read count to gene
I am using this command to get read counts to gene by using the bedtools intersect.
samtools view -Shu -q10 -@ 20 UE-2955-CMLib12_sorted.bam | bedtools intersect -c -a GCA_900659725.1_ASM90065972v1_genomic.gff -b stdin > UE-2955-CMLib{i}_intersect_counts2.bed
The command work for other files but not for one file. Which is slightly bigger in size than other. This file size is 19, 744,118kb
I am getting this following error. slurmstepd: fatal: _msg_socket_accept: pthread_create error Resource temporarily unavailable
Thanks
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Nitin Narwade
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sherafzalk769 •
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sherafzalk769 •
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I guess this error is related to the memory (RAM). Try reducing the number of threads you are using. How much RAM do you have?