search

vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
78 stars 29 forks source link

Warnings when using uncompressed fastqs #16

Closed funnell closed 10 years ago

funnell commented 10 years ago

When using uncompressed fastq files I get the following warnings. I don't see the warnings when using gzipped versions of the same fastq files

$ ./vast-tools align --expr -o /share/scratch/tfunnell_temp/vast -c 6 /share/lustre/archive/SA464/illumina_wtss/A14559/sequence/SA464_A14559_D0R1PACXX_8_1.fastq /share/lusre/archive/SA464/illumina_wtss/A14559/sequence/SA464_A14559_D0R1PACXX_8_2.fastq Use of uninitialized value $fileName2 in substitution (s///) at /share/lustre/tfunnell/local/software/vast-tools/bin/RunDBS_1.pl line 200. [vast align]: Setting output directory to /share/scratch/tfunnell_temp/vast [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /share/scratch/tfunnell_temp/vast/tmp! [vast align]: Mapping reads against mRNA sequences Use of uninitialized value $fq2 in concatenation (.) or string at /share/lustre/tfunnell/local/software/vast-tools/bin/RunDBS_1.pl line 257. [vast align]: Calculating cRPKMs

kcha commented 10 years ago

Hi Tyler,

It looks like you have a typo in the path of your read 2 fastq file (/share/lusre instead of /share/lustre). Can you check if that addresses the issue?

In any case, I will add some extra sanity checks to make sure the inputs are well-formed.

Thanks!

funnell commented 10 years ago

Well that's embarrassing! That was definitely the problem. Yeah some checks would be useful for people like me :)

kcha commented 10 years ago

Ok, I've added some error checks.

Thanks for reporting issues. Hopefully you've had at least one successful run by now! :)

funnell commented 10 years ago

No problem. I've had one successful alignment run so far :)