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nunofonseca / irap

integrated RNA-seq Analysis Pipeline
GNU General Public License v3.0
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Bug? #24

Closed Niklas123Niklas closed 7 years ago

Niklas123Niklas commented 7 years ago

Hey Nuno,

i am having Problems with the new version. If I run .conf files that worked in last version, now I get an error: [INFO] #Genes: 58051 [INFO] #Transcripts: 198002 [INFO] #Exons: 1182163 Having no space between pattern and following word is deprecated at (eval 1) line 1. Bareword found where operator expected at (eval 1) line 1, near "/home/niklas" (Missing operator before niklas?) Bareword found where operator expected at (eval 1) line 1, near "87.gtf" (Missing operator before gtf?) syntax error at (eval 1) line 1, near "/home/niklas" /home/niklas/irap_install/scripts/irap:1616: recipe for target '/home/niklas/irap_install/data/reference/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.lengths.Rdata' failed make: *** [/home/niklas/irap_install/data/reference/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.lengths.Rdata] Error 255

Line 1616 in scripts/irap is irap_gtf2featlength --gtf $< -o $@.tmp --cores $(max_threads) && mv $@.tmp.Rdata $@ && rename "$(gtf_file_abspath).lengths.Rdata.tmp" "$(gtf_file_abspath)" $@.tmp.*

Is this a bug or did I do something wrong?

nunofonseca commented 7 years ago

Hi, Can you post the full ouput of running irap (and add --trace to the list of command line options)? Thanks, Nuno

Niklas123Niklas commented 7 years ago

Hey, I will rerun with: irap --trace conf=RNA_1_4Core.conf

Is this correct? And is there a log file of the run?

nunofonseca commented 7 years ago

No, there is no log file - everything is printed to stdout (but it may be redirected to a file). Could you then run

irap --trace conf=RNA_1_4Core.conf &> logfile

and post the logfile?

Niklas123Niklas commented 7 years ago

Hey,

I did it now, but with the --trace option, I got a different error message. I start a run without trace and see what happens then.

But here is the log. log.txt

nunofonseca commented 7 years ago

Thanks, the log file is quite useful as is. I suspect that you are running iRAP in a debian based distribution. Is that true?

Niklas123Niklas commented 7 years ago

Hey, thats good to hear. I use Ubuntu 12.04.

nunofonseca commented 7 years ago

It seems that the rename command in Debian is different from the other distros and that is causing the error. I'll try to fix it and release a patch in the coming days.

nunofonseca commented 7 years ago

Hi, The issue should be fixed in the new release. Please reopen the ticket if the problem persists. Cheers.