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Old 10-25-2016, 05:19 PM   #1
zhanghao
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Location: BEIJING

Join Date: Nov 2015
Posts: 17
Default BBmap can not produce sorted bam

I used BBmap to map RNAseq data with the command:
/home/bac/software/bbmap/bbmap.sh in1=CYP51C_2_1.fq.gz in2=CYP51C_2_2.fq.gz ref=genome.fasta nodisk out=cyp51c_bb.sam bamscript=bs.sh; sh bs.sh

samtools-1.3.1 is setted in PAYH. But it just produced sam file, seems samtools did not work. It showed:

bs.sh: 2: bs.sh: module: not found
bs.sh: 3: bs.sh: module: not found
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] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
-@, --threads INT
Set number of sorting and compression threads [1]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
[E::hts_open_format] fail to open file 'cyp51c_bb_sorted.bam'
samtools index: failed to open "cyp51c_bb_sorted.bam": No such file or directory

I checked the bs.sh file:

#!/bin/bash
module unload samtools
module load samtools/0.1.19
echo "Note: This script is designed to run with the amount of memory detected by BBMap."
echo " If Samtools crashes, please ensure you are running on the same platform as BBMap,"
echo " or reduce Samtools' memory setting (the -m flag)."
echo "Note: Please ignore any warnings about 'EOF marker is absent'; this is a bug in samtools that occurs when using piped input."
samtools view -bSh1 cyp51c_bb.sam | samtools sort -m 13G -@ 3 - cyp51c_bb_sorted
samtools index cyp51c_bb_sorted.bam
bs.sh (END)
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