Hi Sergej, Your solution by changing the parameters did fix my problem! I followed the directions on the link you provided. Thank you!
Fauna ----- Fauna Yarza PhD Student, Chou Lab Biomedical Sciences Program University of California, San Francisco On Oct 31, 2018, at 3:22 PM, Nowoshilow,Sergej <sergej.nowoshi...@imp.ac.at<mailto:sergej.nowoshi...@imp.ac.at>> wrote: Hi Fauna, It sounds like a system parameter issue to me. would this help? http://posidev.com/blog/2009/06/04/set-ulimit-parameters-on-ubuntu/<https://protect2.fireeye.com/url?k=1498d1e12b05a4ea.1498f6fc-e015f7d37e922723&u=http://posidev.com/blog/2009/06/04/set-ulimit-parameters-on-ubuntu/> Best, Sergej Dr. Sergej Nowoshilow Post-doc in Tanaka Lab Elly Tanaka group Animal models of regeneration Campus-Vienna-Biocenter 1 1030 Vienna email: sergej.nowoshi...@imp.ac.at<mailto:sergej.nowoshi...@imp.ac.at> phone: +43 (0) 1 79730 3203 orcid: 0000-0001-8360-5010<https://orcid.org/0000-0001-8360-5010> This message is confidential and may contain privileges information. It is intended for the named recipients only. If you receive it in error please notify me and permanently delete the original message and any copies. Von: "Yarza, Fauna" <fauna.ya...@ucsf.edu<mailto:fauna.ya...@ucsf.edu>> Datum: Mittwoch, 31. Oktober 2018 um 23:04 An: "samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>" <samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>> Betreff: [Samtools-help] Help splitting a bam file to facilitating sorting Hi all, I am very new to working with sequencing data and have run into a problem when using SAMtools to sort some of my larger files. When running the following samtools sort Sample_aligned.bam > Sample_aligned_sorted.bam this error will be returned Failed to open file ./samtools.7711.2619.tmp.0252.bam samtools sort: fail to open "./samtools.7711.2619.tmp.0252.bam”: Too many open files This error only occurs when trying to sort larger .bam files. I am working locally to avoid running on a cluster, and was wondering if there is a way to split the large .bam files that does not rely on chromosomal information (I do not have this information in my reference transcriptome). My initial idea is to split the original .bam file into 2, sort each file, and then concatenate them with the goal of preserving the sort. Is there a way to do this without creating additional problems downstream (example: not splitting the files by line number and instead using a different metric)? Best, Fauna
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