Entering edit mode
4.5 years ago
sidrah.maryam
▴
60
Hello everyone, I am trying to run scATAC-pro protocol, however, I am receiving the following error: Aligning ... Starting alignment ... [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 3312862 sequences (160000086 bp)... /home/sidrah19220/IP/tools/scATAC-pro/scripts/mapping_bwa.sh: line 44: 256754 Segmentation fault (core dumped) ${BWA_PATH}/bwa mem $BWA_INDEX $BWA_OPTS ${fastqs[0]} ${fastqs[1]} > ${mapRes_dir}/${OUTPUT_PREFIX}.sam BWA Mapping Done! convert to bam ... Converting sam to bam ... Sorting bam file samtools sort: couldn't allocate memory for bam_mem
Please tell me what can be the reason for it.
You are probably out of memory. How much memory is available at your machine and how many threads did you use for mapping and sorting?
Okay thank you so much for clarification. Actually I am doing it on server, and there is enough space available there. However, i will check it again.
I am talking about memory, not disk space. Beyond that it is not only the physical memory but also how much is allocated by the job scheduler. Please add some details how you run the script.
I followed this pipeline: https://github.com/tanlabcode/scATAC-pro#step-by-step-guide-to-running-scATAC-pro
and in the third step of mapping and sorting the issue came up.
While I monitored the memory available, not much of the RAM is being consumed while the execution of task, still the issue was there. It consumed less than 1 GB of memory.