search

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
417 stars 118 forks source link

Assertion iter == dict.end() failed #2

Closed gilesc closed 12 years ago

gilesc commented 12 years ago

Running under Ubuntu 64 bit, I get the following problem under 1.1.18-modified, but NOT under 1.1.12. The problem seems to be confined to rsem-parse-alignments because if I replace rsem-parse-alignments with that from v1.1.12, everything works. Is this an error in v1.1.18 or is this assertion error somehow meaningful?

fastq-dump SRR020782.lite.sra
rsem-calculate-expression -p 8 SRR020782.fastq rsem-reference/human/human SRR020782

...

# reads with at least one reported alignment: 2217543 (25.14%)
# reads that failed to align: 2936010 (33.28%)
# reads with alignments suppressed due to -m: 3668498 (41.58%)
Reported 89680495 alignments to 1 output stream(s)
[samopen] SAM header is present: 37959 sequences.
rsem-parse-alignments: Transcripts.h:103: void Transcripts::buildMappings(int, char**): Assertion `iter == dict.end()' failed.
bli25wisc commented 12 years ago

Hi Cory,

Can you check if you have two transcripts having the same name? RSEM v1.1.12 does not check this and therefore will not give any error message.

Best, Bo

Cory Giles wrote:

Running under Ubuntu 64 bit, I get the following problem under 1.1.18-modified, but NOT under 1.1.12. The problem seems to be confined to rsem-parse-alignments because if I replace rsem-parse-alignments with that from v1.1.12, everything works. Is this an error in v1.1.18 or is this assertion error somehow meaningful?

fastq-dump SRR020782.lite.sra rsem-calculate-expression -p 8 SRR020782.fastq rsem-reference/human/human SRR020782

...

reads with at least one reported alignment: 2217543 (25.14%)

reads that failed to align: 2936010 (33.28%)

reads with alignments suppressed due to -m: 3668498 (41.58%)

Reported 89680495 alignments to 1 output stream(s) [samopen] SAM header is present: 37959 sequences. rsem-parse-alignments: Transcripts.h:103: void Transcripts::buildMappings(int, char**): Assertion `iter == dict.end()' failed.

Reply to this email directly or view it on GitHub: https://github.com/bli25wisc/RSEM/issues/2

gilesc commented 12 years ago

Indeed I did. Thanks!