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Exception caught Cannot open file XXX/.bin_reads/paired_0.off': iostream error #1250
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Hello There is an I/O problem. SPAdes was unable to read one of its intermediate files. So, maybe more information is available in the system log? Does moving output / scratch dir to other volume helps? |
Thank you! Unfortunately I cannot find anything in the syslog and moving the whole spades directory to a mounted NAS drive does not solve the problem. I see the intermediate file and can access by my user, so I do not know why spades cannot handle it. |
Does it reproduce with another dataset? How about running |
Yes, I tried different datasets. The test ran with this result: ========= TEST PASSED CORRECTLY. === Error correction and assembling warnings:
|
Without specifying the threads option, it runs smoothly, but of course it would be good if I could use all or most of the cores of the server... |
You might probably check the open file limit (see |
Description of bug
Hi,
Our server has 512 GB of RAM and 256 cores. I have an issue shown in the spades.log. If I run spades with root privileges, the results are the same. There is a paired_0.off file in the .bin_reads directory. We had an SSD change before this error happened, but the Linux and SPAdes version (however compiled again on the new system), the fastq files and parameters are the same.
Thank you!
spades.log
spades.log
params.txt
params.txt
SPAdes version
3.15.5
Operating System
Ubuntu 22.04.1
Python Version
Python 3.11.5
Method of SPAdes installation
manual
No errors reported in spades.log
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