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TreesLab / NCLscan

We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.
MIT License
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Reference index #10

Closed misik closed 7 years ago

misik commented 7 years ago

Hi,

I've a problem related to create_reference.py. NCLscan-1.6/bin/create_reference.py -c NCLscan-1.6/NCLscan.config sh: NCLscan-1.6/bin/SeqOut: No such file or directory cat: write error: Broken pipe [bwa_index] Pack FASTA... 37.91 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=6907425852, availableWord=498031676 [BWTIncConstructFromPacked] 10 iterations done. 99999996 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999996 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999996 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999996 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999996 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999996 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999996 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999996 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999996 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999996 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999996 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999996 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999996 characters processed. ....

NCLscan-1.6/bin/SeqOut cannot be found but the index can still be generated. The SeqOut file is actually named as SeqOut.cpp in the bin/ folder. Should I change the script as

SeqOut_bin = {NCLscan_bin}/SeqOut.cpp

or is there another way to correct this issue?

Thanks, Meltem

chenchiaying commented 7 years ago

Hi,

Before building the reference index, did you build the C++ code (step 2.4)? The cpp files (e.g. SeqOut.cpp) in bin folder have to do "make" to generate the executive files (e.g. SeqOut).

best, Chia-Ying