bbmap.sh: line 352 RANDOM# Killed

jylee · 02-21-2020, 04:36 PM

Hello all,

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 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...

GenoMax · 02-22-2020, 04:26 AM

Cross-posted on biostars: https://www.biostars.org/p/423541/

I will keep answering there.

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02-21-2020, 04:36 PM	#1
jylee Junior Member Location: East Lansing, MI Join Date: Jun 2019 Posts: 3	bbmap.sh: line 352 RANDOM# Killed Hello all, 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 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...

02-22-2020, 04:26 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Cross-posted on biostars: https://www.biostars.org/p/423541/ I will keep answering there.