bwa mem cannot locate output bam file

Question

[alexadeanfitz]

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

[ATpoint]

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.

[dsarbashis]

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

[ATpoint]

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.