int, long unsigned int>&, std::size_t, std::ostream&): Assertion `l->len == cloc_lengths.at(m->cat_id)' failed.

Is there any problem with having hyphens in the file/sample names? Any other suggestions?

Cheers,

Tom Harrop

[Pedro]

Hi

I'm having that same error! Did you find the source of the error?

Cheers,
Pedro

[Nicolas Rochette]

Hi Pedro,

Are you using the latest version?

Best,

Nicolas

--

[Pedro]

Hi

Yes, Stacks 2.0 Beta7c

The error happens with some of the samples but with others does not. If I remove the sample that throws the error, the program keeps working until the next sample that has an identical problem. I'm trying to see what make those samples different... The error I get is:

tsv2bam: src/tsv2bam.cc:262: void run(const std::vector<int>&, const string&, const std::unordered_map<int, long unsigned int>&, std::size_t, std::ostream&): Assertion `l->len == cloc_lengths.at(m->cat_id)' failed.


Different line, but it does seem the same error as reported in a previous post.

Thanks

[Pedro]

Hi all,

I checked the sample files and I have no clue of what is generating the error...

Any hints?

Cheers

[Tom Harrop]

Hi all,

In my case, the problem went away after I made sure that all the reads were the same length.

Best,

Tom

[Pedro]

Hi Tom,

Thanks, that was the source of my problem also. After trimming all read to same length I manage to run tsv2bam without problems!

Cheers,
Pedro