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nghiavtr / FuSeq

GNU General Public License v3.0
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index version file absent #14

Closed mvheetve closed 4 years ago

mvheetve commented 4 years ago

Hi,

just started with FuSeq today. Currently trying the examples in the documentation to get a grip on things. Encountered this problem when executing code for the first example (k=21):

$ FuSeq_v1.1.2_linux_x86-64/linux/bin/FuSeq -i TxIndexer_idx_k21 -l IU -1 <(gunzip -c SRR064287_1.fastq.gz) -2 <(gunzip -c SRR064287_2.fastq.gz) -p 1 -g Homo_sapiens.GRCh37.75.gtf -o SRR064287_feqDir Logs will be written to SRR064287_feqDir/LogDir [2020-02-04 23:32:32.820] [jointLog] [info] parsing read library format there is 1 lib Exception: [Error: The index version file TxIndexer_idx_k21/versionInfo.json doesn't seem to exist. Please try re-building the sailfish index.] FuSeq_v1.1.2_linux_x86-64/linux/bin/FuSeq tool was invoked improperly. For usage information, try /home/mvheetve/biotools/FuSeq_v1.1.2_linux_x86-64/linux/bin/FuSeq FuSeq --help Exiting.

No problems encountered at the indexing step. Many thanks Mattias

mvheetve commented 4 years ago

Found it. Not enough memory allocated. TxIndexer was killed premature.