Indexing problem, cant generate index

[Eugene Bolotin]

Hi All, I am looking forward to getting Sailfish to work,

I seem to have an indexing problem

I think indexing fails for some reason any help would be appreciated.

I installed the latest version of jellyfish from source using recommended flags.

I got the fa file from the ENSEMBL 75 genome

sailfish index --kmerSize 20 -t Homo_sapiens.GRCh37.75.cdna.all.fa  -o $PWD -f

Version Info: This is the most recent version

writing logs to /illumina/thirdparty/SAILFISH/sailfish-0.6.3/hg19/logs

readFile: Homo_sapiens.GRCh37.75.cdna.all.fa,

file Homo_sapiens.GRCh37.75.cdna.all.fa:

reading from 1 streams

reading from Homo_sapiens.GRCh37.75.cdna.all.fa

hit eof!d 180000 transcripts (90000) transcripts/ss

Running Jellyfish on transcripts

file: Homo_sapiens.GRCh37.75.cdna.all.fa has size 320240654 bytes

running jellyfish with --timing=/illumina/thirdparty/SAILFISH/sailfish-0.6.3/hg19/jf.time -m 20 -t 32 -o /illumina/thirdparty/SAILFISH/sailfish-0.6.3/hg19/jf.counts -s 384288785 Homo_sapiens.GRCh37.75.cdna.all.fa

In Jellyfish process. Counting transcript kmers

Jellyfish terminated with return code 0

Jellyfish finished

transcriptHash size is 99042883

Exiting, log location: /illumina/thirdparty/SAILFISH/sailfish-0.6.3/hg19/logs/sailfish.g2log.20140515-150939.log

Exception : [std::bad_alloc]

sailfish index was invoked improperly.

For usage information, try sailfish index --help

Exiting.

Here are the contents of the log:

 g2log created log file at: Thu May 15 15:09:39 2014

                LOG format: [YYYY/MM/DD hh:mm:ss.uuu* LEVEL FILE:LINE] message

                g2log file shutdown at: 15:10:13

[Eugene Bolotin]

Here is what happens when I run the test file:

sailfish quant -i /illumina/thirdparty/SAILFISH/sailfish-0.6.3/hg19/   -l "T=SE"    -r SRR915774.sra.1_2.fastq -o $PWD

quant -i /illumina/thirdparty/SAILFISH/sailfish-0.6.3/hg19/  -l "T=SE"   -r SRR915774.sra.1_2.fastq -o . -n 100 -f

Version Info: This is the most recent version

Library format { type:single end, relative orientation:none, strandedness:unstranded }

reading index . . . Sailfish terminated with return code 11

sailfish: /illumina/thirdparty/SAILFISH/sailfish-0.6.3/src/QuantificationDriver.cpp:152: int runKmerCounter(const string&, uint32_t, const string&, const std::vector<ReadLibrary>&, const string&, bool): Assertion `status == 0' failed.

Aborted

[Eugene Bolotin]

Hi All,

it was a memory related problem. The index was not generated, it was generated half way before crashing, then sailfish thought that all was good, and also crashing on quant step. I suggest crashing out with an informative message. Like "NOT ENOUGH MEMORY". And crashing out with malformed index with a message "Index is malformed, rerun indexing step."

Thanks,
Eugene

.

[Azar Fazel]

Hi Eugene

I have exactly the same problem with the "sailfish index", can you please let me know how did you solve the problem?

[赵路]

Same here!