novoalign error: Stack Dump

[kle@stowers.orgParticipant]

I tried to run novoalign today, but a block by an error that I do not know how to solve. The command and the error are shown as below.

./novoalign -d ~/Transcriptomes/dd_Smed_v6.pcf.contigs.inx -f ~/Omri_Single_Cell_RNAseq/SRR2051598.sra -o SAM -r Random > ~/Omri_Single_Cell_RNAseq/alignments.sam > ~/Omri_Single_Cell_RNAseq/log.txt

Interrupted..11
Stack Dump …
ip = 0x 4a10cf, sp = 0x 7ffe73244960
ip = 0x 409842, sp = 0x 7ffe73245130
ip = 0x 5de3e0, sp = 0x 7ffe73245140
ip = 0x 414c84, sp = 0x 7ffe73245580
ip = 0x 42eb5c, sp = 0x 7ffe732455b0
ip = 0x 42b11d, sp = 0x 7ffe73245740
ip = 0x 404093, sp = 0x 7ffe73245880
ip = 0x 5df5da, sp = 0x 7ffe73279d40
ip = 0x 409731, sp = 0x 7ffe73279e10

Please let me know if you have any thought or experience about this. Thanks for any help in advance.

• This topic was modified 9 years ago by  kle@stowers.org.

[Colin HercusKeymaster]

Hi TLE,

Novoalign can’t process an sra file. You need to extract the fastq file using

fastq-dump SRR2051598

Cheers, Colin

[Author]

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