ERROR: Sprai/CA didnt produced an output 9-terminator. Check log.

[MjelleLab]

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

2. 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.

[ens-LCampbell]

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: there is no nss2v_v3 or fq2idfq.pl. set right sprai_path in ec.spec when I have set those paths already in the spec files I passed. This is a silly bug, but one I can't seem to get around as the files Organelle_PBA reads during operation are made on the fly and I can't run specific stages again once the run dies.

Can anyone suggest a fix for this please ?

[diriano]

I suggest using https://github.com/rrwick/Unicycler, I have had success assemblying plant mitochondrial and plastid

[ens-LCampbell]

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: bfmt72s, myrealigner, m52bfmt7, nss2v_v3.

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: 'sprai-0.9.9.23/build'

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)

############################################################

============================================================ 0) Checking arguments (Thu 4 Jul 14:50:22 BST 2019)

Input PacBio reads file: artha_pacbioSRR1284093_c025k.fastq
Input type: fastq
Output directory: artha_chl_outdir
Organelle reference fasta file: artha_refchl01_artha.fa
	Organelle reference size: 154478 bp
	Repeat block size coverage detection: 1000
	Coverage ratio to define repeatitive region: 1.6
Completeness fraction: 1.0
Breaks overlap: 0
Highest position to set up origin: 1
Starting-End margin to check circularity: 10
Overlap length to check circularity: 100
Minimum BlasR alignment percentage: 5
Passing BlasR args:
	--nproc=16
Passing Sprai ec options:
	num_threads=16

BEDTOOLS_PATH PATH defined for bedtools executable
BLASR_PATH PATH defined for blasr executable
BLAST_PATH PATH defined for blastn executable
BLAST_PATH PATH defined for makeblastdb executable
CA_PATH PATH defined for runCA executable
CA_PATH PATH defined for pacBioToCA executable
CA_PATH PATH defined for PBcR executable
SAMTOOLS_PATH PATH defined for samtools executable
SPRAI_PATH PATH defined for ezez_vx1.pl executable
SPRAI_PATH PATH defined for ezez4qsub_vx1.pl executable
SPRAI_PATH PATH defined for bfmt72s executable
SPRAI_PATH PATH defined for m52bfmt7 executable
SPRAI_PATH PATH defined for myrealigner executable
SPRAI_PATH PATH defined for nss2v_v3 executable
SPRAI_PATH PATH defined for fa2fq.pl executable
SPRAI_PATH PATH defined for check_circularity.pl executable
SPRAI_PATH PATH defined for dfq2fq_v2.pl executable
SSPACELONG_PATH PATH defined for SSPACE-LongRead.pl executable

and just to show the stage I previously had Organelle_PBA die on me.... is now passing that point:

============================================================ 2) Running assembly (Sprai) (Thu 4 Jul 14:54:06 BST 2019)

Running [date +%Y%m%d_%H%M%S]... 20190704_145406 2.1- Creating the ec.spec file for Sprai.

2.2- Creating the pbasm.spec file for Sprai.

2.3- Running Sprai.

Running [sprai-0.9.9.23/ezez_vx1.pl artha_chl_outdir/02_1_Sprai_ec.spec artha_chl_outdir/02_1_Sprai_pbasm.spec -now 20190704_145406 > artha_chl_outdir/02_1_Sprai_log.txt 2>&1]...

[cgjosephlee]

If you're using ubuntu, you may need to edit L265 in ezez_vx1.pl to

265c265
< my $pipefail = "set -o pipefail;";
---
> my $pipefail = "";

It's because perl uses sh to execute command, and ubuntu directs sh to dash which don't support set command instead of bash.

---

Feel free to try my docker build. https://github.com/cgjosephlee/Organelle_PBA

[liwang0307]

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: 02_1_Sprai_log.txt ca_ikki.log organelle_87.err.txt Thank you very much!