search

aubombarely / Organelle_PBA

A software to assemble chloroplast and mitochodrial genomes using PacBio data
37 stars 15 forks source link

Blasr step is not working #17

Open XuewenWangUGA opened 5 years ago

XuewenWangUGA commented 5 years ago

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

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

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

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

============================================================ 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 commented 5 years ago

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

eikemq commented 5 years ago

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 commented 5 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

cgjosephlee commented 4 years ago

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