Question: bwa mem cannot locate output bam file
0
gravatar for alexadeanfitz
2.1 years ago by
alexadeanfitz10 wrote:

Hello,

Below is the script I ran, first I indexed the reference fasta file, then I ran BWA-MEM and I cannot locate the output aln.bam file

User$ /Users/Alexa/Alexa/SRP135669/fastq/bwa index -a is -p PAO1_index /Users/Alexa/Alexa/SRP135669/fastq/PAO1_index.fasta
[bwa_index] Pack FASTA... 0.05 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.76 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.74 sec
[main] Version: 0.7.12-r1039
[main] CMD: /Users/Alexa/Alexa/SRP135669/fastq/bwa index -a is -p PAO1_index /Users/Alexa/Alexa/SRP135669/fastq/PAO1_index.fasta
[main] Real time: 2.860 sec; CPU: 2.612 sec


User$ /Users/Alexa/Alexa/SRP135669/fastq/run-bwamem -R "@RG\tID:SRR6833341\tDS:SRP135669\tSM:TXBurn\tLB:TXBurn_1\tPL:illumina" PAO1_index /Users/Alexa/Alexa/SRP135669/fastq/SRR6833341_1.fastq
cat /Users/Alexa/Alexa/SRP135669/fastq/SRR6833341_1.fastq \
| /Users/Alexa/Alexa/SRP135669/fastq/bwa mem -p -R'@RG\tID:SRR6833341\tDS:SRP135669\tSM:TXBurn\tLB:TXBurn_1\tPL:illumina' PAO1_index - 2> /Users/Alexa/Alexa/SRP135669/fastq/SRR6833341_1.log.bwamem \
| /Users/Alexa/Alexa/SRP135669/fastq/samtools view -1 - > /Users/Alexa/Alexa/SRP135669/fastq/SRR6833341_1.aln.bam;

Can anyone help me understand what I need to do next? Thank you

rna-seq bwa mem • 743 views
ADD COMMENTlink modified 2.1 years ago by ATpoint38k • written 2.1 years ago by alexadeanfitz10

I do not really know what you are doing, but the syntax is as simple as:

bwa mem <index> read_1.fastq read_2.fastq | samtools view -bo aln.bam -

Try again with this one.

ADD REPLYlink written 2.1 years ago by ATpoint38k

The way you are providing inputs (reads) is not sending the reads to the program. Try instead “-“ put reads with complete path.

ADD REPLYlink written 2.1 years ago by dsarbashis50

By the way, SRR6833341 is an RNA-seq sample. You might therefore rather use a splice-aware aligner like HISAT2, STAR or BBmap rather than BWA mem.

ADD REPLYlink written 2.1 years ago by ATpoint38k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 684 users visited in the last hour