Error running test case

[eldronzhou]

Hi Dr. Wang,

I am running the latest version of SEQLinakge from Docker (actually Singularity on our HPC). I have trouble running through test cases in the documentation downloaded from http://bioinformatics.org/seqlink/download/seqlinkage-example.zip.

I use the following command

seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz --freq EVSEAAF -o LinkageAnalysis \ -K 0.001 --moi AR -W 0 -M 1 --theta-max 0.5 --theta-inc 0.05 -j 8 --run-linkage

and below is the log message:

MESSAGE: Binary trait detected in [/home/gz222/example/seqlinkage-example.fam]
MESSAGE: Checking local resources 5/5 ...
MESSAGE: 12 samples found in [/home/gz222/example/seqlinkage-example.vcf.gz]
MESSAGE: 2 families with a total of 12 samples will be scanned for 28,488 pre-defined units
MESSAGE: 2 units processed {82.82%} ...Process EncoderWorker-7:
Traceback (most recent call last):
File "/opt/miniconda2/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap
self.run()
File "/opt/miniconda2/lib/python2.7/site-packages/SEQLinkage-1.1.0-py2.7.egg/SEQLinkage/Core.py", line 1259, in run
status = m.apply(self.data)
File "/opt/miniconda2/lib/python2.7/site-packages/SEQLinkage-1.1.0-py2.7.egg/SEQLinkage/Core.py", line 333, in apply
self.__FormatHaplotypes(data,recombPos,varnames,uniq_vars)
File "/opt/miniconda2/lib/python2.7/site-packages/SEQLinkage-1.1.0-py2.7.egg/SEQLinkage/Core.py", line 972, in __FormatHaplotypes
start=int(sorted_var[0].split('-')[1])
IndexError: list index out of range
MESSAGE: 2 units (from 15 variants) processed; 2 Mendelian inconsistencies and 0 recombination events handled
MESSAGE: 28,485 units ignored due to absence in VCF file
MESSAGE: Archiving regional marker data to directory [cache]
MESSAGE: 2 units will be converted to LINKAGE format
MESSAGE: 1 units successfully converted to LINKAGE format
MESSAGE: Archiving LINKAGE format to directory [cache]
MESSAGE: Running linkage analysis ...
MESSAGE: Linkage analysis succesfully performed for 1 units
MESSAGE: Report for [LinkageAnalysis] is generated in HTML format

I investigate this issue and find that sorted_var is an empty list when processing the variant 19 288062 rs11542542, which is constant in all individuals. Since this is a test case, I was wondering whether you've encountered this issue when running the latest program from the docker or I guess this issue is specific to my system. Any help would be appreciated.

Thanks,
Geyu

[GracilisMuscle]

Geyu & Dr. Wang,
I, too, get the exact same log message when trying to run the latest version of SEQLinkage from Docker on Unbuntu 20.04 LTS . As this is my first attempt to explore seqlink I don't have anything to add, other than you are not alone in this issue?

Looking forward to a response.

[gaow]

@eldronzhou @GracilisMuscle thanks for the feedback. I've got it on my schedule to look into. Will get back to you very soon!

[eldronzhou]

An update on this thread. The error can be fixed after adding the flag --recomb_cross_fam. I believe the problem is caused by not able to handle variants with no variation in this commit.

[GracilisMuscle]

Excellent! Will try it tonight! Thanks!

…

On Tue, Feb 16, 2021, 7:42 PM Geyu Zhou ***@***.***> wrote: An update on this thread. The error can be fixed after adding the flag --recomb_cross_fam. I believe the problem is caused by not able to handle variants with no variation in this commit <4069280> . — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASD4ADVRLDHOYC2HFJIFKLTS7MGGLANCNFSM4UZEOI2A> .

[chong-cyber]

@eldronzhou @GracilisMuscle Have you guys encountered similar issues in your future usage of SEQLinkage? I was able to run the test sample with no problems but when doing other work I got the same warnings. I have attempted to restore previous versions as well as using making edits on my end but still could not address the issue. Have either of you diagnosed the problem? Thank you very much!

[eldronzhou]

You may want to check if there are variants with no variation (same across all individuals) in your vcf file and remove them before running SEQLinkage.

[chong-cyber]

@eldronzhou Thank you for the quick response! I will take a look and keep you posted.

[DrMiemie]

@eldronzhou thank you very much !this really helps me