read count to gene

Question

[sherafzalk769]

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

[Nitin Narwade]

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?