Closed cbreenmachine closed 2 years ago
Hi Simon,
I've been getting the same bug multiple times on different samples that "(GEM) could not write to file 'stream'".
GEM::FatalError (fm.c:686,fm_write_mem) Could not write to file 'stream' <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< GEM::Unexpected error occurred. Sorry for the inconvenience Feedback and bug reporting it's highly appreciated, => Please report or email (gem.mapper.dev@gmail.com) GEM::Running-Thread (threadID = 3) <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< GEM::Version v3.6.0-bundle-release GEM::CMD gem-mapper -I ../../reference/GENCODE/gembs-index/h38_no_alt.BS.gem --threads 4 --report-file ../data/pool11/329.json --i1 ../data/pool11/329_R1.fastq.gz --i2 ../data/pool11/329_R2.fastq.gz -o ../data/pool11/329.unsorted.sam <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< GEM::Input.State Sequence (File '../data/pool11/329_R1.fastq.gz' Line '361429') @A00835:363:HVVFKDSX2:1:2632:18927:33051/1 TTTTTTTAGGAGAGTTTATTTTATATTTTTTTATATAATTAGGTAATTAATGTTATTAGAAGGTTAGGATATTTGGAATGGTTTAGAGTTTATTTGGGAATTGTGAAATATTTTGTTTTTTGTAGGAGATAAGGTATGTAATTCGATAAT + FFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFF,FFFFFFFFFFFFFF:FFFFFF:FFFF:FFFFFFFFFFFFF:FFFFFFFFFF:,FFFFFFFFFFFFFFFFFFF GEM::Input.State Sequence (File '../data/pool11/329_R2.fastq.gz' Line '40036') @A00835:363:HVVFKDSX2:1:2632:18927:33051/2 CTTATATATCTTTTTCCTTTACTCAAAACAAAACAATTTTTAACACACTAAAAAAAAAAAAAAACCAAATATTTTATACCTTTCTAAAACAACACTATATCCCAAACTACATTTTAAAACTTAATATAAAAATACCAAAATCTAAACACC + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:FFFFF:FFFF,:,FFF:FFFF,,F,F,FFF,FF,FF:F,FFF:FF,:FFFF:,,FFFF:,:F,FF,,,F:FF,,,:F
Do you have any suggestions or advice on how to proceed? Thanks!
-Coleman
Likely running too many instances.
Hi Simon,
I've been getting the same bug multiple times on different samples that "(GEM) could not write to file 'stream'".
Do you have any suggestions or advice on how to proceed? Thanks!
-Coleman