Comments (9)
Can you please report the version and the exact command you used?
from rna-bloom.
Hi,
I use latest conda version, and jar v1.4.3 also has the same problem.
I assembled 30 samples separately, only 3 of them were finished normally, 27 samples got above errors.
here is the log file
rna-bloom.zip
Best,
Kun
from rna-bloom.
Thanks. I am posting part of your command here for future references:
rnabloom -sensitive true -bound 500000 -f true -left ZD_E28_3_1.fq.gz -right ZD_E28_3_2.fq.gz -revcomp-right -t 8 -outdir ZD_E28_3
There are several things wrong with your command:
-sensitive
does not take any arguments.-sensitive true
would not work.-f
does not take any arguments.-f true
would not work. Typically, you don't need to use this option unless the command is a re-run and you want to overwrite all existing files.-bound 500000
is set way too large. I would not expect the fragment size for your paired-end reads to be 500Kbp. Usually, it is well under 1,000 for a typical Illumina RNA-seq sample. Setting a bound that high will result in an extremely long runtime for stage 2.- Since you have installed from
conda
, please include the-ntcard
option to automatically calculate the appropriate Bloom filter sizes. From one of the log files, I noticed that stage 1 was re-run automatically due to a very high Bloom filter false positive rate.
Taking all this together, this modified command should work:
rnabloom -ntcard -sensitive -bound 500 -f -left ZD_E28_3_1.fq.gz -right ZD_E28_3_2.fq.gz -revcomp-right -t 8 -outdir ZD_E28_3
from rna-bloom.
Thank you for pointing out.
Sorry, the .sh files above is the second run, and the log files are the first run's log.
here is the first run command line: rnabloom -left ZD_E28_3_1.fq.gz -right ZD_E28_3_2.fq.gz -revcomp-right -t 8 -outdir ZD_E28_3
all are default except input and output parameters.
I changed the parameters as I want to let rnabloom run through, but failed again.
Best,
Kun
from rna-bloom.
What is the error this time? And, can you please remove the output directory ZD_E28_3
if it already exists and try again?
from rna-bloom.
Also, please use the ntcard
option as mentioned previously.
from rna-bloom.
Hi,
rnabloom finished normally this time (rnabloom -left ZD_E28_3_1.fq.gz -right ZD_E28_3_2.fq.gz -revcomp-right -t 20 -outdir ZD_E28_3 -ntcard), but produced too many transcripts (126327 transcript in rnabloom.transcripts.nr.fa file), the gene number of this species is about 20000, so 126327 transcript is too many. Is there a way or some parameters to reduce transcript number?
Best,
Kun
from rna-bloom.
You may consider using EvidentialGene:
http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html
from rna-bloom.
EvidentialGene is not so easy to use.
from rna-bloom.
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