Parsing error in sam file when converting to bam

Question

[emily.coger]

I am working with single-cell sequencing files and am getting stuck when converting sam to bam. Any help is sincerely appreciated:

This is my initial cutadapt command:

cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT --interleaved --cores=16 -o project/outs/fastq_path/project/PTO035/PTO035_1.fastq.gz -p project/outs/fastq_path/project/PTO035/PTO035_2.fastq.gz project/outs/fastq_path/project/PTO035/PTO035_S1_L001_R1_001.fastq.gz project/outs/fastq_path/project/PTO035/PTO035_S1_L001_R2_001.fastq.gz

This is my command for converting to sam:

bwa mem -C -M -t 16 genome.fa <(zcat project/outs/fastq_path/project/PTO035/PTO035_1.fastq.gz) <(zcat project/outs/fastq_path/project/PTO035/PTO035_2.fastq.gz) > aln_pe3.sam 

When using this command to convert to bam, I get an error:

samtools view -Sb aln_pe3.sam > aln_pe3.bam

Error:

[W::sam_read1_sam] Parse error at line 196
samtools view: error reading file "aln_pe3.sam"

If it helps, this is what line 196 looks like: 
SRR23292069.1   99  chr10   68742898    60  101M    =   68742899    102 GTGAGACACTGCGCCTGGCCAGTGTAGCTATGATTTTCTTTCCTTTTTTATTTGAGACAGAGCCTCACTCGGTTGCCAAGGCTGGAGTGCAGTGGCGTGAT   ?????????????????????????????????????????????????????????????????????????????????????????????????????   NM:i:0  MD:Z:101    MC:Z:101M   AS:i:101    XS:i:37 A00521:358:HWTVNDSX3:1:1101:1669:1000/1

[ATpoint]

There is no need for this process substitution zcat thing, bwa can read gzipped files.

Answer 1

[lakhujanivijay]

Have you already tried running the command like this ?

bwa mem -C -M -t 16 genome.fa project/outs/fastq_path/project/PTO035/PTO035_1.fastq.gz project/outs/fastq_path/project/PTO035/PTO035_2.fastq.gz > aln_pe3.sam

Is there a reason to use zcat when bwa can work on compressed fq file ?