Hello Jedai Masters of Biostars,
I keep facing crash while mapping contig files with BBMap (v.38.76). I am running command "bbmap.sh in=sample_r1.fastq in2=sample_r2.fastq out=./sample_bbmapped.sam bamscript=bs.sh" and process stops on "Started 40 mapping threads" as highlighted in quote below. I can only see "bbmap.sh:line 352: /random number/ Killed". I supposed it could be due to low memory, but using maximum memory set (377G is max on dev-node of my institute) cannot help. I wonder if anyone have had similar issue or know how to fix this. Thank you for your time and consideration!
May the force be with you, Joo-Young
java -da -Xmx377g -Xms377g -cp /mnt/home/leejooy5/Downloads/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 -da -Xmx377g in=Std_host_removed_R1.fastq in2=Std_host_removed_R2.fastq out=./sorted_indexed20200219/Std_megahit_BBmapped.sam bamscript=bs.sh Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, -da, -Xmx377g, in=Std_host_removed_R1.fastq, in2=Std_host_removed_R2.fastq, out=./sorted_indexed20200219/Std_megahit_BBmapped.sam, bamscript=bs.sh] Version 38.76 Retaining first best site only for ambiguous mappings. Found samtools 1.9 Set genome to 1 Loaded Reference: 0.509 seconds. Loading index for chunk 1-1, build 1 Generated Index: 1.078 seconds. Analyzed Index: 2.608 seconds. Started output stream: 0.075 seconds. Cleared Memory: 0.389 seconds. Processing reads in paired-ended mode. Started read stream. **Started 40 mapping threads.** /mnt/home/leejooy5/Downloads/bbmap/**bbmap.sh: line 352: 10803 Killed** java -da -Xmx377g -Xms377g -cp /mnt/home/leejooy5/Downloads/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 -da -Xmx377g in=Std_host_removed_R1.fastq in2=Std_host_removed_R2.fastq out=./sorted_indexed20200219/Std_megahit_BBmapped.sam bamscript=bs.sh Note: This script is designed to run with the amount of memory detected by BBMap. If Samtools crashes, please ensure you are running on the same platform as BBMap, or reduce Samtools' memory setting (the -m flag). Note: Please ignore any warnings about 'EOF marker is absent'; this is a bug in samtools that occurs when using piped input. [bam_sort_core] merging from 0 files and 3 in-memory blocks...