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Old 03-11-2015, 12:08 AM   #1
Alun3.1
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Location: alberta

Join Date: Feb 2015
Posts: 8
Default Assembly quality RSEM-EVAL failing

Hi,

I am trying to run rsem-eval from the Detonate 1.8.1 package to assess the quality of a transcriptome assembly.

I use the following command (on a cluster with ncpus=8:mem=20G):
Code:
rsem-eval-calculate-score -p 8 --no-qualities reads.fasta contigs.fasta RSEM_EVAL_Trinity 290
It outputs 2 folders containing the following files:
Code:
RSEM_EVAL_Trinity.temp/
   RSEM_EVAL_Trinity.1.ebwt
   RSEM_EVAL_Trinity.2.ebwt
   RSEM_EVAL_Trinity.3.ebwt
   RSEM_EVAL_Trinity.4.ebwt
   RSEM_EVAL_Trinity_alignable.fa
   RSEM_EVAL_Trinity_alignable.fa.ridx
   RSEM_EVAL_Trinity.bam
   RSEM_EVAL_Trinity.dat
   RSEM_EVAL_Trinity.gene_res
   RSEM_EVAL_Trinity.grp
   RSEM_EVAL_Trinity.idx.fa
   RSEM_EVAL_Trinity.iso_res
   RSEM_EVAL_Trinity.mparams
   RSEM_EVAL_Trinity.n2g.idx.fa
   RSEM_EVAL_Trinity.omit              #(file is empty)
   RSEM_EVAL_Trinity.rev.1.ebwt
   RSEM_EVAL_Trinity.rev.2.ebwt
   RSEM_EVAL_Trinity.seq
   RSEM_EVAL_Trinity.ti
   RSEM_EVAL_Trinity.transcripts.fa
   RSEM_EVAL_Trinity_un.fa 

RSEM_EVAL_Trinity.stat/
   RSEM_EVAL_Trinity.cnt
   RSEM_EVAL_Trinity.model
   RSEM_EVAL_Trinity.ofg
   RSEM_EVAL_Trinity.theta
and the following error on the ".e" file:
Code:
[samopen] SAM header is present: 114771 sequences.
# reads processed: 21035514
# reads with at least one reported alignment: 17667698 (83.99%)
# reads that failed to align: 3355968 (15.95%)
# reads with alignments suppressed due to -m: 11848 (0.06%)
Reported 31243626 alignments to 1 output stream(s)
rsem-run-em: CalcEvalScore.h:144: CalcEvalScore::CalcEvalScore(Refs&, double, double, int, int, char*, char*): Assertion `N1 == s.size() - 1' failed.
and this on the tail of the ".o" file:
Code:
...
ROUND = 2643, SUM = 20985873.0000002, bChange = 0.00142121, totNum = 1
ROUND = 2644, SUM = 20985873.0000002, bChange = 0.000495484, totNum = 0
Expression Results are written!
"rsem-run-em RSEM_EVAL_Trinity.temp/RSEM_EVAL_Trinity 0 RSEM_EVAL_Trinity RSEM_EVAL_Trinity.temp/RSEM_EVAL_Trinity RSEM_EVAL_Trinity.stat/RSEM_EVAL_Trinity -p 8 --calc-evaluation-score 4.24632071192940157 0.00672688390031380323 370 0" failed! Plase check if you provide correct parameters/options for the pipeline!
I cannot figure out what is wrong. Did someone already have this problem?
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Old 12-05-2016, 01:22 AM   #2
Aghatusha
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Location: Tatarstan

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Posts: 3
Default Same here

Have you found what's wrong with it? Trying to get the scores for assembly quality estimation, I've gotten the same output files.
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Old 12-10-2016, 12:09 AM   #3
Aghatusha
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Posts: 3
Lightbulb Resolved

The problem is in lack of space on hard drive! I tried to run DETONATE on another computer with the same input and 1TB free memory - so it worked fine.
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