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ERROR: Sprai/CA didnt produced an output 9-terminator. Check log. #20
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Im having the exact same issue. I have specified EXPLICITLY the ec.spec and pb spec files when running Organelle_PBA. It mentions that those files are parsed...yet it decides to create its own spec files and use those. The log files states: Can anyone suggest a fix for this please ? |
I suggest using https://github.com/rrwick/Unicycler, I have had success assemblying plant mitochondrial and plastid |
I've since had some luck I believe. If you go to the sprai install folder, check to see if there are these file executables present in there: These files are needed when sprai runs and for some reason, when I installed sprai it didn't put all executables in the same location, instead the above files were located in a folder: Below I have put the main running parameter output from my successful run. Thank you diriano I shall check out unicycler as well as I will be assembling some endosymbiont data from our fly species of interest. OrganelleRef_PBA -i artha_pacbioSRR1284093_c025k.fastq -t fastq -r artha_refchl01_artha.fa -o artha_chl_outdir -b '--nproc=16' -s 'num_threads=16' -V ############################################################ OrganelleRef_PBA Starts (Thu 4 Jul 14:50:22 BST 2019)############################################################ ============================================================
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If you're using ubuntu, you may need to edit L265 in 265c265
< my $pipefail = "set -o pipefail;";
---
> my $pipefail = ""; It's because perl uses Feel free to try my docker build. |
Hi @cgjosephlee , I have this error message. I tried your docker but it still has the same error message. Do you have any suggestions for me? These are the log files: |
I have the same problem as some before me.
sprai-0.9.9.7.tar.gz
I installed and updated Sprai using : lpm update sprai
Running assembly (Sprai) (Fri Jun 7 18:22:43 CEST 2019)
============================================================
2.1- Creating the ec.spec file for Sprai.
2.2- Creating the pbasm.spec file for Sprai.
2.3- Running Sprai.
2.3- Analyzing the results
ERROR: Sprai/CA didnt produced an output 9-terminator. Check log.
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