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rwdavies / STITCH

STITCH - Sequencing To Imputation Through Constructing Haplotypes
http://www.nature.com/ng/journal/v48/n8/abs/ng.3594.html
GNU General Public License v3.0
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sh: /tmp/Rtmp62FCsV/MUYOXGCEGC/files_to_transfer.txt: No such file or directory #44

Closed linlin-pp closed 1 year ago

linlin-pp commented 3 years ago

please help me Following error

[2021-01-28 20:47:12] Done generating inputs [2021-01-28 20:47:12] Copying files onto tempdir sh: /tmp/RtmpFggRHj/ALQXNMCYLW/files_to_transfer.txt: No such file or directory rsync: failed to open files-from file /tmp/RtmpFggRHj/ALQXNMCYLW/files_to_transfer.txt: No such file or directory rsync error: syntax or usage error (code 1) at main.c(1578) [client=3.1.3] [2021-01-28 20:47:13] Done copying files onto tempdir [2021-01-28 20:47:13] Generate allele count [2021-01-28 20:47:13] Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection

Error in check_mclapply_OK(out2) : An error occured during STITCH. The first such error is above Calls: STITCH -> buildAlleleCount -> check_mclapply_OK In addition: Warning messages: 1: In mclapply(1:length(sampleRanges), mc.cores = nCores, FUN = loadBamAndConvert_across_a_range, : scheduled core 5 did not deliver a result, all values of the job will be affected 2: In mclapply(sampleRanges, mc.cores = nCores, FUN = buildAlleleCount_subfunction, : all scheduled cores encountered errors in user code Execution halted srun: error: srv3: task 0: Exited with exit code 1 [xiekr@srv1 chulihou]$ srun -N 1 -w srv3 /nfs2/xiekr/software/STITCH/STITCH.R --chr=NC_013686.1 --bamlist=629bam.list --posfile=Chr18.txt --outputdir=chr18 --method="diploid" --K=10 --nGen=100 --nCores=55

linlin-pp commented 3 years ago

/nfs2/xiekr/software/STITCH/STITCH.R --chr=NC_013669.1 --bamlist=629bam.list --posfile=Chr1.txt --outputdir=chr1 --method="diploid" --K=10 --nGen=100 --nCores=50

rwdavies commented 3 years ago

Did you run out of space in the temporary directory? What does df -h /tmp/ show?

linlin-pp commented 3 years ago

Did you run out of space in the temporary directory? What does df -h /tmp/ show?

Hello, can the following storage path be specified by yourself sh: /tmp/RtmpGHSSBS/YBDJQRBQIN/files_to_transfer.txt: No such file or directory

linlin-pp commented 3 years ago

Hello! Can this path be set by myself /tmp/RtmpGHSSBS/YBDJQRBQIN/files_to_transfer.txt

At 2021-01-28 21:31:46, "rwdavies" notifications@github.com wrote:

Did you run out of space in the temporary directory? What does df -h /tmp/ show?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

linlin-pp commented 3 years ago

![Uploading image.png…]()

rwdavies commented 3 years ago

See option tempdir to set an alternate location for a temporary directory. Though if your tempdir is full, that is probably something you want to take a look at

linlin-pp commented 3 years ago

请参阅tempdir为临时目录设置备用位置的选项。尽管如果您的临时目录已满，那可能就是您想要看的东西

The problem has been solved, thank you!