Blasr step is not working

[XuewenWangUGA]

organelle_PBA step : blasr is not working. I tested that blasr tool is working but not in the Organelle_PBA.

data structure:
dir "test" has the fastq file, reference file
outdir (-o) is artha_chl , as a subdirectory in test

command:
perl $EBROOTORGANELLEREF_PBA/OrganelleRef_PBA -i artha_pacbioSRR1284093_c025k.fastq -r artha_refchl01_artha.fa -o artha_chl -t fastq

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OrganelleRef_PBA Starts (Thu Feb 14 12:53:44 EST 2019)

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============================================================
0) Checking arguments (Thu Feb 14 12:53:44 EST 2019)

Input PacBio reads file: artha_pacbioSRR1284093_c025k.fastq
Input type: fastq
Output directory: artha_chl
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

bedtools is available in the PATH (/usr/local/apps/eb/BEDTools/2.26.0-foss-2016b/bin/bedtools)
blasr is available in the PATH (/usr/local/apps/eb/BLASR/2.2-foss-2016b/bin/blasr)
blastn is available in the PATH (/usr/local/apps/eb/BLAST+/2.7.1-foss-2016b-Python-2.7.14/bin/blastn)
makeblastdb is available in the PATH (/usr/local/apps/eb/BLAST+/2.7.1-foss-2016b-Python-2.7.14/bin/makeblastdb)
runCA is available in the PATH (/usr/local/apps/eb/wgs/8.3rc2-foss-2016b/Linux-amd64/bin/runCA)
pacBioToCA is available in the PATH (/usr/local/apps/eb/wgs/8.3rc2-foss-2016b/Linux-amd64/bin/pacBioToCA)
PBcR is available in the PATH (/usr/local/apps/eb/wgs/8.3rc2-foss-2016b/Linux-amd64/bin/PBcR)
samtools is available in the PATH (/usr/local/apps/eb/SAMtools/1.7-foss-2016b/bin/samtools)
ezez_vx1.pl is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/ezez_vx1.pl)
ezez4qsub_vx1.pl is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/ezez4qsub_vx1.pl)
bfmt72s is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/bfmt72s)
m52bfmt7 is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/m52bfmt7)
myrealigner is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/myrealigner)
nss2v_v3 is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/nss2v_v3)
fa2fq.pl is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/fa2fq.pl)
check_circularity.pl is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/check_circularity.pl)
dfq2fq_v2.pl is available in the PATH (/usr/local/apps/eb/sprai/0.9.9.23-foss-2016b/bin/dfq2fq_v2.pl)
SSPACE-LongRead.pl is available in the PATH (/scratch/xwwang/cpGenome/scripts/OgPbaAssembler/SSPACE-LongRead.pl)

============================================================

1. Running BlasR (Thu Feb 14 12:53:44 EST 2019)
   ============================================================

   1.1- Converting Fastq to Fasta.
   Using Seqtk to convert Fastq to Fasta.
   Input PacBio read file contains 24903 reads

   1.2- Running BlasR mapping.

No BlasR output was created.Please check the input and the running parameters.

[scotthotaling]

I am having the same issue. What version of blasr should be used?

[eikemq]

Hi, I
after struggling with similar problems I recognized, that while installing blasr and sprai with conda/bioconda conda also installed wgs and with this a very old blasr version (1.3) which was linked to the miniconda2/bin folder. As the blasr/bin/blasr version did not worked I installed blasr with apt from the ubuntu repositories and have now the 5.3.2 version which runs fine.

So check with blasr --version which version is installed (that code should only work with higher versions and the old one will give you an error.
Check with which blasr which blasr file is actually used.
Run Organelle_PBA with the option -V to get some debug information.

all the best

[ens-LCampbell]

Im having the exact same issue, the version of blasr thats being used is version 5.3.3. Im only trying to run the test data and this bug keeps appearing. No idea what I can do to solve this issue, any suggestions much appreciated.

[KarinaMartins]

Dear all,
I wonder if one of you was able to solve this issue. I'm trying to run the test data and I'm having the same error message. The installed BlasR is version 5.3.3.
Thank you
Karina

[abeliavskaia]

Same for me: running the pipeline with the test data, blasr version is the latest 5.3.3, error "No BlasR output was created. Please check the input and the running parameters."

[afahrenkrog]

Hello, I also encountered the same issue, any solutions?
Thanks,
Annette

[cgjosephlee]

To use v1.0.8, if you installed sprai via conda, try conda install --force-reinstall blasr to install correct version of blasr (5.3.x).

Or use v1.0.7 if you're using old blasr (e.g. 1.3.x).
https://github.com/aubombarely/Organelle_PBA/blob/590c362ff13bad4a0eced812ddb268aaa773e54d/OrganelleRef_PBA

---

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