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sararselitsky / tDRmapper

MIT License
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bugs out #4

Open alexstaj opened 7 years ago

alexstaj commented 7 years ago 
$ perl Scripts/TdrMappingScripts.pl hg38_mature_pre_for_tdrMapper.fa  input/B1.fastq.gz 
Warning messages:
1: `show_guide` has been deprecated. Please use `show.legend` instead. 
2: Non Lab interpolation is deprecated 
Warning message:
`show_guide` has been deprecated. Please use `show.legend` instead. 
Error in zero_range(from) : x must be length 1 or 2
Calls: ggsave ... train_cartesian -> <Anonymous> -> f -> rescale -> zero_range
Execution halted
alexstaj commented 7 years ago

it didnt map to any pre so it bugs out at producing the pre-pdf. what should I do?

sararselitsky commented 7 years ago

The whole thing stops because there are no pre-tRNA reads?

alexstaj commented 7 years ago

Yes it just stops. Execution halted it says. The last file produced is the pre pdf which is blank.

On Aug 11, 2017 9:02 AM, "Sara Selitsky" notifications@github.com wrote:

The whole thing stops because there are no pre-tRNA reads?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sararselitsky/tDRmapper/issues/4#issuecomment-321806404, or mute the thread https://github.com/notifications/unsubscribe-auth/AC3vBfSp7h_vyGdIxXymkz3Aj10A5rArks5sXFDkgaJpZM4O0DQZ .

sararselitsky commented 7 years ago

What files are outputted when you ran this?

alexstaj commented 7 years ago

so it produced: B1.fastq.gz.hq_cs.mapped B1.fastq.gz.hq_cs.mapped.covg.txt B1.fastq.gz.hq_cs.mapped.covgPre.txt (47 bytes - empty) B1.fastq.gz.hq_cs.mapped.speciesInfo.txt B1.fastq.gz.hq_cs.mapped.top50covg.txt B1.fastq.gz.hq_cs.mapped.top50covgPre.txt (47 bytes - empty) B1.fastq.gz.hq_cs.mapped.top50covg.txt.top50_tdr.pdf B1.fastq.gz.hq_cs.mapped.top50covgPre.txt.top50Pre_tdr.pdf (3.8kB - empty)

and in the directory of B1.fastq.gz it produced:

B1.fastq.gz.hq_cs B1.fastq.gz.hq_cs.notEM B1.fastq.gz.hq_cs.notEM.notPre B1.fastq.gz.hq_cs.notEM.notPre.not1MM B1.fastq.gz.hq_cs.notEM.notPre.not1MM.not1del B1.fastq.gz.hq_cs.notEM.notPre.not1MM.not1del.not2MM B1.fastq.gz.hq_cs.notEM.notPre.not1MM.not1del.not2MM.not2del B1.fastq.gz.hq_cs.notEM.notPre.not1MM.not1del.not2MM.not2del.not3ConsDel

hi I shared a folder to your google drive with my fastq and the hg38 mature and pre fasta.