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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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.Leave a comment:
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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):
It outputs 2 folders containing the following files:Code:rsem-eval-calculate-score -p 8 --no-qualities reads.fasta contigs.fasta RSEM_EVAL_Trinity 290
and the following error on the ".e" file: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 this on the tail of the ".o" 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.
I cannot figure out what is wrong. Did someone already have this problem?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!
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