I tried to convert the SAM file generated by Bowtie(1.2.3) to BAM file with samtools(1.9), but I met the following warnings and errors:
[W::sam_hdr_sanitise] Missing trailing newline on SAM header. Possibly truncated
[E::sam_hdr_error] Missing tab at line 32: "@HISEQ:154:CB8RGANXX:1:2101:1470:1000 16 Fvb7 20495637 255 16M * 0 0 GTTGTGCTACAGCGGN IIIIIIIIIIIIIIII XA:i:1 MD:Z:15A0 NM:i:1 XM:i:3"
[main_samview] failed to write the SAM header
but when I use cat -A to check the newline in my sam file, it looks normal that a $ character appears at every line end. Here is the header region of my sam file :
I think there maybe some problems with my sam file. The commands I used are as below:
bowtie-build -f ref.fasta index
bowtie -f -v 1 -p 8 -S -a -m 50 --best --strata index s3-7-6-hua-2_clean.fa s3-7-6-hua_clean.sam --sam-RG ID:s3-7-6-hua-2_clean
samtools view -bS s3-7-6-hua_clean.sam >s3-7-6-hua_clean.bam
Appreciated for any help!QAQ
•
written
by
Yi Chu •
Your read names @HISEQ:154:etc look like SAM headers, so your SAM file is not usable. Read names in SAM files are not allowed to start with @ characters.
So either your FASTQ file somehow has two @@ characters at the start of its header lines, or your bowtie mapping pipeline is somehow leaving the @ FASTQ header character in as part of the read names.
…or which one of those bowtie arguments is the input sequence data file anyway…
Log in to answer this question.
the message is about a tab, not about a newline.
did you use any tab instead of spaces in the command "bowtie -f -v 1 -p 8 -S -a -m 50 --best --strata index s3-7-6-hua-2_clean.fa s3-7-6-hua_clean.sam --sam-RG ID:s3-7-6-hua-2_clean" , it could mess the @PG line in the header.
Thank you for your help:D! It turns out that the '@' character brings the problem~