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Re: [Seqan-dev] Mason2 exception error

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Thank you Marcel. I just submitted my issue.


Στις Δευ, 10 Μαΐ 2021, 12:06 π.μ. ο χρήστης Marcel Ehrhardt <marehr2@zedat.fu-berlin.de> έγραψε:

Hi Christos,

this seems like a bug, can you open a bug ticket at https://github.com/seqan/seqan/issues?

Could you also provide links to the used files?

Thank you!

On 5/8/21 8:42 PM, Christos Matzoros wrote:

Hello, I use mason2 to create paired-end reads as shown bellow:

./mason_simulator -ir /home/chris/Desktop/GRCh38_latest_genomic.fa --num-threads 12 -n 1000000 --illumina-read-length 150 --input-vcf /home/chris/mason_output/variation/hg_out.vcf --out /home/chris/mason_output/simulator_output/pair_end_left_reads.fq --out-right /home/chris/mason_output/simulator_output/pair_end_right_reads.fq


and I get the following error:


MASON SIMULATOR
===============

____INITIALIZING______________________________________________________________

Opening reference and variants file ... OK
Initializing fragment-to-contig distribution ... OK
Initializing simulation threads ... OK
Opening output file /home/chris/mason_output/simulator_output/pair_end_left_reads.fq ... OK
Opening output file /home/chris/mason_output/simulator_output/pair_end_right_reads.fq .../home/osboxes/seqan/include/seqan/basic/basic_exception.h:363 FAILED!  (Uncaught exception of type MasonIOException: Could not open right/single-end output file.)

stack trace:
  0                      [0x4c401d]
  1                      [0x4c96a6]
  2                      [0x4c96f1]
  3                      [0x4d4c38]
  4                      [0x467abf]
  5                      [0x468312]
  6                      [0x400b42]
  7                      [0x53c62b]
  8                      [0x405f51]

Aborted (core dumped)


I really don't know where is the problem.
Any advice would be very helpful. 

Thank you,
Chris


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