#30 SNP-frequency-diff.pl output error

[adedayo Adeyanju]

Hi,

I am trying to run SNP-frequency-diff.pl:
The code i am using is below:
perl /group/bioinfo/apps/apps/popoolation2_1201/snp-frequency-diff.pl --input LB_HB_java.sync --output-prefix LB_HB --min-count 2 --min-coverage 4 --max-coverage 2%
I get the following error:
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 14.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 15.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 16.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 17.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 18.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 22.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 23.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 24.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 25.

Thanks for your anticipated support.

[Chris Allan]

Hi,
I have the same error.
Use of uninitialized value $rc in uc at /mnt/lustre/projects/tu32/callan/popoolation2_1201/popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> line 218. Did you ever find a resolution?
Regards,
Chris

[adedayo Adeyanju]

The error was created from the output of the (Create a synchronized file)
java -jar /group/bioinfo/apps/apps/popoolation2_1201/mpileup2sync.jar
--input p1_p2.mpileup --output p1_p2_java.sync --fastq-type sanger
--min-qual 20 --threads 20

initially, I was using Illumina as my fastq type which is correct but it
seems the software did not recognize this

I used sanger as my --fastq-type instead of Illumina and that seemed to
solve the problem.

On Thu, Jul 6, 2017 at 7:25 AM, Chris Allan cjaln200@users.sf.net wrote:

Hi,
I have the same error.
Use of uninitialized value $rc in uc at /mnt/lustre/projects/tu32/
callan/popoolation2_1201/popoolation2_1201/Modules/Synchronized.pm line
31, <$ifh> line 218. Did you ever find a resolution?
Regards,
Chris

---

• [tickets:#30] https://sourceforge.net/p/popoolation2/tickets/30/
  SNP-frequency-diff.pl output error*

Status: New
Created: Sun Mar 19, 2017 02:26 PM UTC by adedayo Adeyanju
Last Updated: Sun Mar 19, 2017 02:26 PM UTC
Owner: Robert Kofler

Hi,

I am trying to run SNP-frequency-diff.pl:
The code i am using is below:
perl /group/bioinfo/apps/apps/popoolation2_1201/snp-frequency-diff.pl
--input LB_HB_java.sync --output-prefix LB_HB --min-count 2 --min-coverage
4 --max-coverage 2%
I get the following error:
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 14.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 15.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 16.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 17.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 18.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 22.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 23.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 24.
Use of uninitialized value $rc in uc at /depot/bioinfo/apps/apps/
popoolation2_1201/Modules/Synchronized.pm line 31, <$ifh> l
ine 25.

Thanks for your anticipated support.

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[Chris Allan]

Thanks for your reply. I also used Illumina hiseq sequencing but actually set fastq-type option to sanger when running mpileup2sync...strange! I think i'll submit my own ticket!
Regards,
Chris

[Balan Ramesh]

I have the same issue.